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Miyazako H, Hoshino T. Rapid pattern formation in model cell membranes when using an electron beam. Colloids Surf B Biointerfaces 2022. [DOI: 10.1016/j.colsurfb.2022.112967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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2
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Komatsu R, Tanimoto Y, Ando K, Yasuhara K, Iwasaki Y, Hayashi F, Morigaki K. Nanofluidic Model Membrane for the Single-Molecule Observation of Membrane Proteins. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7234-7243. [PMID: 35641430 DOI: 10.1021/acs.langmuir.2c00724] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Membrane proteins play essential roles in the cell, and they constitute one of the most important targets of drugs. Studying membrane proteins in a controlled model membrane environment can provide unambiguous, quantitative information on their molecular properties and functions. However, reconstituting membrane proteins in a model system poses formidable technological challenges. Here, we developed a novel model membrane platform for highly sensitive observation of membrane proteins by combining a micropatterned lipid membrane and a nanofluidic channel. A micropatterned model membrane was generated by lithographically integrating a polymerized lipid bilayer and a natural (fluid) lipid bilayer. A nanofluidic channel having a defined thickness was formed between the fluid bilayer and a polydimethylsiloxane (PDMS) slab by attaching the polymeric bilayer and PDMS slab using an adhesion layer composed of silica nanoparticles that are coated with a biocompatible polymer brush. As we reconstituted rhodopsin (Rh), a G-protein-coupled receptor (GPCR), from a detergent-solubilized state into the fluid bilayer, only successfully reconstituted Rh molecules diffused laterally in the lipid bilayer and migrated into the nanogap junction, where they could be observed with a vastly improved signal-to-background ratio. The nanogap junction effectively separates the sites of reconstitution and observation and provides a novel platform for studying the molecular properties and functions of membrane proteins at the single-molecular level.
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Affiliation(s)
- Ryota Komatsu
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yasushi Tanimoto
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Koji Ando
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Kazuma Yasuhara
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Yasuhiko Iwasaki
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita 564-0836, Japan
| | - Fumio Hayashi
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Kenichi Morigaki
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
- Biosignal Research Center, Kobe University, Kobe 657-8501, Japan
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Lan C, Stulz A, Barthes NPF, Lauw S, Salavei P, Jung M, Heerklotz H, Ulbrich MH. Designed membrane protein heterodimers and control of their affinity by binding domain and membrane linker properties. NANOSCALE 2021; 13:20692-20702. [PMID: 34878479 DOI: 10.1039/d1nr06574b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many membrane proteins utilize dimerization to transmit signals across the cell membrane via regulation of the lateral binding affinity. The complexity of natural membrane proteins hampers the understanding of this regulation on a biophysical level. We designed simplified membrane proteins from well-defined soluble dimerization domains with tunable affinities, flexible linkers, and an inert membrane anchor. Live-cell single-molecule imaging demonstrates that their dimerization affinity indeed depends on the strength of their binding domains. We confirm that as predicted, the 2-dimensional affinity increases with the 3-dimensional binding affinity of the binding domains and decreases with linker lengths. Models of extended and coiled linkers delineate an expected range of 2-dimensional affinities, and our observations for proteins with medium binding strength agree well with the models. Our work helps in understanding the function of membrane proteins and has important implications for the design of synthetic receptors.
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Affiliation(s)
- Chenyang Lan
- Faculty of Biology, University of Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
| | - Anja Stulz
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | | | - Susan Lauw
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany.
- Core Facility Signalling Factory & Robotics, University of Freiburg, Germany
| | - Pavel Salavei
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany.
- Core Facility Signalling Factory & Robotics, University of Freiburg, Germany
| | - Manfred Jung
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Heiko Heerklotz
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany.
- Leslie Dan Faculty of Pharmacy, University of Toronto, Germany
| | - Maximilian H Ulbrich
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany.
- Internal Medicine IV, University of Freiburg Medical Center and Faculty of Medicine, University of Freiburg, Germany
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Schneider F, Sych T, Eggeling C, Sezgin E. Influence of nanobody binding on fluorescence emission, mobility, and organization of GFP-tagged proteins. iScience 2021; 24:101891. [PMID: 33364580 PMCID: PMC7753935 DOI: 10.1016/j.isci.2020.101891] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/02/2020] [Accepted: 12/01/2020] [Indexed: 12/22/2022] Open
Abstract
Advanced fluorescence microscopy studies require specific and monovalent molecular labeling with bright and photostable fluorophores. This necessity led to the widespread use of fluorescently labeled nanobodies against commonly employed fluorescent proteins (FPs). However, very little is known how these nanobodies influence their target molecules. Here, we tested commercially available nanobodies and observed clear changes of the fluorescence properties, mobility and organization of green fluorescent protein (GFP) tagged proteins after labeling with the anti-GFP nanobody. Intriguingly, we did not observe any co-diffusion of fluorescently labeled nanobodies with the GFP-labeled proteins. Our results suggest significant binding of the nanobodies to a non-emissive, likely oligomerized, form of the FPs, promoting disassembly into monomeric form after binding. Our findings have significant implications on the application of nanobodies and GFP labeling for studying dynamic and quantitative protein organization in the plasma membrane of living cells using advanced imaging techniques.
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Affiliation(s)
- Falk Schneider
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
- Jena Center of Soft Matters, Friedrich-Schiller-University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
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Birchenough HL, Jowitt TA. Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D): Preparing Functionalized Lipid Layers for the Study of Complex Protein-Ligand Interactions. Methods Mol Biol 2021; 2263:183-197. [PMID: 33877598 DOI: 10.1007/978-1-0716-1197-5_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Quartz crystal microbalance with dissipation monitoring (QCM-D) is one of the most widely used techniques for the deposition of lipid layers and provides a useful tool for protein-ligand analysis. By using functionalized lipids, for example, with nitrilotriacetic acid (NTA) or biotin, one can couple a molecule to the surface to investigate ligand interactions. Using lipid layers in this way allows for the analysis of complex binding events such as conformational changes, fibrillation, and hierarchical clustering on the surface, which is difficult to interpret with conventional surface sensor techniques. Deposition of lipids and subsequent molecular interactions are easily monitored using both the frequency and the dissipation, which have distinct features in bilayer formation and make QCM-D the ideal technique to use. Here we describe the formation of biotinylated lipid bilayers using two different types of lipids and the subsequent addition of avidin, which can then be used as a basis for linking biotinylated molecules to the surface. These protocols can be adapted to use other lipid moieties and linking chemistries.
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Affiliation(s)
- Holly L Birchenough
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Wellcome Trust Centre for Cell Matrix Research, University of Manchester, Manchester, UK
| | - Thomas A Jowitt
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- Wellcome Trust Centre for Cell Matrix Research, University of Manchester, Manchester, UK.
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Kappa but not delta or mu opioid receptors form homodimers at low membrane densities. Cell Mol Life Sci 2021; 78:7557-7568. [PMID: 34657173 PMCID: PMC8629795 DOI: 10.1007/s00018-021-03963-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/25/2021] [Accepted: 09/29/2021] [Indexed: 11/03/2022]
Abstract
Opioid receptors (ORs) have been observed as homo- and heterodimers, but it is unclear if the dimers are stable under physiological conditions, and whether monomers or dimers comprise the predominant fraction in a cell. Here, we use three live-cell imaging approaches to assess dimerization of ORs at expression levels that are 10-100 × smaller than in classical biochemical assays. At membrane densities around 25/µm2, a split-GFP assay reveals that κOR dimerizes, while µOR and δOR stay monomeric. At receptor densities < 5/µm2, single-molecule imaging showed no κOR dimers, supporting the concept that dimer formation depends on receptor membrane density. To directly observe the transition from monomers to dimers, we used a single-molecule assay to assess membrane protein interactions at densities up to 100 × higher than conventional single-molecule imaging. We observe that κOR is monomeric at densities < 10/µm2 and forms dimers at densities that are considered physiological. In contrast, µOR and δOR stay monomeric even at the highest densities covered by our approach. The observation of long-lasting co-localization of red and green κOR spots suggests that it is a specific effect based on OR dimerization and not an artefact of coincidental encounters.
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Birchenough HL, Swann MJ, Zindy E, Day AJ, Jowitt TA. Enhanced avidin binding to lipid bilayers using PDP-PE lipids with PEG-biotin linkers. NANOSCALE ADVANCES 2020; 2:1625-1633. [PMID: 36132312 PMCID: PMC9417969 DOI: 10.1039/d0na00060d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/07/2020] [Indexed: 06/15/2023]
Abstract
Two of the most important aspects of lipid bilayers that have increased their popularity in the field of nanotechnology and biosensors are their fluid nature, which is highly beneficial in ensuring the spatial organization of attached molecules, and the relative ease in which they can be manipulated to change the surface chemistry. Here we have used two different types of functionalized lipids to study the interaction of avidin, which is a common approach to attach further ligands for study. We have tested the commonly used Biotinyl-Cap-PE lipids at different molar percentages and reveal that avidin is not evenly distributed, but forms what looks like clusters even at low percentage occupancy which hampers the level of avidin that can be associated with the surface. We have then successfully employed the novel strategy of using PDP-PE lipids which contain a reducible disulphide to which we added maleamide-PEG-biotin spacers of different lengths. There is a more even distribution of avidin on these layers and thereby increasing the amount and efficiency of avidin association. The reduced levels of avidin that was being associated with the Biotinyl-Cap-PE layers as compared to the PDP-PE lipids could be analysed with QCM-D and interferometry approaches, but it was only with SEEC microscopy that the reason for the reduced occupancy was resolved.
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Affiliation(s)
| | - Marcus J Swann
- Swann Scientific Consulting Ltd 110 Sandy Lane Lymm WA13 9HR UK
| | - Egor Zindy
- Wellcome Trust Centre for Cell-Matrix Research UK
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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Evolution and development of model membranes for physicochemical and functional studies of the membrane lateral heterogeneity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2012-2017. [DOI: 10.1016/j.bbamem.2018.03.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/08/2018] [Accepted: 03/11/2018] [Indexed: 12/19/2022]
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