1
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Barbotin A, Billaudeau C, Sezgin E, Carballido-López R. Quantification of membrane fluidity in bacteria using TIR-FCS. Biophys J 2024:S0006-3495(24)00407-7. [PMID: 38877702 DOI: 10.1016/j.bpj.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
Plasma membrane fluidity is an important phenotypic feature that regulates the diffusion, function, and folding of transmembrane and membrane-associated proteins. In bacterial cells, variations in membrane fluidity are known to affect respiration, transport, and antibiotic resistance. Membrane fluidity must therefore be tightly regulated to adapt to environmental variations and stresses such as temperature fluctuations or osmotic shocks. Quantitative investigation of bacterial membrane fluidity has been, however, limited due to the lack of available tools, primarily due to the small size and membrane curvature of bacteria that preclude most conventional analysis methods used in eukaryotes. Here, we develop an assay based on total internal reflection-fluorescence correlation spectroscopy (TIR-FCS) to directly measure membrane fluidity in live bacteria via the diffusivity of fluorescent membrane markers. With simulations validated by experiments, we could determine how the small size, high curvature, and geometry of bacteria affect diffusion measurements and correct subsequent measurements for unbiased diffusion coefficient estimation. We used this assay to quantify the fluidity of the cytoplasmic membranes of the Gram-positive bacteria Bacillus subtilis (rod-shaped) and Staphylococcus aureus (coccus) at high (37°C) and low (20°C) temperatures in a steady state and in response to a cold shock, caused by a shift from high to low temperature. The steady-state fluidity was lower at 20°C than at 37°C, yet differed between B. subtilis and S. aureus at 37°C. Upon cold shock, the membrane fluidity decreased further below the steady-state fluidity at 20°C and recovered within 30 min in both bacterial species. Our minimally invasive assay opens up exciting perspectives for the study of a wide range of phenomena affecting the bacterial membrane, from disruption by chemicals or antibiotics to viral infection or change in nutrient availability.
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Affiliation(s)
- Aurélien Barbotin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Cyrille Billaudeau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Rut Carballido-López
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
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2
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Doktorova M, Khelashvili G, Brown MF. Efficient calculation of orientation-dependent lipid dynamics from membrane simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.23.542012. [PMID: 37292992 PMCID: PMC10245828 DOI: 10.1101/2023.05.23.542012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular dynamics simulations of lipid membranes have become increasingly impactful in biophysics because they offer atomistic resolution of structural fluctuations in relation to their functional outputs. Yet quantitative characterization of multiscale processes is a formidable challenge due to the distribution of motions that evade analysis of discrete simulation data. Here we investigate the efficient calculation of CH bond relaxation rates from membrane simulations. Widely used computational approaches offer numerical simplicity but fall short of capturing crucial aspects of the orientation dependence of the dynamics. To circumvent this problem, we introduced a robust framework based on liquid crystal theory which considers explicitly the CH bond motions with respect to the director axis (bilayer normal). Analysis of the orientation dependence of the dynamics shows excellent agreement with experiment, illustrating how the ordering potential affects the calculated relaxation rates. Furthermore, a fit-based resampling of the autocorrelation function of the bond fluctuations validates the new approach for low-temporal resolution data. The recovered relaxation rates indicate that at short timescales, both with and without cholesterol, the local motions of CH bonds describe the bilayer microviscosity and resemble liquid hydrocarbons. Our results establish the critical role of the orientational anisotropy in analysis of membrane simulations, explain fundamental aspects of lipid dynamics, and provide guidelines for extracting information that can be compared to experimental data.
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Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology & Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
- Department of Physics, University of Arizona, Tucson, AZ, USA
- Program in Applied Mathematics, University of Arizona, Tucson, AZ, USA
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3
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Tripathy M, Srivastava A. Lipid packing in biological membranes governs protein localization and membrane permeability. Biophys J 2023; 122:2727-2743. [PMID: 37254482 PMCID: PMC10397809 DOI: 10.1016/j.bpj.2023.05.028] [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: 12/16/2022] [Revised: 04/18/2023] [Accepted: 05/25/2023] [Indexed: 06/01/2023] Open
Abstract
Plasma membrane (PM) heterogeneity has long been implicated in various cellular functions. However, mechanistic principles governing functional regulations of lipid environment are not well understood due to the inherent complexities associated with the relevant length and timescales that limit both direct experimental measurements and their interpretation. In this context, computer simulations hold immense potential to investigate molecular-level interactions and mechanisms that lead to PM heterogeneity and its functions. Herein, we investigate spatial and dynamic heterogeneity in model membranes with coexisting liquid ordered and liquid disordered phases and characterize the membrane order in terms of the local topological changes in lipid environment using the nonaffine deformation framework. Furthermore, we probe the packing defects in these membranes, which can be considered as the conjugate of membrane order assessed in terms of the nonaffine parameter. In doing so, we formalize the connection between membrane packing and local membrane order and use that to explore the mechanistic principles behind their functions. Our observations suggest that heterogeneity in mixed phase membranes is a consequence of local lipid topology and its temporal evolution, which give rise to disparate lipid packing in ordered and disordered domains. This in turn governs the distinct nature of packing defects in these domains that can play a crucial role in preferential localization of proteins in mixed phase membranes. Furthermore, we observe that lipid packing also leads to contrasting distribution of free volume in the membrane core region in ordered and disordered membranes, which can lead to distinctive membrane permeability of small molecules. Our results, thus, indicate that heterogeneity in mixed phase membranes closely governs the membrane functions that may emerge from packing-related basic design principles.
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Affiliation(s)
- Madhusmita Tripathy
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bangalore, Karnataka, India.
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bangalore, Karnataka, India.
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4
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Schlegel J, Porebski B, Andronico L, Hanke L, Edwards S, Brismar H, Murrell B, McInerney GM, Fernandez-Capetillo O, Sezgin E. A Multiparametric and High-Throughput Platform for Host-Virus Binding Screens. NANO LETTERS 2023; 23:3701-3707. [PMID: 36892970 PMCID: PMC10176574 DOI: 10.1021/acs.nanolett.2c04884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Speed is key during infectious disease outbreaks. It is essential, for example, to identify critical host binding factors to pathogens as fast as possible. The complexity of host plasma membrane is often a limiting factor hindering fast and accurate determination of host binding factors as well as high-throughput screening for neutralizing antimicrobial drug targets. Here, we describe a multiparametric and high-throughput platform tackling this bottleneck and enabling fast screens for host binding factors as well as new antiviral drug targets. The sensitivity and robustness of our platform were validated by blocking SARS-CoV-2 particles with nanobodies and IgGs from human serum samples.
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Affiliation(s)
- Jan Schlegel
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Luca Andronico
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Steven Edwards
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, 17165 Solna, Sweden
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, 17165 Solna, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
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5
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Wang HY, Chan SH, Dey S, Castello-Serrano I, Rosen MK, Ditlev JA, Levental KR, Levental I. Coupling of protein condensates to ordered lipid domains determines functional membrane organization. SCIENCE ADVANCES 2023; 9:eadf6205. [PMID: 37126554 PMCID: PMC10132753 DOI: 10.1126/sciadv.adf6205] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
During T cell activation, the transmembrane adaptor protein LAT (linker for activation of T cells) forms biomolecular condensates with Grb2 and Sos1, facilitating signaling. LAT has also been associated with cholesterol-rich condensed lipid domains; However, the potential coupling between protein condensation and lipid phase separation and its role in organizing T cell signaling were unknown. Here, we report that LAT/Grb2/Sos1 condensates reconstituted on model membranes can induce and template lipid domains, indicating strong coupling between lipid- and protein-based phase separation. Correspondingly, activation of T cells induces cytoplasmic protein condensates that associate with and stabilize raft-like membrane domains. Inversely, lipid domains nucleate and stabilize LAT protein condensates in both reconstituted and living systems. This coupling of lipid and protein assembly is functionally important, as uncoupling of lipid domains from cytoplasmic protein condensates abrogates T cell activation. Thus, thermodynamic coupling between protein condensates and ordered lipid domains regulates the functional organization of living membranes.
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Affiliation(s)
- Hong-Yin Wang
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Sze Ham Chan
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Simli Dey
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Ivan Castello-Serrano
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jonathon A Ditlev
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Program in Molecular Medicine, Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kandice R Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
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6
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Li Q, Ferrare JT, Silver J, Wilson JO, Arteaga-Castaneda L, Qiu W, Vershinin M, King SJ, Neuman KC, Xu J. Cholesterol in the cargo membrane amplifies tau inhibition of kinesin-1-based transport. Proc Natl Acad Sci U S A 2023; 120:e2212507120. [PMID: 36626558 PMCID: PMC9934065 DOI: 10.1073/pnas.2212507120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 12/08/2022] [Indexed: 01/11/2023] Open
Abstract
Intracellular cargos are often membrane-enclosed and transported by microtubule-based motors in the presence of microtubule-associated proteins (MAPs). Whereas increasing evidence reveals how MAPs impact the interactions between motors and microtubules, critical questions remain about the impact of the cargo membrane on transport. Here we combined in vitro optical trapping with theoretical approaches to determine the effect of a lipid cargo membrane on kinesin-based transport in the presence of MAP tau. Our results demonstrate that attaching kinesin to a fluid lipid membrane reduces the inhibitory effect of tau on kinesin. Moreover, adding cholesterol, which reduces kinesin diffusion in the cargo membrane, amplifies the inhibitory effect of tau on kinesin binding in a dosage-dependent manner. We propose that reduction of kinesin diffusion in the cargo membrane underlies the effect of cholesterol on kinesin binding in the presence of tau, and we provide a simple model for this proposed mechanism. Our study establishes a direct link between cargo membrane cholesterol and MAP-based regulation of kinesin-1. The cholesterol effects uncovered here may more broadly extend to other lipid alterations that impact motor diffusion in the cargo membrane, including those associated with aging and neurological diseases.
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Affiliation(s)
- Qiaochu Li
- Department of Physics, University of California, Merced, CA95343
| | - James T. Ferrare
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - Jonathan Silver
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - John O. Wilson
- Department of Physics, University of California, Merced, CA95343
| | | | - Weihong Qiu
- Department of Physics, Oregon State University, Corvallis, OR97331
| | - Michael Vershinin
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT84112
| | - Stephen J. King
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL32827
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - Jing Xu
- Department of Physics, University of California, Merced, CA95343
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7
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Giakoumatos EC, Gascoigne L, Gumí-Audenis B, García ÁG, Tuinier R, Voets IK. Impact of poly(ethylene glycol) functionalized lipids on ordering and fluidity of colloid supported lipid bilayers. SOFT MATTER 2022; 18:7569-7578. [PMID: 36165127 PMCID: PMC9555145 DOI: 10.1039/d2sm00806h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Colloid supported lipid bilayers (CSLBs) are highly appealing building blocks for functional colloids. In this contribution, we critically evaluate the impact on lipid ordering and CSLB fluidity of inserted additives. We focus on poly(ethylene glycol) (PEG) bearing lipids, which are commonly introduced to promote colloidal stability. We investigate whether their effect on the CSLB is related to the incorporated amount and chemical nature of the lipid anchor. To this end, CSLBs were prepared from lipids with a low or high melting temperature (Tm), DOPC, and DPPC, respectively. Samples were supplemented with either 0, 5 or 10 mol% of either a low or high Tm PEGylated lipid, DOPE-PEG2000 or DSPE-PEG2000, respectively. Lipid ordering was probed via differential scanning calorimetry and fluidity by fluorescence recovery after photobleaching. We find that up to 5 mol% of either PEGylated lipids could be incorporated into both membranes without any pronounced effects. However, the fluorescence recovery of the liquid-like DOPC membrane was markedly decelerated upon incorporating 10 mol% of either PEGylated lipids, whilst insertion of the anchoring lipids (DOPE and DSPE without PEG2000) had no detectable impact. Therefore, we conclude that the amount of incorporated PEG stabilizer, not the chemical nature of the lipid anchor, should be tuned carefully to achieve sufficient colloidal stability without compromising the membrane dynamics. These findings offer guidance for the experimental design of studies using CSLBs, such as those focusing on the consequences of intra- and inter-particle inhomogeneities for multivalent binding and the impact of additive mobility on superselectivity.
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Affiliation(s)
- Emma C Giakoumatos
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Levena Gascoigne
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Berta Gumí-Audenis
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Álvaro González García
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Remco Tuinier
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Ilja K Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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8
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Céspedes PF, Jainarayanan A, Fernández-Messina L, Valvo S, Saliba DG, Kurz E, Kvalvaag A, Chen L, Ganskow C, Colin-York H, Fritzsche M, Peng Y, Dong T, Johnson E, Siller-Farfán JA, Dushek O, Sezgin E, Peacock B, Law A, Aubert D, Engledow S, Attar M, Hester S, Fischer R, Sánchez-Madrid F, Dustin ML. T-cell trans-synaptic vesicles are distinct and carry greater effector content than constitutive extracellular vesicles. Nat Commun 2022; 13:3460. [PMID: 35710644 PMCID: PMC9203538 DOI: 10.1038/s41467-022-31160-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/07/2022] [Indexed: 12/19/2022] Open
Abstract
The immunological synapse is a molecular hub that facilitates the delivery of three activation signals, namely antigen, costimulation/corepression and cytokines, from antigen-presenting cells (APC) to T cells. T cells release a fourth class of signaling entities, trans-synaptic vesicles (tSV), to mediate bidirectional communication. Here we present bead-supported lipid bilayers (BSLB) as versatile synthetic APCs to capture, characterize and advance the understanding of tSV biogenesis. Specifically, the integration of juxtacrine signals, such as CD40 and antigen, results in the adaptive tailoring and release of tSV, which differ in size, yields and immune receptor cargo compared with steadily released extracellular vesicles (EVs). Focusing on CD40L+ tSV as model effectors, we show that PD-L1 trans-presentation together with TSG101, ADAM10 and CD81 are key in determining CD40L vesicular release. Lastly, we find greater RNA-binding protein and microRNA content in tSV compared with EVs, supporting the specialized role of tSV as intercellular messengers.
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Affiliation(s)
- Pablo F Céspedes
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK.
| | - Ashwin Jainarayanan
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Lola Fernández-Messina
- Immunology Service, Hospital de la Princesa, Instituto Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Madrid, Spain
- Intercellular communication in the inflammatory response. Vascular Physiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Salvatore Valvo
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - David G Saliba
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Elke Kurz
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Audun Kvalvaag
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Lina Chen
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Charity Ganskow
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Huw Colin-York
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
| | - Marco Fritzsche
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Errin Johnson
- Sir William Dunn School of Pathology, The University of Oxford, Oxford, UK
| | | | - Omer Dushek
- Sir William Dunn School of Pathology, The University of Oxford, Oxford, UK
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Simon Engledow
- Oxford Genomics Centre, Wellcome Centre for Human Genetics, The University of Oxford, Oxford, UK
| | - Moustafa Attar
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
- Oxford Genomics Centre, Wellcome Centre for Human Genetics, The University of Oxford, Oxford, UK
| | - Svenja Hester
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, The University of Oxford, Oxford, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, The University of Oxford, Oxford, UK
| | - Francisco Sánchez-Madrid
- Immunology Service, Hospital de la Princesa, Instituto Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Madrid, Spain
- Intercellular communication in the inflammatory response. Vascular Physiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK.
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9
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Membrane surfaces regulate assembly of ribonucleoprotein condensates. Nat Cell Biol 2022; 24:461-470. [PMID: 35411085 PMCID: PMC9035128 DOI: 10.1038/s41556-022-00882-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/26/2022] [Accepted: 03/03/2022] [Indexed: 12/20/2022]
Abstract
Biomolecular condensates organize biochemistry, yet little is known about how cells control the position and scale of these structures. In cells, condensates often appear as relatively small assemblies that do not coarsen into a single droplet despite their propensity to fuse. Here we report that ribonucleoprotein condensates of the Q-rich protein Whi3 interact with the endoplasmic reticulum, prompting us to examine how membrane association controls condensate size. Reconstitution reveals that membrane recruitment promotes Whi3 condensation under physiological conditions. These assemblies rapidly arrest, resembling size distributions seen in cells. The temporal ordering of molecular interactions and the slow diffusion of membrane-bound complexes can limit condensate size. Our experiments reveal a tradeoff between locally-enhanced protein concentration at membranes, favoring condensation, and an accompanying reduction in diffusion, restricting coarsening. Given that many condensates bind endomembranes, we predict that the biophysical properties of lipid bilayers are key for controlling condensate sizes throughout the cell.
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10
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Genetically encoded photo-switchable molecular sensors for optoacoustic and super-resolution imaging. Nat Biotechnol 2022; 40:598-605. [PMID: 34845372 PMCID: PMC9005348 DOI: 10.1038/s41587-021-01100-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/17/2021] [Indexed: 02/07/2023]
Abstract
Reversibly photo-switchable proteins are essential for many super-resolution fluorescence microscopic and optoacoustic imaging methods. However, they have yet to be used as sensors that measure the distribution of specific analytes at the nanoscale or in the tissues of live animals. Here we constructed the prototype of a photo-switchable Ca2+ sensor based on GCaMP5G that can be switched with 405/488-nm light and describe its molecular mechanisms at the structural level, including the importance of the interaction of the core barrel structure of the fluorescent protein with the Ca2+ receptor moiety. We demonstrate super-resolution imaging of Ca2+ concentration in cultured cells and optoacoustic Ca2+ imaging in implanted tumor cells in mice under controlled Ca2+ conditions. Finally, we show the generalizability of the concept by constructing examples of photo-switching maltose and dopamine sensors based on periplasmatic binding protein and G-protein-coupled receptor-based sensors.
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11
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Single-molecule manipulation of macromolecules on GUV or SUV membranes using optical tweezers. Biophys J 2021; 120:5454-5465. [PMID: 34813728 DOI: 10.1016/j.bpj.2021.11.2884] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/16/2021] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
Despite their wide applications in soluble macromolecules, optical tweezers have rarely been used to characterize the dynamics of membrane proteins, mainly due to the lack of model membranes compatible with optical trapping. Here, we examined optical trapping and mechanical properties of two potential model membranes, giant and small unilamellar vesicles (GUVs and SUVs, respectively) for studies of membrane protein dynamics. We found that optical tweezers can stably trap GUVs containing iodixanol with controlled membrane tension. The trapped GUVs with high membrane tension can serve as a force sensor to accurately detect reversible folding of a DNA hairpin or membrane binding of synaptotagmin-1 C2AB domain attached to the GUV. We also observed that SUVs are rigid enough to resist large pulling forces and are suitable for detecting protein conformational changes induced by force. Our methodologies may facilitate single-molecule manipulation studies of membrane proteins using optical tweezers.
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Sych T, Gurdap CO, Wedemann L, Sezgin E. How Does Liquid-Liquid Phase Separation in Model Membranes Reflect Cell Membrane Heterogeneity? MEMBRANES 2021; 11:323. [PMID: 33925240 PMCID: PMC8146956 DOI: 10.3390/membranes11050323] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 11/22/2022]
Abstract
Although liquid-liquid phase separation of cytoplasmic or nuclear components in cells has been a major focus in cell biology, it is only recently that the principle of phase separation has been a long-standing concept and extensively studied in biomembranes. Membrane phase separation has been reconstituted in simplified model systems, and its detailed physicochemical principles, including essential phase diagrams, have been extensively explored. These model membrane systems have proven very useful to study the heterogeneity in cellular membranes, however, concerns have been raised about how reliably they can represent native membranes. In this review, we will discuss how phase-separated membrane systems can mimic cellular membranes and where they fail to reflect the native cell membrane heterogeneity. We also include a few humble suggestions on which phase-separated systems should be used for certain applications, and which interpretations should be avoided to prevent unreliable conclusions.
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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; (T.S.); (C.O.G.); (L.W.)
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Marrink SJ, Levental I. Computational and Experimental Advances in Biomembranes: Resolving Their Complexity. J Phys Chem B 2020; 124:9975-9976. [PMID: 33176427 DOI: 10.1021/acs.jpcb.0c09401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Ilya Levental
- University of Virginia, Charlottesville, Virginia 22903, United States
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14
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Plochberger B, Sych T, Weber F, Novacek J, Axmann M, Stangl H, Sezgin E. Lipoprotein Particles Interact with Membranes and Transfer Their Cargo without Receptors. Biochemistry 2020; 59:4421-4428. [PMID: 33147967 PMCID: PMC7677925 DOI: 10.1021/acs.biochem.0c00748] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Lipid transfer from lipoprotein particles to cells is essential for lipid homeostasis. High-density lipoprotein (HDL) particles are mainly captured by cell membrane-associated scavenger receptor class B type 1 (SR-B1) from the bloodstream, while low-density and very-low-density lipoprotein (LDL and VLDL, respectively) particles are mostly taken up by receptor-mediated endocytosis. However, the role of the target lipid membrane itself in the transfer process has been largely neglected so far. Here, we study how lipoprotein particles (HDL, LDL, and VLDL) interact with synthetic lipid bilayers and cell-derived membranes and transfer their cargo subsequently. Employing cryo-electron microscopy, spectral imaging, and fluorescence (cross) correlation spectroscopy allowed us to observe integration of all major types of lipoprotein particles into the membrane and delivery of their cargo in a receptor-independent manner. Importantly, the biophysical properties of the target cell membranes change upon delivery of cargo. The concept of receptor-independent interaction of lipoprotein particles with membranes helps us to better understand lipoprotein particle biology and can be exploited for novel treatments of dyslipidemia diseases.
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Affiliation(s)
- Birgit Plochberger
- TU Wien, Institute of Applied Physics, Vienna 1040, Austria.,Johannes Kepler University Linz, Institute of Biophysics, Linz 4020, Austria.,Upper Austria University of Applied Sciences, Campus Linz, Linz 4020, Austria
| | - Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Florian Weber
- Upper Austria University of Applied Sciences, Campus Linz, Linz 4020, Austria.,Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Jiri Novacek
- CEITEC, Masaryk University, University Campus Bohunice, Brno 62500, Czech Republic
| | - Markus Axmann
- Medical University of Vienna, Center for Pathobiochemistry and Genetics, Institute of Medical Chemistry, Vienna 1090, Austria
| | - Herbert Stangl
- Medical University of Vienna, Center for Pathobiochemistry and Genetics, Institute of Medical Chemistry, Vienna 1090, Austria
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden.,MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, U.K
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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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Céspedes PF, Beckers D, Dustin ML, Sezgin E. Model membrane systems to reconstitute immune cell signaling. FEBS J 2020; 288:1070-1090. [DOI: 10.1111/febs.15488] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/26/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Pablo F. Céspedes
- Kennedy Institute of Rheumatology Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences University of Oxford UK
| | - Daniel Beckers
- MRC Human Immunology Unit MRC Weatherall Institute of Molecular Medicine University of Oxford UK
| | - Michael L. Dustin
- Kennedy Institute of Rheumatology Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences University of Oxford UK
| | - Erdinc Sezgin
- MRC Human Immunology Unit MRC Weatherall Institute of Molecular Medicine University of Oxford UK
- Science for Life Laboratory Department of Women's and Children's Health Karolinska Institutet Stockholm Sweden
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