1
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Narayan KB, Baeyens L, James HP, Swain A, Baumgart T. Fluorescence imaging of lamellipodin-mediated biomolecular condensates on solid supported lipid bilayer membranes. Methods Enzymol 2024; 700:33-48. [PMID: 38971606 DOI: 10.1016/bs.mie.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
Biomolecular condensates play a major role in numerous cellular processes, including several that occur on the surface of lipid bilayer membranes. There is increasing evidence that cellular membrane trafficking phenomena, including the internalization of the plasma membrane through endocytosis, are mediated by multivalent protein-protein interactions that can lead to phase separation. We have recently found that proteins involved in the clathrin-independent endocytic pathway named Fast Endophilin Mediated Endocytosis can undergo liquid-liquid phase separation (LLPS) in solution and on lipid bilayer membranes. Here, the protein solution concentrations required for phase separation to be observed are significantly smaller compared to those required for phase separation in solution. LLPS is challenging to systematically characterize in cellular systems in general, and on biological membranes in particular. Model membrane approaches are more suitable for this purpose as they allow for precise control over the nature and amount of the components present in a mixture. Here we describe a method that enables the imaging of LLPS domain formation on solid supported lipid bilayers. These allow for facile imaging, provide long-term stability, and avoid clustering of vesicles and vesicle-attached features (such as buds and tethers) in the presence of multi-valent membrane interacting proteins.
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Affiliation(s)
- Karthik B Narayan
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Laura Baeyens
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Honey Priya James
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Aparna Swain
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA.
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2
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Walker G, Brown C, Ge X, Kumar S, Muzumdar MD, Gupta K, Bhattacharyya M. Oligomeric organization of membrane proteins from native membranes at nanoscale spatial and single-molecule resolution. NATURE NANOTECHNOLOGY 2024; 19:85-94. [PMID: 38012273 PMCID: PMC10981947 DOI: 10.1038/s41565-023-01547-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/16/2023] [Indexed: 11/29/2023]
Abstract
The oligomeric organization of membrane proteins in native cell membranes is a critical regulator of their function. High-resolution quantitative measurements of oligomeric assemblies and how they change under different conditions are indispensable to understanding membrane protein biology. We report Native-nanoBleach, a total internal reflection fluorescence microscopy-based single-molecule photobleaching step analysis technique to determine the oligomeric distribution of membrane proteins directly from native membranes at an effective spatial resolution of ~10 nm. We achieved this by capturing target membrane proteins in native nanodiscs with their proximal native membrane environment using amphipathic copolymers. We applied Native-nanoBleach to quantify the oligomerization status of structurally and functionally diverse membrane proteins, including a receptor tyrosine kinase (TrkA) and a small GTPase (KRas) under growth-factor binding and oncogenic mutations, respectively. Our data suggest that Native-nanoBleach provides a sensitive, single-molecule platform to quantify membrane protein oligomeric distributions in native membranes under physiologically and clinically relevant conditions.
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Affiliation(s)
- Gerard Walker
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Caroline Brown
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Xiangyu Ge
- Department of Pathology, Yale University, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Shailesh Kumar
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Mandar D Muzumdar
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
- Department of Genetics, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Yale University, New Haven, CT, USA
- Yale Cancer Center, New Haven, USA
| | - Kallol Gupta
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
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3
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Cawley J, Berger BA, Odudimu AT, Singh AN, Santa DE, McDarby AI, Honerkamp-Smith AR, Wittenberg NJ. Imaging Giant Vesicle Membrane Domains with a Luminescent Europium Tetracycline Complex. ACS OMEGA 2023; 8:29314-29323. [PMID: 37599986 PMCID: PMC10433515 DOI: 10.1021/acsomega.3c02721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023]
Abstract
Microdomains in lipid bilayer membranes are routinely imaged using organic fluorophores that preferentially partition into one of the lipid phases, resulting in fluorescence contrast. Here, we show that membrane microdomains in giant unilamellar vesicles (GUVs) can be visualized with europium luminescence using a complex of europium III (Eu3+) and tetracycline (EuTc). EuTc is unlike typical organic lipid probes in that it is a coordination complex with a unique excitation/emission wavelength combination (396/617 nm), a very large Stokes shift (221 nm), and a very narrow emission bandwidth (8 nm). The probe preferentially interacts with liquid disordered domains in GUVs, which results in intensity contrast across the surface of phase-separated GUVs. Interestingly, EuTc also alters GM1 ganglioside partitioning. GM1 typically partitions into liquid ordered domains, but after labeling phase-separated GUVs with EuTc, cholera toxin B-subunit (CTxB), which binds GM1, labels liquid disordered domains. We also demonstrate that EuTc, but not free Eu3+ or Tc, significantly reduces lipid diffusion coefficients. Finally, we show that EuTc can be used to label cellular membranes similar to a traditional membrane probe. EuTc may find utility as a membrane imaging probe where its large Stokes shift and sharp emission band would enable multicolor imaging.
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Affiliation(s)
- Jennie
L. Cawley
- Department
of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, Pennsylvania 18015, United States
| | - Brett A. Berger
- Department
of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, Pennsylvania 18015, United States
| | - Adeyemi T. Odudimu
- Department
of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, Pennsylvania 18015, United States
| | - Aarshi N. Singh
- Department
of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, Pennsylvania 18015, United States
| | - Dane E. Santa
- Department
of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, Pennsylvania 18015, United States
| | - Ariana I. McDarby
- Department
of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, Pennsylvania 18015, United States
| | - Aurelia R. Honerkamp-Smith
- Department
of Physics, Lehigh University, 17 Memorial Drive East, Bethlehem, Pennsylvania 18015, United States
| | - Nathan J. Wittenberg
- Department
of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, Pennsylvania 18015, United States
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4
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Kinnun JJ, Scott HL, Bolmatov D, Collier CP, Charlton TR, Katsaras J. Biophysical studies of lipid nanodomains using different physical characterization techniques. Biophys J 2023; 122:931-949. [PMID: 36698312 PMCID: PMC10111277 DOI: 10.1016/j.bpj.2023.01.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
For the past 50 years, evidence for the existence of functional lipid domains has been steadily accumulating. Although the notion of functional lipid domains, also known as "lipid rafts," is now widely accepted, this was not always the case. This ambiguity surrounding lipid domains could be partly attributed to the fact that they are highly dynamic, nanoscopic structures. Since most commonly used techniques are sensitive to microscale structural features, it is therefore, not surprising that it took some time to reach a consensus regarding their existence. In this review article, we will discuss studies that have used techniques that are inherently sensitive to nanoscopic structural features (i.e., neutron scatting, nuclear magnetic resonance, and Förster resonance energy transfer). We will also mention techniques that may be of use in the future (i.e., cryoelectron microscopy, droplet interface bilayers, inelastic x-ray scattering, and neutron reflectometry), which can further our understanding of the different and unique physicochemical properties of nanoscopic lipid domains.
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Affiliation(s)
- Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Haden L Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Dima Bolmatov
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Timothy R Charlton
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - John Katsaras
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
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5
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Walker G, Brown C, Ge X, Kumar S, Muzumdar MD, Gupta K, Bhattacharyya M. Determination of oligomeric organization of membrane proteins from native membranes at nanoscale-spatial and single-molecule resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.19.529138. [PMID: 36865290 PMCID: PMC9980011 DOI: 10.1101/2023.02.19.529138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The oligomeric organization of membrane proteins in native cell membranes is a critical regulator of their function. High-resolution quantitative measurements of oligomeric assemblies and how they change under different conditions are indispensable to the understanding of membrane protein biology. We report a single-molecule imaging technique (Native-nanoBleach) to determine the oligomeric distribution of membrane proteins directly from native membranes at an effective spatial resolution of ∼10 nm. We achieved this by capturing target membrane proteins in "native nanodiscs" with their proximal native membrane environment using amphipathic copolymers. We established this method using structurally and functionally diverse membrane proteins with well-established stoichiometries. We then applied Native-nanoBleach to quantify the oligomerization status of a receptor tyrosine kinase (TrkA) and a small GTPase (KRas) under conditions of growth-factor binding or oncogenic mutations, respectively. Native-nanoBleach provides a sensitive, single-molecule platform to quantify membrane protein oligomeric distributions in native membranes at an unprecedented spatial resolution.
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6
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Luchini A, Tidemand FG, Johansen NT, Sebastiani F, Corucci G, Fragneto G, Cárdenas M, Arleth L. Dark peptide discs for the investigation of membrane proteins in supported lipid bilayers: the case of synaptobrevin 2 (VAMP2). NANOSCALE ADVANCES 2022; 4:4526-4534. [PMID: 36341300 PMCID: PMC9595196 DOI: 10.1039/d2na00384h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Supported lipid bilayers (SLBs) are commonly used as model systems mimicking biological membranes. Recently, we reported a new method to produce SLBs with incorporated membrane proteins, which is based on the application of peptide discs [Luchini et al., Analytical Chemistry, 2020, 92, 1081-1088]. Peptide discs are small discoidal particles composed of a lipid core and an outer belt of self-assembled 18A peptides. SLBs including membrane proteins can be formed by depositing the peptide discs on a solid support and subsequently removing the peptide by buffer rinsing. Here, we introduce a new variant of the 18A peptide, named dark peptide (d18A). d18A exhibits UV absorption at 214 nm, whereas the absorption at 280 nm is negligible. This improves sample preparation as it enables a direct quantification of the membrane protein concentration in the peptide discs by measuring UV absorption at 280 nm. We describe the application of the peptide discs prepared with d18A (dark peptide discs) to produce SLBs with a membrane protein, synaptobrevin 2 (VAMP2). The collected data showed the successful formation of SLBs with high surface coverage and incorporation of VAMP2 in a single orientation with the extramembrane domain exposed towards the bulk solvent. Compared to 18A, we found that d18A was more efficiently removed from the SLB. Our data confirmed the structural organisation of VAMP2 as including both α-helical and β-sheet secondary structure. We further verified the orientation of VAMP2 in the SLBs by characterising the binding of VAMP2 with α-synuclein. These results point at the produced SLBs as relevant membrane models for biophysical studies as well as nanostructured biomaterials.
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Affiliation(s)
| | - Frederik Grønbæk Tidemand
- Department of Plant and Environmental Sciences, University of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Nicolai Tidemand Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Federica Sebastiani
- Biofilms Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University Per Albin Hanssons Väg 35 21432 Malmö Sweden
| | - Giacomo Corucci
- Institut Laue-Langevin 71 Avenue des Martyrs, BP 156 38042 Grenoble France
- Université Grenoble Alpes, Ecole Doctorale de Physique 110 Rue de la Chimie 38400 Saint-Martin-d'Hères France
| | - Giovanna Fragneto
- Institut Laue-Langevin 71 Avenue des Martyrs, BP 156 38042 Grenoble France
- Université Grenoble Alpes, Ecole Doctorale de Physique 110 Rue de la Chimie 38400 Saint-Martin-d'Hères France
| | - Marité Cárdenas
- Biofilms Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University Per Albin Hanssons Väg 35 21432 Malmö Sweden
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5 2100 Copenhagen Denmark
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Bonet NF, Cava DG, Vélez M. Quartz crystal microbalance and atomic force microscopy to characterize mimetic systems based on supported lipids bilayer. Front Mol Biosci 2022; 9:935376. [PMID: 35992275 PMCID: PMC9382308 DOI: 10.3389/fmolb.2022.935376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 11/23/2022] Open
Abstract
Quartz Crystal Microbalance (QCM) with dissipation and Atomic Force Microscopy (AFM) are two characterization techniques that allow describing processes taking place at solid-liquid interfaces. Both are label-free and, when used in combination, provide kinetic, thermodynamic and structural information at the nanometer scale of events taking place at surfaces. Here we describe the basic operation principles of both techniques, addressing a non-specialized audience, and provide some examples of their use for describing biological events taking place at supported lipid bilayers (SLBs). The aim is to illustrate current strengths and limitations of the techniques and to show their potential as biophysical characterization techniques.
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8
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Almeida‐Marrero V, Bethlehem F, Longo S, Bertolino MC, Torres T, Huskens J, de la Escosura A. Tailored Multivalent Targeting of Siglecs with Photosensitizing Liposome Nanocarriers. Angew Chem Int Ed Engl 2022; 61:e202206900. [PMID: 35652453 PMCID: PMC9401027 DOI: 10.1002/anie.202206900] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Indexed: 11/18/2022]
Abstract
The modification of surfaces with multiple ligands allows the formation of platforms for the study of multivalency in diverse processes. Herein we use this approach for the implementation of a photosensitizer (PS)-nanocarrier system that binds efficiently to siglec-10, a member of the CD33 family of siglecs (sialic acid (SA)-binding immunoglobulin-like lectins). In particular, a zinc phthalocyanine derivative bearing three SA moieties (PcSA) has been incorporated in the membrane of small unilamellar vesicles (SUVs), retaining its photophysical properties upon insertion into the SUV's membrane. The interaction of these biohybrid systems with human siglec-10-displaying supported lipid bilayers (SLBs) has shown the occurrence of weakly multivalent, superselective interactions between vesicle and SLB. The SLB therefore acts as an excellent cell membrane mimic, while the binding with PS-loaded SUVs shows the potential for targeting siglec-expressing cells with photosensitizing nanocarriers.
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Affiliation(s)
- Verónica Almeida‐Marrero
- Department of Organic ChemistryUniversidad Autónoma de MadridCampus de Cantoblanco28049MadridSpain
| | - Fleur Bethlehem
- Department of Molecules & MaterialsMESA+ Institute for NanotechnologyFaculty of Science and TechnologyUniversity of TwenteP.O. Box 2177500 AEEnschedeThe Netherlands
| | - Sara Longo
- Department of Molecules & MaterialsMESA+ Institute for NanotechnologyFaculty of Science and TechnologyUniversity of TwenteP.O. Box 2177500 AEEnschedeThe Netherlands
| | - M. Candelaria Bertolino
- Department of Molecules & MaterialsMESA+ Institute for NanotechnologyFaculty of Science and TechnologyUniversity of TwenteP.O. Box 2177500 AEEnschedeThe Netherlands
| | - Tomás Torres
- Department of Organic ChemistryUniversidad Autónoma de MadridCampus de Cantoblanco28049MadridSpain
- Institute for Advanced Research in Chemistry (IAdChem)Campus de Cantoblanco28049MadridSpain
- Tomás TorresIMDEA NanoscienceCampus de Cantoblanco28049MadridSpain
| | - Jurriaan Huskens
- Department of Molecules & MaterialsMESA+ Institute for NanotechnologyFaculty of Science and TechnologyUniversity of TwenteP.O. Box 2177500 AEEnschedeThe Netherlands
| | - Andrés de la Escosura
- Department of Organic ChemistryUniversidad Autónoma de MadridCampus de Cantoblanco28049MadridSpain
- Institute for Advanced Research in Chemistry (IAdChem)Campus de Cantoblanco28049MadridSpain
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9
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Almeida-Marrero V, Bethlehem F, Longo S, Bertolino MC, Torres T, Huskens J, de la Escosura A. Tailored Multivalent Targeting of Siglecs with Photosensitizing Liposome Nanocarriers. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Verónica Almeida-Marrero
- Universidad Autonoma de Madrid - Campus de Cantoblanco: Universidad Autonoma de Madrid Organic Chemistry SPAIN
| | - Fleur Bethlehem
- University of Twente Institute for Nanotechnology: Universiteit Twente MESA+ Institute for Nanotechnology MESA+ NETHERLANDS
| | - Sara Longo
- University of Twente Institute for Nanotechnology: Universiteit Twente MESA+ Institute for Nanotechnology MESA+ NETHERLANDS
| | - M. Candelaria Bertolino
- University of Twente Institute for Nanotechnology: Universiteit Twente MESA+ Institute for Nanotechnology MESA+ NETHERLANDS
| | - Tomas Torres
- Universidad Autonoma de Madrid - Campus de Cantoblanco: Universidad Autonoma de Madrid Departmento de Química Orgánica Cantoblanco 28049 Madrid SPAIN
| | - Jurriaan Huskens
- University of Twente Institute for Nanotechnology: Universiteit Twente MESA+ Institute for Nanotechnology MESA+ NETHERLANDS
| | - Andrés de la Escosura
- Universidad Autonoma de Madrid - Campus de Cantoblanco: Universidad Autonoma de Madrid Organic Chemistry C/ Francisco Tomás y Valiente 7, Facultad de CienciasMódulo 01, Planta 4, L-401 28049 Madrid SPAIN
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10
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Cava DG, Vélez M. Supported Lipid Bilayers (SLBs) to Study Amyloid-Lipid Membrane Interactions with Atomic Force Microscopy. Methods Mol Biol 2022; 2538:109-116. [PMID: 35951296 DOI: 10.1007/978-1-0716-2529-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Supported lipid bilayers (SLBs) are model membrane systems that can be used to study the interaction between amyloid fibers and membranes with atomic force microscopy (AFM). This chapter describes the preparation of SLBs on mica that can then be used as a substrate for fiber absorption. AFM can then be used to study the topography of the lipid-protein surface to study the evolution of the fibers, as well as the modifications on the membrane induced by their presence.
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Affiliation(s)
- Daniel G Cava
- Instituto de Catálisis y Petroleoquímica (CSIC), (Cantoblanco) Madrid, Spain
| | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica (CSIC), (Cantoblanco) Madrid, Spain.
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11
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Claus RA, Graeler MH. Sphingolipidomics in Translational Sepsis Research-Biomedical Considerations and Perspectives. Front Med (Lausanne) 2021; 7:616578. [PMID: 33553212 PMCID: PMC7854573 DOI: 10.3389/fmed.2020.616578] [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: 10/12/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Scientific Background: Sphingolipids are a highly diverse group of lipids with respect to physicochemical properties controlling either structure, distribution, or function, all of them regulating cellular response in health and disease. Mass spectrometry, on the other hand, is an analytical technique characterizing ionized molecules or fragments thereof by mass-to-charge ratios, which has been prosperingly developed for rapid and reliable qualitative and quantitative identification of lipid species. Parallel to best performance of in-depth chromatographical separation of lipid classes, preconditions of precise quantitation of unique molecular species by preprocessing of biological samples have to be fulfilled. As a consequence, “lipid profiles” across model systems and human individuals, esp. complex (clinical) samples, have become eminent over the last couple of years due to sensitivity, specificity, and discriminatory capability. Therefore, it is significance to consider the entire experimental strategy from sample collection and preparation, data acquisition, analysis, and interpretation. Areas Covered: In this review, we outline considerations with clinical (i.e., human) samples with special emphasis on sample handling, specific physicochemical properties, target measurements, and resulting profiling of sphingolipids in biomedicine and translational research to maximize sensitivity and specificity as well as to provide robust and reproducible results. A brief commentary is also provided regarding new insights of “clinical sphingolipidomics” in translational sepsis research. Expert Opinion: The role of mass spectrometry of sphingolipids and related species (“sphingolipidomics”) to investigate cellular and compartment-specific response to stress, e.g., in generalized infection and sepsis, is on the rise and the ability to integrate multiple datasets from diverse classes of biomolecules by mass spectrometry measurements and metabolomics will be crucial to fostering our understanding of human health as well as response to disease and treatment.
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Affiliation(s)
- Ralf A Claus
- Department for Anesthesiology and Intensive Care Medicine, Sepsis Research, Jena University Hospital, Jena, Germany
| | - Markus H Graeler
- Department for Anesthesiology and Intensive Care Medicine, Sepsis Research, Jena University Hospital, Jena, Germany.,Center for Sepsis Care & Control, Jena University Hospital, Jena, Germany.,Center for Molecular Biomedicine (CMB), Jena University Hospital, Jena, Germany
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12
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Pore-forming proteins: From defense factors to endogenous executors of cell death. Chem Phys Lipids 2020; 234:105026. [PMID: 33309552 DOI: 10.1016/j.chemphyslip.2020.105026] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
Pore-forming proteins (PFPs) and small antimicrobial peptides (AMPs) represent a large family of molecules with the common ability to punch holes in cell membranes to alter their permeability. They play a fundamental role as infectious bacteria's defensive tools against host's immune system and as executors of endogenous machineries of regulated cell death in eukaryotic cells. Despite being highly divergent in primary sequence and 3D structure, specific folds of pore-forming domains have been conserved. In fact, pore formation is considered an ancient mechanism that takes place through a general multistep process involving: membrane partitioning and insertion, oligomerization and pore formation. However, different PFPs and AMPs assemble and form pores following different mechanisms that could end up either in the formation of protein-lined or protein-lipid pores. In this review, we analyze the current findings in the mechanism of action of different PFPs and AMPs that support a wide role of membrane pore formation in nature. We also provide the newest insights into the development of state-of-art techniques that have facilitated the characterization of membrane pores. To understand the physiological role of these peptides/proteins or develop clinical applications, it is essential to uncover the molecular mechanism of how they perforate membranes.
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13
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Woodward X, Kelly CV. Single-lipid dynamics in phase-separated supported lipid bilayers. Chem Phys Lipids 2020; 233:104991. [PMID: 33121937 DOI: 10.1016/j.chemphyslip.2020.104991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 11/26/2022]
Abstract
Phase separation is a fundamental organizing mechanism on cellular membranes. Lipid phases have complex dependencies on the membrane composition, curvature, tension, and temperature. Lipid diffusion rates vary by up to ten-fold between liquid-disordered (Ld) and liquid-ordered (Lo) phases depending on the membrane composition, measurement technique, and the surrounding environment. This manuscript reports the lipid diffusion on phase-separated supported lipid bilayers (SLBs) with varying temperature, composition, and lipid phase. Lipid diffusion is measured by single-particle tracking (SPT) and fluorescence correlation spectroscopy (FCS) via custom data acquisition and analysis protocols that apply to diverse membranes systems. Traditionally, SPT is sensitive to diffuser aggregation, whereas the diffusion rates reported by FCS are unaffected by the presence of immobile aggregates. Within this manuscript, we report (1) improved single-particle tracking analysis of lipid diffusion, (2) comparison and consistency between diffusion measurement methods for non-Brownian diffusers, and (3) the application of these methods to measure the phase, temperature, and composition dependencies in lipid diffusion. We demonstrate improved SPT analysis methods that yield consistent FCS and SPT diffusion results even when most fluorescent lipids are frequently confined within aggregates within the membrane. With varying membrane composition and temperature, we demonstrate differences in diffusion between the Ld and Lo phases of SLBs.
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Affiliation(s)
- Xinxin Woodward
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States
| | - Christopher V Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States.
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14
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Tzoneva R, Stoyanova T, Petrich A, Popova D, Uzunova V, Momchilova A, Chiantia S. Effect of Erufosine on Membrane Lipid Order in Breast Cancer Cell Models. Biomolecules 2020; 10:E802. [PMID: 32455962 PMCID: PMC7277205 DOI: 10.3390/biom10050802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/11/2022] Open
Abstract
Alkylphospholipids are a novel class of antineoplastic drugs showing remarkable therapeutic potential. Among them, erufosine (EPC3) is a promising drug for the treatment of several types of tumors. While EPC3 is supposed to exert its function by interacting with lipid membranes, the exact molecular mechanisms involved are not known yet. In this work, we applied a combination of several fluorescence microscopy and analytical chemistry approaches (i.e., scanning fluorescence correlation spectroscopy, line-scan fluorescence correlation spectroscopy, generalized polarization imaging, as well as thin layer and gas chromatography) to quantify the effect of EPC3 in biophysical models of the plasma membrane, as well as in cancer cell lines. Our results indicate that EPC3 affects lipid-lipid interactions in cellular membranes by decreasing lipid packing and increasing membrane disorder and fluidity. As a consequence of these alterations in the lateral organization of lipid bilayers, the diffusive dynamics of membrane proteins are also significantly increased. Taken together, these findings suggest that the mechanism of action of EPC3 could be linked to its effects on fundamental biophysical properties of lipid membranes, as well as on lipid metabolism in cancer cells.
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Affiliation(s)
- Rumiana Tzoneva
- Bulgarian Academy of Sciences, Institute of Biophysics and Biomedical Engineering, 1113 Sofia, Bulgaria; (R.T.); (T.S.); (D.P.); (V.U.); (A.M.)
| | - Tihomira Stoyanova
- Bulgarian Academy of Sciences, Institute of Biophysics and Biomedical Engineering, 1113 Sofia, Bulgaria; (R.T.); (T.S.); (D.P.); (V.U.); (A.M.)
| | - Annett Petrich
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Street 24-25, 14476 Potsdam, Germany;
| | - Desislava Popova
- Bulgarian Academy of Sciences, Institute of Biophysics and Biomedical Engineering, 1113 Sofia, Bulgaria; (R.T.); (T.S.); (D.P.); (V.U.); (A.M.)
| | - Veselina Uzunova
- Bulgarian Academy of Sciences, Institute of Biophysics and Biomedical Engineering, 1113 Sofia, Bulgaria; (R.T.); (T.S.); (D.P.); (V.U.); (A.M.)
| | - Albena Momchilova
- Bulgarian Academy of Sciences, Institute of Biophysics and Biomedical Engineering, 1113 Sofia, Bulgaria; (R.T.); (T.S.); (D.P.); (V.U.); (A.M.)
| | - Salvatore Chiantia
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Street 24-25, 14476 Potsdam, Germany;
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15
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Shelby ML, He W, Dang AT, Kuhl TL, Coleman MA. Cell-Free Co-Translational Approaches for Producing Mammalian Receptors: Expanding the Cell-Free Expression Toolbox Using Nanolipoproteins. Front Pharmacol 2019; 10:744. [PMID: 31333463 PMCID: PMC6616253 DOI: 10.3389/fphar.2019.00744] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 12/28/2022] Open
Abstract
Membranes proteins make up more than 60% of current drug targets and account for approximately 30% or more of the cellular proteome. Access to this important class of proteins has been difficult due to their inherent insolubility and tendency to aggregate in aqueous solutions. Understanding membrane protein structure and function demands novel means of membrane protein production that preserve both their native conformational state as well as function. Over the last decade, cell-free expression systems have emerged as an important complement to cell-based expression of membrane proteins due to their simple and customizable experimental parameters. One approach to overcome the solubility and stability limitations of purified membrane proteins is to support them in stable, native-like states within nanolipoprotein particles (NLPs), aka nanodiscs. This has become common practice to facilitate biochemical and biophysical characterization of proteins of interest. NLP technology can be easily coupled with cell-free systems to achieve functional membrane protein production for this purpose. Our approach involves utilizing cell-free expression systems in the presence of NLPs or using co-translation techniques to perform one-pot expression and self-assembly of membrane protein/NLP complexes. We describe how cell-free reactions can be modified to render control over nanoparticle size and monodispersity in support of membrane protein production. These modifications have been exploited to facilitate co-expression of full-length functional membrane proteins such as G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). In particular, we summarize the state of the art in NLP-assisted cell-free coexpression of these important classes of membrane proteins as well as evaluate the advances in and prospects for this technology that will drive drug discovery against these targets. We conclude with a prospective on the use of NLPs to produce as well as deliver functional mammalian membrane-bound proteins for a range of applications.
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Affiliation(s)
- Megan L Shelby
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Wei He
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Amanda T Dang
- University of California at Davis, Davis, CA, United States
| | - Tonya L Kuhl
- University of California at Davis, Davis, CA, United States
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, Livermore, CA, United States.,University of California at Davis, Davis, CA, United States
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16
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Engineering the interface between lipid membranes and nanoporous gold: A study by quartz crystal microbalance with dissipation monitoring. Biointerphases 2018; 13:011002. [PMID: 29304551 DOI: 10.1116/1.5010249] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Nanoporous gold (np-Au) is a nanostructured metal with many desirable attributes. Despite the growing number of applications of nanoporous materials, there are still open questions regarding their fabrication and subsequent surface functionalization. For example, the hydrophobic nature of gold surfaces makes the formation of planar supported lipid layers challenging. Here, the authors engineer the interface between np-Au and 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid layers using well-differentiated approaches based on vesicle adsorption and solvent exchange methods. The results reveal that the nanotopography of the np-Au surface plays a clear role in the vesicle adsorption process. Compared to vesicle adsorption, the solvent exchange method proves successful in the formation of planar supported lipid bilayers in both np-Au and planar Au surfaces, being less sensitive to the surface morphological features. The influence of nanostructured surfaces on lipid layer formation is determined by the driving mechanisms behind each process, i.e., the balance of adhesion and cohesion forces in vesicle adsorption and lyotropic lipid phase transitions in solvent exchange, respectively. A better understanding of such interactions will contribute to the development of a variety of applications, from electrochemical biosensors to drug screening and delivery systems, using nanoporous gold coated with stimuli-responsive lipid layers.
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17
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Kiessling V, Liang B, Kreutzberger AJB, Tamm LK. Planar Supported Membranes with Mobile SNARE Proteins and Quantitative Fluorescence Microscopy Assays to Study Synaptic Vesicle Fusion. Front Mol Neurosci 2017; 10:72. [PMID: 28360838 PMCID: PMC5352703 DOI: 10.3389/fnmol.2017.00072] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/03/2017] [Indexed: 12/31/2022] Open
Abstract
Synaptic vesicle membrane fusion, the process by which neurotransmitter gets released at the presynaptic membrane is mediated by a complex interplay between proteins and lipids. The realization that the lipid bilayer is not just a passive environment where other molecular players like SNARE proteins act, but is itself actively involved in the process, makes the development of biochemical and biophysical assays particularly challenging. We summarize in vitro assays that use planar supported membranes and fluorescence microscopy to address some of the open questions regarding the molecular mechanisms of SNARE-mediated membrane fusion. Most of the assays discussed in this mini-review were developed in our lab over the last 15 years. We emphasize the sample requirements that we found are important for the successful application of these methods.
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Affiliation(s)
- Volker Kiessling
- Center for Membrane and Cell Physiology, University of VirginiaCharlottesville, VA, USA; Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, VA, USA
| | - Binyong Liang
- Center for Membrane and Cell Physiology, University of VirginiaCharlottesville, VA, USA; Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, VA, USA
| | - Alex J B Kreutzberger
- Center for Membrane and Cell Physiology, University of VirginiaCharlottesville, VA, USA; Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, VA, USA
| | - Lukas K Tamm
- Center for Membrane and Cell Physiology, University of VirginiaCharlottesville, VA, USA; Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, VA, USA
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18
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Yamada S, Isogai T, Tero R, Tanaka-Takiguchi Y, Ujihara T, Kinoshita M, Takiguchi K. Septin Interferes with the Temperature-Dependent Domain Formation and Disappearance of Lipid Bilayer Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:12823-12832. [PMID: 27934514 DOI: 10.1021/acs.langmuir.6b03452] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Domain formation or compartmentalization in a lipid bilayer membrane has been thought to take place dynamically in cell membranes and play important roles in the spatiotemporal regulation of their physiological functions. In addition, the membrane skeleton, which is a protein assembly beneath the cell membrane, also regulates the properties as well as the morphology of membranes because of its role as a diffusion barrier against constitutive molecules of the membrane or as a scaffold for physiological reactions. Therefore, it is important to study the relationship between lipid bilayer membranes and proteins that form the membrane skeleton. Among cytoskeletal systems, septin is unique because it forms arrays on liposomes that contain phosphoinositides, and this property is thought to contribute to the formation of the annulus in sperm flagellum. In this study, a supported lipid bilayer (SLB) was used to investigate the effect of septin on lipid bilayers because SLBs rather than liposomes are suitable for observation of the membrane domains formed. We found that SLBs containing phosphatidylinositol (PI) reversibly form domains by decreasing the temperature and that septin affects both the formation and the disappearance of the cooling-induced domain. Septin inhibits the growth of cooling-induced domains during decreases in temperature and inhibits the dispersion and the disappearance of those domains during increases in temperature. These results indicate that septin complexes, i.e., filaments or oligomers assembling on the surface of lipid bilayer membranes, can regulate the dynamics of domain formation via their behavior as an anchor for PI molecules.
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Affiliation(s)
| | | | - Ryugo Tero
- The Electronics-Inspired Interdisciplinary Research Institute, Toyohashi University of Technology , Toyohashi 441-8580, Japan
| | | | | | | | - Kingo Takiguchi
- Structural Biology Research Center, Nagoya University , Nagoya 464-8601, Japan
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19
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Yang ST, Lim SI, Kiessling V, Kwon I, Tamm LK. Site-specific fluorescent labeling to visualize membrane translocation of a myristoyl switch protein. Sci Rep 2016; 6:32866. [PMID: 27605302 PMCID: PMC5015116 DOI: 10.1038/srep32866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/16/2016] [Indexed: 12/20/2022] Open
Abstract
Fluorescence approaches have been widely used for elucidating the dynamics of protein-membrane interactions in cells and model systems. However, non-specific multi-site fluorescent labeling often results in a loss of native structure and function, and single cysteine labeling is not feasible when native cysteines are required to support a protein's folding or catalytic activity. Here, we develop a method using genetic incorporation of non-natural amino acids and bio-orthogonal chemistry to site-specifically label with a single fluorescent small molecule or protein the myristoyl-switch protein recoverin, which is involved in rhodopsin-mediated signaling in mammalian visual sensory neurons. We demonstrate reversible Ca(2+)-responsive translocation of labeled recoverin to membranes and show that recoverin favors membranes with negative curvature and high lipid fluidity in complex heterogeneous membranes, which confers spatio-temporal control over down-stream signaling events. The site-specific orthogonal labeling technique is promising for structural, dynamical, and functional studies of many lipid-anchored membrane protein switches.
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Affiliation(s)
- Sung-Tae Yang
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Sung In Lim
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Volker Kiessling
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Inchan Kwon
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904, USA
- School of Materials Science and Engineering, and Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Lukas K. Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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20
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The role of cholesterol in membrane fusion. Chem Phys Lipids 2016; 199:136-143. [PMID: 27179407 DOI: 10.1016/j.chemphyslip.2016.05.003] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/07/2016] [Accepted: 05/10/2016] [Indexed: 12/21/2022]
Abstract
Cholesterol modulates the bilayer structure of biological membranes in multiple ways. It changes the fluidity, thickness, compressibility, water penetration and intrinsic curvature of lipid bilayers. In multi-component lipid mixtures, cholesterol induces phase separations, partitions selectively between different coexisting lipid phases, and causes integral membrane proteins to respond by changing conformation or redistribution in the membrane. But, which of these often overlapping properties are important for membrane fusion?-Here we review a range of recent experiments that elucidate the multiple roles that cholesterol plays in SNARE-mediated and viral envelope glycoprotein-mediated membrane fusion.
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