1
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Gregor C, Grimm F, Rehman J, Wurm CA, Egner A. Click Chemistry with Cell-Permeable Fluorophores Expands the Choice of Bioorthogonal Markers for Two-Color Live-Cell STED Nanoscopy. Cells 2024; 13:683. [PMID: 38667298 PMCID: PMC11049381 DOI: 10.3390/cells13080683] [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: 02/02/2024] [Revised: 03/17/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
STED nanoscopy allows for the direct observation of dynamic processes in living cells and tissues with diffraction-unlimited resolution. Although fluorescent proteins can be used for STED imaging, these labels are often outperformed in photostability by organic fluorescent dyes. This feature is especially crucial for time-lapse imaging. Unlike fluorescent proteins, organic fluorophores cannot be genetically fused to a target protein but require different labeling strategies. To achieve simultaneous imaging of more than one protein in the interior of the cell with organic fluorophores, bioorthogonal labeling techniques and cell-permeable dyes are needed. In addition, the fluorophores should preferentially emit in the red spectral range to reduce the potential phototoxic effects that can be induced by the STED light, which further restricts the choice of suitable markers. In this work, we selected five different cell-permeable organic dyes that fulfill all of the above requirements and applied them for SPIEDAC click labeling inside living cells. By combining click-chemistry-based protein labeling with other orthogonal and highly specific labeling methods, we demonstrate two-color STED imaging of different target structures in living specimens using different dye pairs. The excellent photostability of the dyes enables STED imaging for up to 60 frames, allowing the observation of dynamic processes in living cells over extended time periods at super-resolution.
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Affiliation(s)
- Carola Gregor
- Department of Optical Nanoscopy, Institut für Nanophotonik Göttingen e.V., 37077 Göttingen, Germany;
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Florian Grimm
- Abberior GmbH, Hans-Adolf-Krebs Weg 1, 37077 Göttingen, Germany; (F.G.); (J.R.)
| | - Jasmin Rehman
- Abberior GmbH, Hans-Adolf-Krebs Weg 1, 37077 Göttingen, Germany; (F.G.); (J.R.)
| | - Christian A. Wurm
- Abberior GmbH, Hans-Adolf-Krebs Weg 1, 37077 Göttingen, Germany; (F.G.); (J.R.)
| | - Alexander Egner
- Department of Optical Nanoscopy, Institut für Nanophotonik Göttingen e.V., 37077 Göttingen, Germany;
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
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2
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Tomishige N, Bin Nasim M, Murate M, Pollet B, Didier P, Godet J, Richert L, Sako Y, Mély Y, Kobayashi T. HIV-1 Gag targeting to the plasma membrane reorganizes sphingomyelin-rich and cholesterol-rich lipid domains. Nat Commun 2023; 14:7353. [PMID: 37990014 PMCID: PMC10663554 DOI: 10.1038/s41467-023-42994-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
Although the human immunodeficiency virus type 1 lipid envelope has been reported to be enriched with host cell sphingomyelin and cholesterol, the molecular mechanism of the enrichment is not well understood. Viral Gag protein plays a central role in virus budding. Here, we report the interaction between Gag and host cell lipids using different quantitative and super-resolution microscopy techniques in combination with specific probes that bind endogenous sphingomyelin and cholesterol. Our results indicate that Gag in the inner leaflet of the plasma membrane colocalizes with the outer leaflet sphingomyelin-rich domains and cholesterol-rich domains, enlarges sphingomyelin-rich domains, and strongly restricts the mobility of sphingomyelin-rich domains. Moreover, Gag multimerization induces sphingomyelin-rich and cholesterol-rich lipid domains to be in close proximity in a curvature-dependent manner. Our study suggests that Gag binds, coalesces, and reorganizes pre-existing lipid domains during assembly.
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Affiliation(s)
- Nario Tomishige
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.
- Cellular Informatics Laboratory, RIKEN CPR, Wako, Saitama, Japan.
| | - Maaz Bin Nasim
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
- Faculty of Pharmacy, The University of Lahore, Lahore, Pakistan
| | - Motohide Murate
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
- Cellular Informatics Laboratory, RIKEN CPR, Wako, Saitama, Japan
| | - Brigitte Pollet
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Julien Godet
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN CPR, Wako, Saitama, Japan
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.
| | - Toshihide Kobayashi
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.
- Cellular Informatics Laboratory, RIKEN CPR, Wako, Saitama, Japan.
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3
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Socrier L, Sharma A, Chen T, Flato K, Kettelhoit K, Enderlein J, Werz DB, Steinem C. Fluorophore position of headgroup-labeled Gb 3 glycosphingolipids in lipid bilayers. Biophys J 2023; 122:4104-4112. [PMID: 37735870 PMCID: PMC10598288 DOI: 10.1016/j.bpj.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023] Open
Abstract
Fluorescent lipid probes are an invaluable tool for investigating lipid membranes. In particular, localizing certain receptor lipids such as glycosphingolipids within phase-separated membranes is of pivotal interest to understanding the influence of protein-receptor lipid binding on membrane organization. However, fluorescent labeling can readily alter the phase behavior of a lipid membrane because of the interaction of the fluorescent moiety with the membrane interface. Here, we investigated Gb3 glycosphingolipids, serving as receptor lipids for the protein Shiga toxin, with a headgroup attached BODIPY fluorophore separated by a polyethylene glycol (PEG) spacer of different lengths. We found that the diffusion coefficients of the fluorescently labeled Gb3 species in 1,2-dioleoyl-sn-glycero-3-phosphocholine/Gb3 (98:2, n/n) supported lipid bilayers are unaltered by the PEG spacer length. However, quenching as well as graphene-induced energy transfer experiments indicated that the length of the PEG spacer (n = 3 and n = 13) alters the position of the BODIPY fluorophore. In particular, the graphene-induced energy transfer technique provided accurate end-to-end distances between the fluorophores in the two leaflets of the bilayer thus enabling us to quantify the distance between the membrane interface and the fluorophore with sub-nanometer resolution. The spacer with three oligo ethylene glycol groups positioned the BODIPY fluorophore directly at the membrane interface favoring its interaction with the bilayer and thus may disturb lipid packing. However, the longer PEG spacer (n = 13) separated the BODIPY moiety from the membrane surface by 1.5 nm.
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Affiliation(s)
- Larissa Socrier
- Max-Planck-Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Akshita Sharma
- III. Institute of Physics - Biophysics, Georg-August-Universität, Göttingen, Germany
| | - Tao Chen
- III. Institute of Physics - Biophysics, Georg-August-Universität, Göttingen, Germany
| | - Kira Flato
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Göttingen, Germany
| | | | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg-August-Universität, Göttingen, Germany
| | - Daniel B Werz
- Institute of Organic Chemistry, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Claudia Steinem
- Max-Planck-Institute for Dynamics and Self-Organization, Göttingen, Germany; Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Göttingen, Germany.
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4
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Woodward X, Javanainen M, Fábián B, Kelly CV. Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion. Biophys J 2023:S0006-3495(23)00001-2. [PMID: 36604961 DOI: 10.1016/j.bpj.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/23/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
The precise spatiotemporal control of nanoscale membrane shape and composition is the result of a complex interplay of individual and collective molecular behaviors. Here, we employed single-molecule localization microscopy and computational simulations to observe single-lipid diffusion and sorting in model membranes with varying compositions, phases, temperatures, and curvatures. Supported lipid bilayers were created over 50-nm-radius nanoparticles to mimic the size of naturally occurring membrane buds, such as endocytic pits and the formation of viral envelopes. The curved membranes recruited liquid-disordered lipid phases while altering the diffusion and sorting of tracer lipids. Disorder-preferring fluorescent lipids sorted to and experienced faster diffusion on the nanoscale curvature only when embedded in a membrane capable of sustaining lipid phase separation at low temperatures. The curvature-induced sorting and faster diffusion even occurred when the sample temperature was above the miscibility temperature of the planar membrane, implying that the nanoscale curvature could induce phase separation in otherwise homogeneous membranes. Further confirmation and understanding of these results are provided by continuum and coarse-grained molecular dynamics simulations with explicit and spontaneous curvature-phase coupling, respectively. The curvature-induced membrane compositional heterogeneity and altered dynamics were achieved only with a coupling of the curvature with a lipid phase separation. These cross-validating results demonstrate the complex interplay of lipid phases, molecular diffusion, and nanoscale membrane curvature that are critical for membrane functionality.
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Affiliation(s)
- Xinxin Woodward
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic; Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Balázs Fábián
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Christopher V Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan.
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5
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Ragaller F, Andronico L, Sykora J, Kulig W, Rog T, Urem YB, Abhinav, Danylchuk DI, Hof M, Klymchenko A, Amaro M, Vattulainen I, Sezgin E. Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties. Open Biol 2022; 12:220175. [PMID: 36099931 PMCID: PMC9470265 DOI: 10.1098/rsob.220175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The plasma membrane, as a highly complex cell organelle, serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a detailed investigation of biophysical properties of the plasma membrane is of utmost importance for a comprehensive understanding of biological processes occurring therein. During the past two decades, several environment-sensitive probes have been developed and become popular tools to investigate membrane properties. Although these probes are assumed to report on membrane order in similar ways, their individual mechanisms remain to be elucidated. In this study, using model membrane systems, we characterized the probes Pro12A, NR12S and NR12A in depth and examined their sensitivity to parameters with potential biological implications, such as the degree of lipid saturation, double bond position and configuration (cis versus trans), phospholipid headgroup and cholesterol content. Applying spectral imaging together with atomistic molecular dynamics simulations and time-dependent fluorescent shift analyses, we unravelled individual sensitivities of these probes to different biophysical properties, their distinct localizations and specific relaxation processes in membranes. Overall, Pro12A, NR12S and NR12A serve together as a toolbox with a wide range of applications allowing to select the most appropriate probe for each specific research question.
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Affiliation(s)
- Franziska Ragaller
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Luca Andronico
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Jan Sykora
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Rog
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Yagmur Balim Urem
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Abhinav
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Andrey Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Mariana Amaro
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
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6
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Sezgin E. Giant plasma membrane vesicles to study plasma membrane structure and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183857. [PMID: 34990591 DOI: 10.1016/j.bbamem.2021.183857] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/25/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022]
Abstract
The plasma membrane (PM) is a highly heterogenous structure intertwined with the cortical actin cytoskeleton and extracellular matrix. This complex architecture makes it difficult to study the processes taking place at the PM. Model membrane systems that are simple mimics of the PM overcome this bottleneck and allow us to study the biophysical principles underlying the processes at the PM. Among them, cell-derived giant plasma membrane vesicles (GPMVs) are considered the most physiologically relevant system, retaining the compositional complexity of the PM to a large extent. GPMVs have become a key tool in membrane research in the last few years. In this review, I will provide a brief overview of this system, summarize recent applications and discuss the limitations.
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Affiliation(s)
- Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden.
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7
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Westra M, Gutierrez Y, MacGillavry HD. Contribution of Membrane Lipids to Postsynaptic Protein Organization. Front Synaptic Neurosci 2021; 13:790773. [PMID: 34887741 PMCID: PMC8649999 DOI: 10.3389/fnsyn.2021.790773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/02/2021] [Indexed: 11/13/2022] Open
Abstract
The precise subsynaptic organization of proteins at the postsynaptic membrane controls synaptic transmission. In particular, postsynaptic receptor complexes are concentrated in distinct membrane nanodomains to optimize synaptic signaling. However, despite the clear functional relevance of subsynaptic receptor organization to synaptic transmission and plasticity, the mechanisms that underlie the nanoscale organization of the postsynaptic membrane remain elusive. Over the last decades, the field has predominantly focused on the role of protein-protein interactions in receptor trafficking and positioning in the synaptic membrane. In contrast, the contribution of lipids, the principal constituents of the membrane, to receptor positioning at the synapse remains poorly understood. Nevertheless, there is compelling evidence that the synaptic membrane is enriched in specific lipid species and that deregulation of lipid homeostasis in neurons severely affects synaptic functioning. In this review we focus on how lipids are organized at the synaptic membrane, with special emphasis on how current models of membrane organization could contribute to protein distribution at the synapse and synaptic transmission. Finally, we will present an outlook on how novel technical developments could be applied to study the dynamic interplay between lipids and proteins at the postsynaptic membrane.
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Affiliation(s)
- Manon Westra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Yolanda Gutierrez
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Harold D MacGillavry
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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8
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Show your true color: Mammalian cell surface staining for tracking cellular identity in multiplexing and beyond. Curr Opin Chem Biol 2021; 66:102102. [PMID: 34861482 DOI: 10.1016/j.cbpa.2021.102102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/18/2021] [Accepted: 10/27/2021] [Indexed: 12/23/2022]
Abstract
Fluorescence microscopy revolutionized cell biology and changed requirements for dyes towards higher brightness, novel capacities, and specific targets. With the need for multiplexing assays in high-throughput methodologies, surface staining gained particular interest because it allows rapid application of exogenous stains to track cellular identity in mixed populations. Indeed, the last decade has enriched the toolbox of general lipid stains, fluorescent lipid analogues, sugar-binding lectins, and protein-specific antibodies enabling the first rationally designed plasma membrane-specific dyes. Still, multiple challenges exist, and the unique properties of each dye must be considered when selecting a staining approach for a specific application. Recent advances are also promising that future dyes will provide ultimate brightness and photostability in diverse colors and reduced sizes for high-resolution imaging.
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9
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Ochmann SE, Joshi H, Büber E, Franquelim HG, Stegemann P, Saccà B, Keyser UF, Aksimentiev A, Tinnefeld P. DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity. NANO LETTERS 2021; 21:8634-8641. [PMID: 34662130 DOI: 10.1021/acs.nanolett.1c02584] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Signal transmission in neurons goes along with changes in the transmembrane potential. To report them, different approaches, including optical voltage-sensing dyes and genetically encoded voltage indicators, have evolved. Here, we present a DNA nanotechnology-based system and demonstrated its functionality on liposomes. Using DNA origami, we incorporated and optimized different properties such as membrane targeting and voltage sensing modularly. As a sensing unit, we used a hydrophobic red dye anchored to the membrane and an anionic green dye at the DNA to connect the nanostructure and the membrane dye anchor. Voltage-induced displacement of the anionic donor unit was read out by fluorescence resonance energy transfer (FRET) changes of single sensors attached to liposomes. A FRET change of ∼5% for ΔΨ = 100 mV was observed. The working mechanism of the sensor was rationalized by molecular dynamics simulations. Our approach holds potential for an application as nongenetically encoded membrane sensors.
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Affiliation(s)
- Sarah E Ochmann
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Himanshu Joshi
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61820, United States
| | - Ece Büber
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | | | - Pierre Stegemann
- Center of Medical Biotechnology (ZMB) and Center for Nano Integration Duisburg-Essen (CENIDE), University of Duisburg-Essen, 45117 Essen, Germany
| | - Barbara Saccà
- Center of Medical Biotechnology (ZMB) and Center for Nano Integration Duisburg-Essen (CENIDE), University of Duisburg-Essen, 45117 Essen, Germany
| | - Ulrich F Keyser
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61820, United States
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 81377 München, Germany
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10
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Lorizate M, Terrones O, Nieto-Garai JA, Rojo-Bartolomé I, Ciceri D, Morana O, Olazar-Intxausti J, Arboleya A, Martin A, Szynkiewicz M, Calleja-Felipe M, Bernardino de la Serna J, Contreras FX. Super-Resolution Microscopy Using a Bioorthogonal-Based Cholesterol Probe Provides Unprecedented Capabilities for Imaging Nanoscale Lipid Heterogeneity in Living Cells. SMALL METHODS 2021; 5:e2100430. [PMID: 34928061 DOI: 10.1002/smtd.202100430] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/26/2021] [Indexed: 06/14/2023]
Abstract
Despite more than 20 years of work since the lipid raft concept was proposed, the existence of these nanostructures remains highly controversial due to the lack of noninvasive methods to investigate their native nanorganization in living unperturbed cells. There is an unmet need for probes for direct imaging of nanoscale membrane dynamics with high spatial and temporal resolution in living cells. In this paper, a bioorthogonal-based cholesterol probe (chol-N3 ) is developed that, combined with nanoscopy, becomes a new powerful method for direct visualization and characterization of lipid raft at unprecedented resolution in living cells. The chol-N3 probe mimics cholesterol in synthetic and cellular membranes without perturbation. When combined with live-cell super-resolution microscopy, chol-N3 demonstrates the existence of cholesterol-rich nanodomains of <50 nm at the plasma membrane of resting living cells. Using this tool, the lipid membrane structure of such subdiffraction limit domains is identified, and the nanoscale spatiotemporal organization of cholesterol in the plasma membrane of living cells reveals multiple cholesterol diffusion modes at different spatial localizations. Finally, imaging across thick organ samples outlines the potential of this new method to address essential biological questions that were previously beyond reach.
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Affiliation(s)
- Maier Lorizate
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Oihana Terrones
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Iratxe Rojo-Bartolomé
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Dalila Ciceri
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Ornella Morana
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - June Olazar-Intxausti
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Aroa Arboleya
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Alexia Martin
- National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Marta Szynkiewicz
- Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Research Complex at Harwell, Oxford, OX11 0FA, UK
| | - Maria Calleja-Felipe
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Jorge Bernardino de la Serna
- National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
- Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Research Complex at Harwell, Oxford, OX11 0FA, UK
- NIHR Imperial Biomedical Research Centre, London, SW7 2AZ, UK
| | - F-Xabier Contreras
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48011, Spain
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11
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Javanainen M, Martinez-Seara H, Kelly CV, Jungwirth P, Fábián B. Anisotropic diffusion of membrane proteins at experimental timescales. J Chem Phys 2021; 155:015102. [PMID: 34241397 DOI: 10.1063/5.0054973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Single-particle tracking (SPT) experiments of lipids and membrane proteins provide a wealth of information about the properties of biomembranes. Careful analysis of SPT trajectories can reveal deviations from ideal Brownian behavior. Among others, this includes confinement effects and anomalous diffusion, which are manifestations of both the nanoscale structure of the underlying membrane and the structure of the diffuser. With the rapid increase in temporal and spatial resolution of experimental methods, a new aspect of the motion of the particle, namely, anisotropic diffusion, might become relevant. This aspect that so far received only little attention is the anisotropy of the diffusive motion and may soon provide an additional proxy to the structure and topology of biomembranes. Unfortunately, the theoretical framework for detecting and interpreting anisotropy effects is currently scattered and incomplete. Here, we provide a computational method to evaluate the degree of anisotropy directly from molecular dynamics simulations and also point out a way to compare the obtained results with those available from SPT experiments. In order to probe the effects of anisotropic diffusion, we performed coarse-grained molecular dynamics simulations of peripheral and integral membrane proteins in flat and curved bilayers. In agreement with the theoretical basis, our computational results indicate that anisotropy can persist up to the rotational relaxation time [τ=(2Dr)-1], after which isotropic diffusion is observed. Moreover, the underlying topology of the membrane bilayer can couple with the geometry of the particle, thus extending the spatiotemporal domain over which this type of motion can be detected.
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Affiliation(s)
- Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
| | - Christopher V Kelly
- Department of Physics and Astronomy, Wayne State University, 666 W Hancock Street, Detroit, Michigan 48201, USA
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
| | - Balázs Fábián
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
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12
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Chmielińska A, Stepien P, Bonarek P, Girych M, Enkavi G, Rog T, Dziedzicka-Wasylewska M, Polit A. Can di-4-ANEPPDHQ reveal the structural differences between nanodiscs and liposomes? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183649. [PMID: 33991503 DOI: 10.1016/j.bbamem.2021.183649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/15/2021] [Accepted: 05/10/2021] [Indexed: 11/17/2022]
Abstract
The potential-sensitive di-4-ANEPPDHQ dye is presently gaining popularity in structural studies of the lipid bilayer. Within the bilayer, dye environmental sensitivity originates from the excitation induced charge redistribution and is usually attributed to solvent relaxation. Here, di-4-ANEPPDHQ is utilized to compare the structure of neutral and negatively charged lipid bilayers between two model systems: the nanodiscs and the liposomes. Using the well-established approach of measuring solvatochromic shifts of the steady-state spectra to study the bilayer structural changes has proved insufficient in this case. By applying an in-depth analysis of time-resolved fluorescence decays and emission spectra, we distinguished and characterized two and three distinct emissive di-4-ANEPPDHQ species in the liposomes and the nanodiscs, respectively. These emissive species were ascribed to the dual emission of the dye rather than to solvent relaxation. An additional, long-lived component present in the nanodiscs was associated with a unique domain of high order, postulated recently. Our results reveal that the di-4-ANEPPDHQ steady-state fluorescence should be interpreted with caution. With the experimental approach presented here, the di-4-ANEPPDHQ sensitivity was improved. We confirmed that the bilayer structure is, indeed, altered in the nanodiscs. Moreover, molecular dynamic simulations showed a distribution of the probe in the nanodiscs plane, which is sensitive to lipid composition. In POPC nanodiscs, probe frequently interacts with MSP, while in POPC-POPG nanodiscs, such interactions are rare. We did not observe, however, any impact of those interactions on the probe fluorescence.
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Affiliation(s)
- Anna Chmielińska
- Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Piotr Stepien
- Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Piotr Bonarek
- Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, Gustaf Hällströmin katu 2, 00014 Helsinki, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, Gustaf Hällströmin katu 2, 00014 Helsinki, Finland
| | - Tomasz Rog
- Department of Physics, University of Helsinki, Gustaf Hällströmin katu 2, 00014 Helsinki, Finland
| | - Marta Dziedzicka-Wasylewska
- Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Agnieszka Polit
- Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
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13
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Bunker A, Róg T. Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery. Front Mol Biosci 2020; 7:604770. [PMID: 33330633 PMCID: PMC7732618 DOI: 10.3389/fmolb.2020.604770] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.
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Affiliation(s)
- Alex Bunker
- Division of Pharmaceutical Biosciences, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, University of Helsinki, Helsinki, Finland
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14
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Filipe HAL, Moreno MJ, Loura LMS. The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations. Molecules 2020; 25:E3424. [PMID: 32731549 PMCID: PMC7435664 DOI: 10.3390/molecules25153424] [Citation(s) in RCA: 9] [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: 07/08/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022] Open
Abstract
Fluorescent probes have been employed for more than half a century to study the structure and dynamics of model and biological membranes, using spectroscopic and/or microscopic experimental approaches. While their utilization has led to tremendous progress in our knowledge of membrane biophysics and physiology, in some respects the behavior of bilayer-inserted membrane probes has long remained inscrutable. The location, orientation and interaction of fluorophores with lipid and/or water molecules are often not well known, and they are crucial for understanding what the probe is actually reporting. Moreover, because the probe is an extraneous inclusion, it may perturb the properties of the host membrane system, altering the very properties it is supposed to measure. For these reasons, the need for independent methodologies to assess the behavior of bilayer-inserted fluorescence probes has been recognized for a long time. Because of recent improvements in computational tools, molecular dynamics (MD) simulations have become a popular means of obtaining this important information. The present review addresses MD studies of all major classes of fluorescent membrane probes, focusing in the period between 2011 and 2020, during which such work has undergone a dramatic surge in both the number of studies and the variety of probes and properties accessed.
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Affiliation(s)
- Hugo A. L. Filipe
- Chemistry Department, Coimbra Chemistry Center, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal;
| | - Maria João Moreno
- Coimbra Chemistry Center and CNC—Center for Neuroscience and Cell Biology, Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal;
| | - Luís M. S. Loura
- Coimbra Chemistry Center and CNC—Center for Neuroscience and Cell Biology, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
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15
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Yano Y, Hanashima S, Tsuchikawa H, Yasuda T, Slotte JP, London E, Murata M. Sphingomyelins and ent-Sphingomyelins Form Homophilic Nano-Subdomains within Liquid Ordered Domains. Biophys J 2020; 119:539-552. [PMID: 32710823 PMCID: PMC7399500 DOI: 10.1016/j.bpj.2020.06.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/19/2020] [Accepted: 06/26/2020] [Indexed: 12/29/2022] Open
Abstract
Sphingomyelin (SM), a major component of small domains (or lipid rafts) in mammalian cell membranes, forms a liquid-ordered phase in the presence of cholesterol (Cho). However, the nature of molecular interactions within the ordered SM/Cho phase remains elusive. We previously revealed that stearoyl-SM (SSM) and its enantiomer (ent-SSM) separately form nano-subdomains within the liquid-ordered phase involving homophilic SSM-SSM and ent-SSM-ent-SSM interactions. In this study, the details of the subdomain formation by SSMs at the nanometer range were examined using Förster resonance energy transfer (FRET) measurements in lipid bilayers containing SSM and ent-SSM, dioleoyl-phosphatidylcholine and Cho. Although microscopy detected a stereochemical effect on partition coefficient favoring stereochemically homophilic interactions in the liquid-ordered state, it showed no significant difference in large-scale liquid-ordered domain formation by the two stereoisomers. In contrast to the uniform domains seen microscopy, FRET analysis using fluorescent donor- and acceptor-labeled SSM showed distinct differences in SM and ent-SM colocalization within nanoscale distances. Donor- and acceptor-labeled SSM showed significantly higher FRET efficiency than did donor-labeled SSM and acceptor-labeled ent-SSM in lipid vesicles composed of “racemic” (1:1) mixtures of SSM/ent-SSM with dioleoylphosphatidylcholine and Cho. The difference in FRET efficiency indicated that SSM and ent-SSM assemble to form separate nano-subdomains. The average size of the subdomains decreased as temperature increased, and at physiological temperatures, the subdomains were found to have a single-digit nanometer radius. These results suggest that (even in the absence of ent-SM) SM-SM interactions play a crucial role in forming nano-subdomains within liquid-ordered domains and may be a key feature of lipid microdomains (or rafts) in biological membranes.
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Affiliation(s)
- Yo Yano
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Tomokazu Yasuda
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York.
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan.
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16
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Levental I, Levental KR, Heberle FA. Lipid Rafts: Controversies Resolved, Mysteries Remain. Trends Cell Biol 2020; 30:341-353. [PMID: 32302547 DOI: 10.1016/j.tcb.2020.01.009] [Citation(s) in RCA: 316] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 01/08/2023]
Abstract
The lipid raft hypothesis postulates that lipid-lipid interactions can laterally organize biological membranes into domains of distinct structures, compositions, and functions. This proposal has in equal measure exhilarated and frustrated membrane research for decades. While the physicochemical principles underlying lipid-driven domains has been explored and is well understood, the existence and relevance of such domains in cells remains elusive, despite decades of research. Here, we review the conceptual underpinnings of the raft hypothesis and critically discuss the supporting and contradicting evidence in cells, focusing on why controversies about the composition, properties, and even the very existence of lipid rafts remain unresolved. Finally, we highlight several recent breakthroughs that may resolve existing controversies and suggest general approaches for moving beyond questions of the existence of rafts and towards understanding their physiological significance.
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Affiliation(s)
- Ilya Levental
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 70030, USA.
| | - Kandice R Levental
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 70030, USA
| | - Frederick A Heberle
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 33830, USA
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17
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Yu Y, Li M, Yu Y. Tracking Single Molecules in Biomembranes: Is Seeing Always Believing? ACS NANO 2019; 13:10860-10868. [PMID: 31589406 PMCID: PMC7179047 DOI: 10.1021/acsnano.9b07445] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The spatial organization of molecules in cell membranes and their dynamic interactions play a central role in regulating cell functions. Single-particle tracking (SPT), a technique in which single molecules are imaged and tracked in real time, has led to breakthrough discoveries regarding these spatiotemporal complexities of cell membranes. There are, however, emerging concerns about factors that might produce misleading interpretations of SPT results. Here, we briefly review the application of SPT to understanding the nanoscale heterogeneities of plasma membranes, with a focus on the unique challenges, pitfalls, and limitations that confront the use of nanoparticles as imaging probes for tracking the dynamics of single molecules in cell membranes.
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18
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Liao YH, Lin CH, Cheng CY, Wong WC, Juo JY, Hsieh CL. Monovalent and Oriented Labeling of Gold Nanoprobes for the High-Resolution Tracking of a Single-Membrane Molecule. ACS NANO 2019; 13:10918-10928. [PMID: 31259529 DOI: 10.1021/acsnano.9b01176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Single-molecule tracking is a powerful method to study molecular dynamics in living systems including biological membranes. High-resolution single-molecule tracking requires a bright and stable signal, which has typically been facilitated by nanoparticles due to their superb optical properties. However, there are concerns about using a nanoparticle to label a single molecule because of its relatively large size and the possibility of cross-linking multiple target molecules, both of which could affect the original molecular dynamics. In this work, using various labeling schemes, we investigate the effects using nanoparticles to measure the diffusion of single-membrane molecules. By conjugating a low density of streptavidin (sAv) to gold nanoparticles (AuNPs) of different sizes (10, 15, 20, 30, and 40 nm), we isolate and quantify the effect of the particle size on the diffusion of biotinylated lipids in supported lipid bilayers (SLBs). We find that single sAv tends to cross-link two biotinylated lipids, leading to a much slower diffusion in SLBs. We further demonstrate a simple and robust strategy for the monovalent and oriented labeling of a single lipid molecule with a AuNP by using naturally dimeric rhizavidin (rAv) as a bridge, thus connecting the biotinylated nanoparticle surface and biotinylated target molecule. The rAv-AuNP conjugate demonstrates fast and free diffusion in SLBs (2-3 μm2/s for rAv-AuNP sizes of 10-40 nm), which is comparable to the diffusion of dye-labeled lipids, indicating that the adverse size and cross-linking effects are successfully avoided. We also note that the diffusion of dye-labeled lipids critically depends on the choice of dye, which could report different diffusion coefficients by about 20% (2.2 μm2/s of ATTO647N and 2.6 μm2/s of ATTO532). By comparing the diffusion of the uniformly and randomly oriented labeling of a single lipid molecule with a AuNP, we conclude that oriented labeling is favorable for measuring the diffusion of single-membrane molecules. Our work shows that the measured diffusion of the membrane molecule is highly sensitive to the molecular design of the cross-linker for labeling. The demonstrated approach of monovalent and oriented AuNP labeling provides the opportunity to study single-molecule membrane dynamics at much higher spatiotemporal resolutions and, most importantly, without labeling artifacts.
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Affiliation(s)
- Yi-Hung Liao
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
| | - Chih-Hsiang Lin
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
| | - Ching-Ya Cheng
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
| | - Wai Cheng Wong
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
| | - Jz-Yuan Juo
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
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19
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Favard C, Chojnacki J, Merida P, Yandrapalli N, Mak J, Eggeling C, Muriaux D. HIV-1 Gag specifically restricts PI(4,5)P2 and cholesterol mobility in living cells creating a nanodomain platform for virus assembly. SCIENCE ADVANCES 2019; 5:eaaw8651. [PMID: 31616784 PMCID: PMC6774721 DOI: 10.1126/sciadv.aaw8651] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 09/09/2019] [Indexed: 06/10/2023]
Abstract
HIV-1 Gag protein assembles at the plasma membrane of infected cells for viral particle formation. Gag targets lipids, mainly PI(4,5)P2, at the inner leaflet of this membrane. Here, we address the question whether Gag is able to trap specifically PI(4,5)P2 or other lipids during HIV-1 assembly in the host CD4+ T lymphocytes. Lipid dynamics within and away from HIV-1 assembly sites were determined using super-resolution microscopy coupled with scanning fluorescence correlation spectroscopy in living cells. Analysis of HIV-1-infected cells revealed that, upon assembly, HIV-1 is able to specifically trap PI(4,5)P2 and cholesterol, but not phosphatidylethanolamine or sphingomyelin. Furthermore, our data showed that Gag is the main driving force to restrict the mobility of PI(4,5)P2 and cholesterol at the cell plasma membrane. This is the first direct evidence highlighting that HIV-1 creates its own specific lipid environment by selectively recruiting PI(4,5)P2 and cholesterol as a membrane nanoplatform for virus assembly.
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Affiliation(s)
- C. Favard
- Montpellier Infectious Disease Research Institute, IRIM, CNRS–Université Montpellier, 1919, route de Mende, 34293 Montpellier Cedex, France
| | - J. 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
| | - P. Merida
- Montpellier Infectious Disease Research Institute, IRIM, CNRS–Université Montpellier, 1919, route de Mende, 34293 Montpellier Cedex, France
| | - N. Yandrapalli
- Montpellier Infectious Disease Research Institute, IRIM, CNRS–Université Montpellier, 1919, route de Mende, 34293 Montpellier Cedex, France
| | - J. Mak
- Institute for Glycomics, Griffith University Gold Coast, Southport, QLD, Australia
| | - C. 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
| | - D. Muriaux
- Montpellier Infectious Disease Research Institute, IRIM, CNRS–Université Montpellier, 1919, route de Mende, 34293 Montpellier Cedex, France
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20
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Pinkwart K, Schneider F, Lukoseviciute M, Sauka-Spengler T, Lyman E, Eggeling C, Sezgin E. Nanoscale dynamics of cholesterol in the cell membrane. J Biol Chem 2019; 294:12599-12609. [PMID: 31270209 PMCID: PMC6709632 DOI: 10.1074/jbc.ra119.009683] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/26/2019] [Indexed: 12/22/2022] Open
Abstract
Cholesterol constitutes ∼30-40% of the mammalian plasma membrane, a larger fraction than of any other single component. It is a major player in numerous signaling processes as well as in shaping molecular membrane architecture. However, our knowledge of the dynamics of cholesterol in the plasma membrane is limited, restricting our understanding of the mechanisms regulating its involvement in cell signaling. Here, we applied advanced fluorescence imaging and spectroscopy approaches on in vitro (model membranes) and in vivo (live cells and embryos) membranes as well as in silico analysis to systematically study the nanoscale dynamics of cholesterol in biological membranes. Our results indicate that cholesterol diffuses faster than phospholipids in live membranes, but not in model membranes. Interestingly, a detailed statistical diffusion analysis suggested two-component diffusion for cholesterol in the plasma membrane of live cells. One of these components was similar to a freely diffusing phospholipid analogue, whereas the other one was significantly faster. When a cholesterol analogue was localized to the outer leaflet only, the fast diffusion of cholesterol disappeared, and it diffused similarly to phospholipids. Overall, our results suggest that cholesterol diffusion in the cell membrane is heterogeneous and that this diffusional heterogeneity is due to cholesterol's nanoscale interactions and localization in the membrane.
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Affiliation(s)
- Kerstin Pinkwart
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Falk Schneider
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Martyna Lukoseviciute
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Edward Lyman
- Departments of Physics and Astronomy and Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,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
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
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21
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Poojari C, Wilkosz N, Lira RB, Dimova R, Jurkiewicz P, Petka R, Kepczynski M, Róg T. Behavior of the DPH fluorescence probe in membranes perturbed by drugs. Chem Phys Lipids 2019; 223:104784. [PMID: 31199906 DOI: 10.1016/j.chemphyslip.2019.104784] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/09/2019] [Accepted: 06/08/2019] [Indexed: 12/22/2022]
Abstract
1,6-Diphenyl-1,3,5-hexatriene (DPH) is one of the most commonly used fluorescent probes to study dynamical and structural properties of lipid bilayers and cellular membranes via measuring steady-state or time-resolved fluorescence anisotropy. In this study, we present a limitation in the use of DPH to predict the order of lipid acyl chains when the lipid bilayer is doped with itraconazole (ITZ), an antifungal drug. Our steady-state fluorescence anisotropy measurements showed a significant decrease in fluorescence anisotropy of DPH embedded in the ITZ-containing membrane, suggesting a substantial increase in membrane fluidity, which indirectly indicates a decrease in the order of the hydrocarbon chains. This result or its interpretation is in disagreement with the fluorescence recovery after photobleaching measurements and molecular dynamics (MD) simulation data. The results of these experiments and calculations indicate an increase in the hydrocarbon chain order. The MD simulations of the bilayer containing both ITZ and DPH provide explanations for these observations. Apparently, in the presence of the drug, the DPH molecules are pushed deeper into the hydrophobic membrane core below the lipid double bonds, and the probe predominately adopts the orientation of the ITZ molecules that is parallel to the membrane surface, instead of orienting parallel to the lipid acyl chains. For this reason, DPH anisotropy provides information related to the less ordered central region of the membrane rather than reporting the properties of the upper segments of the lipid acyl chains.
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Affiliation(s)
- Chetan Poojari
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101 Tampere, Finland
| | - Natalia Wilkosz
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Rafael B Lira
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry AS CR, v.v.i, Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Rafał Petka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland.
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, PO Box 64, FI-00014, Helsinki, Finland.
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22
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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23
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Sezgin E, Schneider F, Galiani S, Urbančič I, Waithe D, Lagerholm BC, Eggeling C. Measuring nanoscale diffusion dynamics in cellular membranes with super-resolution STED-FCS. Nat Protoc 2019; 14:1054-1083. [PMID: 30842616 DOI: 10.1038/s41596-019-0127-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/04/2019] [Indexed: 11/08/2022]
Abstract
Super-resolution microscopy techniques enable optical imaging in live cells with unprecedented spatial resolution. They unfortunately lack the temporal resolution required to directly investigate cellular dynamics at scales sufficient to measure molecular diffusion. These fast time scales are, on the other hand, routinely accessible by spectroscopic techniques such as fluorescence correlation spectroscopy (FCS). To enable the direct investigation of fast dynamics at the relevant spatial scales, FCS has been combined with super-resolution stimulated emission depletion (STED) microscopy. STED-FCS has been applied in point or scanning mode to reveal nanoscale diffusion behavior of molecules in live cells. In this protocol, we describe the technical details of performing point STED-FCS (pSTED-FCS) and scanning STED-FCS (sSTED-FCS) measurements, from calibration and sample preparation to data acquisition and analysis. We give particular emphasis to 2D diffusion dynamics in cellular membranes, using molecules tagged with organic fluorophores. These measurements can be accomplished within 4-6 h by those proficient in fluorescence imaging.
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Affiliation(s)
- Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Falk Schneider
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Silvia Galiani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Iztok Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Solid State Physics Department, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Dominic Waithe
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Christian 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.
- Institute of Applied Optics, Friedrich-Schiller-University Jena, Jena, Germany.
- Department of Biophysical Imaging, Leibniz Institute of Photonic Technology e.V., Jena, Germany.
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24
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Javanainen M, Martinez-Seara H. Rapid diffusion of cholesterol along polyunsaturated membranes via deep dives. Phys Chem Chem Phys 2019; 21:11660-11669. [PMID: 31119241 DOI: 10.1039/c9cp02022e] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cholesterol regulates the function of membrane proteins either via direct or membrane-mediated effects. Therefore, its ready availability is crucial for many protein-governed cellular processes. Recent studies suggest that cholesterol can partition to the core of polyunsaturated membranes, where cholesterol binding sites of many membrane proteins are also located. This core region is characterized by a lower viscosity. Therefore, we hypothesized that cholesterol partitioning into the membrane interior increases the rate of its diffusion in polyunsaturated membrane environments. We studied the behavior of cholesterol in membranes with increasing level of lipid chain unsaturation using a combination of atomistic and coarse-grained molecular dynamics simulations. Our simulations suggest a strong correlation between entropy-driven enhanced cholesterol partitioning to the membrane core and its faster lateral diffusion, which indicates that the less viscous membrane core indeed provides an efficient means for cholesterol movement in polyunsaturated membrane environments.
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Affiliation(s)
- Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, CZ-166 10 Prague 6, Czech Republic.
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