1
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Peter MF, Ruland JA, Kim Y, Hendricks P, Schneberger N, Siebrasse JP, Thomas GH, Kubitscheck U, Hagelueken G. Conformational coupling of the sialic acid TRAP transporter HiSiaQM with its substrate binding protein HiSiaP. Nat Commun 2024; 15:217. [PMID: 38191530 PMCID: PMC10774421 DOI: 10.1038/s41467-023-44327-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 12/08/2023] [Indexed: 01/10/2024] Open
Abstract
The tripartite ATP-independent periplasmic (TRAP) transporters use an extra cytoplasmic substrate binding protein (SBP) to transport a wide variety of substrates in bacteria and archaea. The SBP can adopt an open- or closed state depending on the presence of substrate. The two transmembrane domains of TRAP transporters form a monomeric elevator whose function is strictly dependent on the presence of a sodium ion gradient. Insights from experimental structures, structural predictions and molecular modeling have suggested a conformational coupling between the membrane elevator and the substrate binding protein. Here, we use a disulfide engineering approach to lock the TRAP transporter HiSiaPQM from Haemophilus influenzae in different conformational states. The SBP, HiSiaP, is locked in its substrate-bound form and the transmembrane elevator, HiSiaQM, is locked in either its assumed inward- or outward-facing states. We characterize the disulfide-locked constructs and use single-molecule total internal reflection fluorescence (TIRF) microscopy to study their interactions. Our experiments demonstrate that the SBP and the transmembrane elevator are indeed conformationally coupled, meaning that the open and closed state of the SBP recognize specific conformational states of the transporter and vice versa.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
- Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Jan A Ruland
- Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Yeojin Kim
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Philipp Hendricks
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Niels Schneberger
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Jan Peter Siebrasse
- Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
| | - Ulrich Kubitscheck
- Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Gregor Hagelueken
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.
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2
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Margheritis E, Kappelhoff S, Cosentino K. Pore-Forming Proteins: From Pore Assembly to Structure by Quantitative Single-Molecule Imaging. Int J Mol Sci 2023; 24:ijms24054528. [PMID: 36901959 PMCID: PMC10003378 DOI: 10.3390/ijms24054528] [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] [Received: 01/05/2023] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Pore-forming proteins (PFPs) play a central role in many biological processes related to infection, immunity, cancer, and neurodegeneration. A common feature of PFPs is their ability to form pores that disrupt the membrane permeability barrier and ion homeostasis and generally induce cell death. Some PFPs are part of the genetically encoded machinery of eukaryotic cells that are activated against infection by pathogens or in physiological programs to carry out regulated cell death. PFPs organize into supramolecular transmembrane complexes that perforate membranes through a multistep process involving membrane insertion, protein oligomerization, and finally pore formation. However, the exact mechanism of pore formation varies from PFP to PFP, resulting in different pore structures with different functionalities. Here, we review recent insights into the molecular mechanisms by which PFPs permeabilize membranes and recent methodological advances in their characterization in artificial and cellular membranes. In particular, we focus on single-molecule imaging techniques as powerful tools to unravel the molecular mechanistic details of pore assembly that are often obscured by ensemble measurements, and to determine pore structure and functionality. Uncovering the mechanistic elements of pore formation is critical for understanding the physiological role of PFPs and developing therapeutic approaches.
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3
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Scott S, Weiss M, Selhuber-Unkel C, Barooji YF, Sabri A, Erler JT, Metzler R, Oddershede LB. Extracting, quantifying, and comparing dynamical and biomechanical properties of living matter through single particle tracking. Phys Chem Chem Phys 2023; 25:1513-1537. [PMID: 36546878 DOI: 10.1039/d2cp01384c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A panoply of new tools for tracking single particles and molecules has led to an explosion of experimental data, leading to novel insights into physical properties of living matter governing cellular development and function, health and disease. In this Perspective, we present tools to investigate the dynamics and mechanics of living systems from the molecular to cellular scale via single-particle techniques. In particular, we focus on methods to measure, interpret, and analyse complex data sets that are associated with forces, materials properties, transport, and emergent organisation phenomena within biological and soft-matter systems. Current approaches, challenges, and existing solutions in the associated fields are outlined in order to support the growing community of researchers at the interface of physics and the life sciences. Each section focuses not only on the general physical principles and the potential for understanding living matter, but also on details of practical data extraction and analysis, discussing limitations, interpretation, and comparison across different experimental realisations and theoretical frameworks. Particularly relevant results are introduced as examples. While this Perspective describes living matter from a physical perspective, highlighting experimental and theoretical physics techniques relevant for such systems, it is also meant to serve as a solid starting point for researchers in the life sciences interested in the implementation of biophysical methods.
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Affiliation(s)
- Shane Scott
- Institute of Physiology, Kiel University, Hermann-Rodewald-Straße 5, 24118 Kiel, Germany
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Christine Selhuber-Unkel
- Institute for Molecular Systems Engineering, Heidelberg University, D-69120 Heidelberg, Germany.,Max Planck School Matter to Life, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Younes F Barooji
- Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen, Denmark.
| | - Adal Sabri
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Janine T Erler
- BRIC, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht Str. 24/25, D-14476 Potsdam, Germany.,Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
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4
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Lo CH, Zeng J. Application of polymersomes in membrane protein study and drug discovery: Progress, strategies, and perspectives. Bioeng Transl Med 2023; 8:e10350. [PMID: 36684106 PMCID: PMC9842050 DOI: 10.1002/btm2.10350] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 01/25/2023] Open
Abstract
Membrane proteins (MPs) play key roles in cellular signaling pathways and are responsible for intercellular and intracellular interactions. Dysfunctional MPs are directly related to the pathogenesis of various diseases, and they have been exploited as one of the most sought-after targets in the pharmaceutical industry. However, working with MPs is difficult given that their amphiphilic nature requires protection from biological membrane or membrane mimetics. Polymersomes are bilayered nano-vesicles made of self-assembled block copolymers that have been widely used as cell membrane mimetics for MP reconstitution and in engineering of artificial cells. This review highlights the prevailing trend in the application of polymersomes in MP study and drug discovery. We begin with a review on the techniques for synthesis and characterization of polymersomes as well as methods of MP insertion to form proteopolymersomes. Next, we review the structural and functional analysis of the different types of MPs reconstituted in polymersomes, including membrane transport proteins, MP complexes, and membrane receptors. We then summarize the factors affecting reconstitution efficiency and the quality of reconstituted MPs for structural and functional studies. Additionally, we discuss the potential in using proteopolymersomes as platforms for high-throughput screening (HTS) in drug discovery to identify modulators of MPs. We conclude by providing future perspectives and recommendations on advancing the study of MPs and drug development using proteopolymersomes.
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Affiliation(s)
- Chih Hung Lo
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical SchoolBostonMassachusettsUSA
| | - Jialiu Zeng
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
- Department of Biomedical EngineeringBoston UniversityBostonMassachusettsUSA
- Department of ChemistryBoston UniversityBostonMassachusettsUSA
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5
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Peter MF, Ruland JA, Depping P, Schneberger N, Severi E, Moecking J, Gatterdam K, Tindall S, Durand A, Heinz V, Siebrasse JP, Koenig PA, Geyer M, Ziegler C, Kubitscheck U, Thomas GH, Hagelueken G. Structural and mechanistic analysis of a tripartite ATP-independent periplasmic TRAP transporter. Nat Commun 2022; 13:4471. [PMID: 35927235 PMCID: PMC9352664 DOI: 10.1038/s41467-022-31907-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022] Open
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are found widely in bacteria and archaea and consist of three structural domains, a soluble substrate-binding protein (P-domain), and two transmembrane domains (Q- and M-domains). HiSiaPQM and its homologs are TRAP transporters for sialic acid and are essential for host colonization by pathogenic bacteria. Here, we reconstitute HiSiaQM into lipid nanodiscs and use cryo-EM to reveal the structure of a TRAP transporter. It is composed of 16 transmembrane helices that are unexpectedly structurally related to multimeric elevator-type transporters. The idiosyncratic Q-domain of TRAP transporters enables the formation of a monomeric elevator architecture. A model of the tripartite PQM complex is experimentally validated and reveals the coupling of the substrate-binding protein to the transporter domains. We use single-molecule total internal reflection fluorescence (TIRF) microscopy in solid-supported lipid bilayers and surface plasmon resonance to study the formation of the tripartite complex and to investigate the impact of interface mutants. Furthermore, we characterize high-affinity single variable domains on heavy chain (VHH) antibodies that bind to the periplasmic side of HiSiaQM and inhibit sialic acid uptake, providing insight into how TRAP transporter function might be inhibited in vivo.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Jan A Ruland
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Peer Depping
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
- Aston Centre for Membrane Proteins and Lipids Research, Aston St., B4 7ET, Birmingham, UK
| | - Niels Schneberger
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Emmanuele Severi
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
- Biosciences Institute, Newcastle University, Newcastle, NE2 4HH, UK
| | - Jonas Moecking
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Karl Gatterdam
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Sarah Tindall
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
| | - Alexandre Durand
- Institut de Génétique et de Biologie Molecule et Cellulaire, 1 Rue Laurent Fries, 67404, Illkirch Cedex, France
| | - Veronika Heinz
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Jan Peter Siebrasse
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Paul-Albert Koenig
- Core Facility Nanobodies, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Christine Ziegler
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Ulrich Kubitscheck
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
| | - Gregor Hagelueken
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.
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6
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Açarı İK, Sel E, Özcan İ, Ateş B, Köytepe S, Thakur VK. Chemistry and engineering of brush type polymers: Perspective towards tissue engineering. Adv Colloid Interface Sci 2022; 305:102694. [PMID: 35597039 DOI: 10.1016/j.cis.2022.102694] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/21/2022] [Accepted: 05/06/2022] [Indexed: 11/01/2022]
Abstract
In tissue engineering, it is imperative to control the behaviour of cells/stem cells, such as adhesion, proliferation, propagation, motility, and differentiation for tissue regeneration. Surfaces that allow cells to behave in this way are critical as support materials in tissue engineering. Among these surfaces, brush-type polymers have an important potential for tissue engineering and biomedical applications. Brush structure and length, end groups, bonding densities, hydrophilicity, surface energy, structural flexibility, thermal stability, surface chemical reactivity, rheological and tribological properties, electron and energy transfer ability, cell binding and absorption abilities for various biological molecules of brush-type polymers were increased its importance in tissue engineering applications. In addition, thanks to these functional properties and adjustable surface properties, brush type polymers are used in different high-tech applications such as electronics, sensors, anti-fouling, catalysis, purification and energy etc. This review comprehensively highlights the use of brush-type polymers in tissue engineering applications. Considering the superior properties of brush-type polymer structures, it is believed that in the future, it will be an effective tool in structure designs containing many different biomolecules (enzymes, proteins, etc.) in the field of tissue engineering.
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7
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Nagai R, Sugimachi A, Tanimoto Y, Suzuki KGN, Hayashi F, Weikert D, Gmeiner P, Kasai RS, Morigaki K. Functional Reconstitution of Dopamine D2 Receptor into a Supported Model Membrane in a Nanometric Confinement. Adv Biol (Weinh) 2021; 5:e2100636. [PMID: 34761565 DOI: 10.1002/adbi.202100636] [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] [Received: 03/01/2021] [Revised: 10/22/2021] [Indexed: 11/07/2022]
Abstract
Dopamine D2 receptor (D2R), a G-protein-coupled receptor (GPCR), plays critical roles in neural functions and represents the target for a wide variety of drugs used to treat neurological diseases. However, its fundamental physicochemical properties, such as dimerization and affinity to different lipid environments, remain unknown. Here, reconstitution and characterization of D2R in a supported model membrane in nanometric confinement are reported. D2R is expressed in Chinese hamster ovary (CHO) cells and transferred into the supported model membrane as cell membrane blebs. D2R molecules are reconstituted with an elevated density in the cleft between the substrate and poly(dimethylsiloxane) (PDMS) elastomer. Reconstituted D2R retains the physiological functions, as evaluated from its binding to an antagonist and dimerization lifetime. The transient dimer formation of D2R, similar to the live cell, suggests that it is an innate property that does not depend on the cellular structures such as actin filaments. Although the mechanism of this unique reconstitution process is currently not fully understood, the finding points to a new possibility of using a nanometric space (<100 nm thick) as a platform for reconstituting and studying membrane proteins under the quasi-physiological conditions, which are difficult to be created by other methods.
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Affiliation(s)
- Rurika Nagai
- Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Ayane Sugimachi
- Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Yasushi Tanimoto
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan
| | - Kenichi G N Suzuki
- Institute for Glyco-Core Research (iGCORE), Gifu University, Gifu, 501-1193, Japan
| | - Fumio Hayashi
- Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Dorothee Weikert
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Rinshi S Kasai
- Institute for Glyco-Core Research (iGCORE), Gifu University, Gifu, 501-1193, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, 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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8
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Schoppe J, Schubert E, Apelbaum A, Yavavli E, Birkholz O, Stephanowitz H, Han Y, Perz A, Hofnagel O, Liu F, Piehler J, Raunser S, Ungermann C. Flexible open conformation of the AP-3 complex explains its role in cargo recruitment at the Golgi. J Biol Chem 2021; 297:101334. [PMID: 34688652 PMCID: PMC8591511 DOI: 10.1016/j.jbc.2021.101334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 01/17/2023] Open
Abstract
Vesicle formation at endomembranes requires the selective concentration of cargo by coat proteins. Conserved adapter protein complexes at the Golgi (AP-3), the endosome (AP-1), or the plasma membrane (AP-2) with their conserved core domain and flexible ear domains mediate this function. These complexes also rely on the small GTPase Arf1 and/or specific phosphoinositides for membrane binding. The structural details that influence these processes, however, are still poorly understood. Here we present cryo-EM structures of the full-length stable 300 kDa yeast AP-3 complex. The structures reveal that AP-3 adopts an open conformation in solution, comparable to the membrane-bound conformations of AP-1 or AP-2. This open conformation appears to be far more flexible than AP-1 or AP-2, resulting in compact, intermediate, and stretched subconformations. Mass spectrometrical analysis of the cross-linked AP-3 complex further indicates that the ear domains are flexibly attached to the surface of the complex. Using biochemical reconstitution assays, we also show that efficient AP-3 recruitment to the membrane depends primarily on cargo binding. Once bound to cargo, AP-3 clustered and immobilized cargo molecules, as revealed by single-molecule imaging on polymer-supported membranes. We conclude that its flexible open state may enable AP-3 to bind and collect cargo at the Golgi and could thus allow coordinated vesicle formation at the trans-Golgi upon Arf1 activation.
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Affiliation(s)
- Jannis Schoppe
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
| | - Evelyn Schubert
- Department of Structural Biochemistry, Max-Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Amir Apelbaum
- Department of Structural Biochemistry, Max-Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Erdal Yavavli
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
| | - Oliver Birkholz
- Department of Biology/Chemistry, Biophysics Section, Osnabrück University, Osnabrück, Germany
| | - Heike Stephanowitz
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Berlin, Germany
| | - Yaping Han
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
| | - Angela Perz
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
| | - Oliver Hofnagel
- Department of Structural Biochemistry, Max-Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Fan Liu
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Berlin, Germany
| | - Jacob Piehler
- Department of Biology/Chemistry, Biophysics Section, Osnabrück University, Osnabrück, Germany; Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max-Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany; Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany.
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9
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Why Do Tethered-Bilayer Lipid Membranes Suit for Functional Membrane Protein Reincorporation? APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11114876] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Membrane proteins (MPs) are essential for cellular functions. Understanding the functions of MPs is crucial as they constitute an important class of drug targets. However, MPs are a challenging class of biomolecules to analyze because they cannot be studied outside their native environment. Their structure, function and activity are highly dependent on the local lipid environment, and these properties are compromised when the protein does not reside in the cell membrane. Mammalian cell membranes are complex and composed of different lipid species. Model membranes have been developed to provide an adequate environment to envisage MP reconstitution. Among them, tethered-Bilayer Lipid Membranes (tBLMs) appear as the best model because they allow the lipid bilayer to be decoupled from the support. Thus, they provide a sufficient aqueous space to envisage the proper accommodation of large extra-membranous domains of MPs, extending outside. Additionally, as the bilayer remains attached to tethers covalently fixed to the solid support, they can be investigated by a wide variety of surface-sensitive analytical techniques. This review provides an overview of the different approaches developed over the last two decades to achieve sophisticated tBLMs, with a more and more complex lipid composition and adapted for functional MP reconstitution.
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10
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Martinez WE, Arenas JE, Mok L, Wong NY, Lozano MM, Lin WC, Gutierrez MG, Sierra Chavera R, McGivern JG. Bioelectronic Measurement of Target Engagement to a Membrane-Bound Transporter. SLAS DISCOVERY 2021; 26:1004-1013. [PMID: 33980065 DOI: 10.1177/24725552211013067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ability to detect and characterize drug binding to a target protein is of high priority in drug discovery research. However, there are inherent challenges when the target of interest is an integral membrane protein (IMP). Assuming successful purification of the IMP, traditional approaches for measuring binding such as surface plasmon resonance (SPR) and fluorescence resonance energy transfer (FRET) have been proven valuable. However, the mass dependence of SPR signals may preclude the detection of binding events when the ligand has a significantly smaller mass than the target protein. In FRET-based experiments, protein labeling through modification may inadvertently alter protein dynamics. Graphene Bio-Electronic Sensing Technology (GBEST) aims to overcome these challenges. Label-free characterization takes place in a microfluidic chamber wherein a fluid lipid membrane is reconstituted directly above the GBEST sensor surface. By leveraging the high conductivity, sensitivity, and electrical properties of monolayer graphene, minute changes in electrostatic charges arising from the binding and unbinding of a ligand to a native IMP target can be detected in real time and in a mass-independent manner. Using crude membrane fractions prepared from cells overexpressing monocarboxylate transporter 1 (MCT1), we demonstrate the ability to (1) form a fluid lipid bilayer enriched with MCT1 directly on top of the GBEST sensor and (2) obtain kinetic binding data for an anti-MCT1 antibody. Further development of this novel technology will enable characterization of target engagement by both low- and high-molecular-weight drug candidates to native IMP targets in a physiologically relevant membrane environment.
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Affiliation(s)
- William E Martinez
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Avalor Therapeutics, Seattle, WA, USA
| | - Jaime E Arenas
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA
| | - Leo Mok
- Discovery Technologies, Amgen Research, South San Francisco, CA, USA
| | - Ngo Yin Wong
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Ximedica, LLC, San Francisco, CA, USA
| | - Monica M Lozano
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Profusa, Inc., Emeryville, CA, USA
| | - Wan-Chen Lin
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Imgenix Corp., Paoli, PA, USA
| | - M Gertrude Gutierrez
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Pharmaceutical Science & Technology, AstraZeneca, South San Francisco, CA, USA
| | - Rodrigo Sierra Chavera
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Sierra Intelligence, Bahrain
| | - Joseph G McGivern
- Discovery Technologies, Amgen Research, South San Francisco, CA, USA.,Denali Therapeutics, South San Francisco, CA, USA
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11
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Hernández-Rocamora VM, Baranova N, Peters K, Breukink E, Loose M, Vollmer W. Real-time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin-binding proteins. eLife 2021; 10:61525. [PMID: 33625355 PMCID: PMC7943195 DOI: 10.7554/elife.61525] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Natalia Baranova
- Institute for Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Utrecht, Netherlands
| | - Martin Loose
- Institute for Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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12
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Ca 2+-Daptomycin targets cell wall biosynthesis by forming a tripartite complex with undecaprenyl-coupled intermediates and membrane lipids. Nat Commun 2020; 11:1455. [PMID: 32193379 PMCID: PMC7081307 DOI: 10.1038/s41467-020-15257-1] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/25/2020] [Indexed: 11/08/2022] Open
Abstract
The lipopeptide daptomycin is used as an antibiotic to treat severe infections with gram-positive pathogens, such as methicillin resistant Staphylococcus aureus (MRSA) and drug-resistant enterococci. Its precise mechanism of action is incompletely understood, and a specific molecular target has not been identified. Here we show that Ca2+-daptomycin specifically interacts with undecaprenyl-coupled cell envelope precursors in the presence of the anionic phospholipid phosphatidylglycerol, forming a tripartite complex. We use microbiological and biochemical assays, in combination with fluorescence and optical sectioning microscopy of intact staphylococcal cells and model membrane systems. Binding primarily occurs at the staphylococcal septum and interrupts cell wall biosynthesis. This is followed by delocalisation of components of the peptidoglycan biosynthesis machinery and massive membrane rearrangements, which may account for the pleiotropic cellular events previously reported. The identification of carrier-bound cell wall precursors as specific targets explains the specificity of daptomycin for bacterial cells. Our work reconciles apparently inconsistent previous results, and supports a concise model for the mode of action of daptomycin.
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13
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Baranova N, Radler P, Hernández-Rocamora VM, Alfonso C, López-Pelegrín M, Rivas G, Vollmer W, Loose M. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nat Microbiol 2020; 5:407-417. [PMID: 31959972 PMCID: PMC7048620 DOI: 10.1038/s41564-019-0657-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/06/2019] [Indexed: 11/14/2022]
Abstract
Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery is coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1 and in live cells where they circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the cell thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ-FtsA filaments, but despite their directed collective behavior, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signaling activity at the division site.
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Affiliation(s)
- Natalia Baranova
- Institute for Science and Technology Austria, Klosterneuburg, Austria
| | - Philipp Radler
- Institute for Science and Technology Austria, Klosterneuburg, Austria
| | | | | | | | - Germán Rivas
- Centro de Investigaciones Biológicas, Madrid, Spain
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Martin Loose
- Institute for Science and Technology Austria, Klosterneuburg, Austria.
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14
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Wong WC, Juo JY, Lin CH, Liao YH, Cheng CY, Hsieh CL. Characterization of Single-Protein Dynamics in Polymer-Cushioned Lipid Bilayers Derived from Cell Plasma Membranes. J Phys Chem B 2019; 123:6492-6504. [DOI: 10.1021/acs.jpcb.9b03789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wai Cheng Wong
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei 10617, Taiwan
| | - Jz-Yuan Juo
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei 10617, Taiwan
| | - Chih-Hsiang Lin
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei 10617, Taiwan
| | - Yi-Hung Liao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei 10617, Taiwan
| | - Ching-Ya Cheng
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei 10617, Taiwan
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei 10617, Taiwan
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15
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Mapar M, Jõemetsa S, Pace H, Zhdanov VP, Agnarsson B, Höök F. Spatiotemporal Kinetics of Supported Lipid Bilayer Formation on Glass via Vesicle Adsorption and Rupture. J Phys Chem Lett 2018; 9:5143-5149. [PMID: 30137991 DOI: 10.1021/acs.jpclett.8b02092] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Supported lipid bilayers (SLBs) represent one of the most popular mimics of the cell membrane. Herein, we have used total internal reflection fluorescence microscopy for in-depth characterization of the vesicle-mediated SLB formation mechanism on a common silica-rich substrate, borosilicate glass. Fluorescently labeling a subset of vesicles allowed us to monitor the adsorption of individual labeled vesicles, resolve the onset of SLB formation from small seeds of SLB patches, and track their growth via SLB-edge-induced autocatalytic rupture of adsorbed vesicles. This made it possible to perform the first quantitative measurement of the SLB front velocity, which is shown to increase up to 1 order of magnitude with time. This effect can be classified as dramatic because in many other physical, chemical, or biological kinetic processes the front velocity is either constant or decreasing with time. The observation was successfully described with a theoretical model and Monte Carlo simulations implying rapid local diffusion of lipids upon vesicle rupture.
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Affiliation(s)
- Mokhtar Mapar
- Division of Biological Physics, Department of Physics , Chalmers University of Technology , 41296 Göteborg , Sweden
| | - Silver Jõemetsa
- Division of Biological Physics, Department of Physics , Chalmers University of Technology , 41296 Göteborg , Sweden
| | - Hudson Pace
- Division of Biological Physics, Department of Physics , Chalmers University of Technology , 41296 Göteborg , Sweden
| | - Vladimir P Zhdanov
- Division of Biological Physics, Department of Physics , Chalmers University of Technology , 41296 Göteborg , Sweden
- Boreskov Institute of Catalysis , Russian Academy of Sciences , Novosibirsk 630090 , Russia
| | - Björn Agnarsson
- Division of Biological Physics, Department of Physics , Chalmers University of Technology , 41296 Göteborg , Sweden
| | - Fredrik Höök
- Division of Biological Physics, Department of Physics , Chalmers University of Technology , 41296 Göteborg , Sweden
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16
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Chavent M, Duncan AL, Rassam P, Birkholz O, Hélie J, Reddy T, Beliaev D, Hambly B, Piehler J, Kleanthous C, Sansom MSP. How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins. Nat Commun 2018; 9:2846. [PMID: 30030429 PMCID: PMC6054660 DOI: 10.1038/s41467-018-05255-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 06/15/2018] [Indexed: 01/07/2023] Open
Abstract
The spatiotemporal organisation of membranes is often characterised by the formation of large protein clusters. In Escherichia coli, outer membrane protein (OMP) clustering leads to OMP islands, the formation of which underpins OMP turnover and drives organisation across the cell envelope. Modelling how OMP islands form in order to understand their origin and outer membrane behaviour has been confounded by the inherent difficulties of simulating large numbers of OMPs over meaningful timescales. Here, we overcome these problems by training a mesoscale model incorporating thousands of OMPs on coarse-grained molecular dynamics simulations. We achieve simulations over timescales that allow direct comparison to experimental data of OMP behaviour. We show that specific interaction surfaces between OMPs are key to the formation of OMP clusters, that OMP clusters present a mesh of moving barriers that confine newly inserted proteins within islands, and that mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs. In Escherichia coli, outer membrane protein (OMP) cluster and form islands, but the origin and behaviour of those clusters remains poorly understood. Here authors use coarse grained molecular dynamics simulation and show that their mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs.
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Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 Route de Narbonne, Toulouse, 31400, France
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Patrice Rassam
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401, Illkirch, France
| | - Oliver Birkholz
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,SEMMLE, Blue Boar Court, 9 Alfred St, Oxford, OX1 4EH, UK
| | - Tyler Reddy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Theoretical Biology and Biophysics, T-6, Los Alamos National Laboratory, Los Alamos, NM, 87525, USA
| | - Dmitry Beliaev
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter (550), Woodstock Road, Oxford, OX2 6GG, UK
| | - Ben Hambly
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter (550), Woodstock Road, Oxford, OX2 6GG, UK
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
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17
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Lee TH, Hirst DJ, Kulkarni K, Del Borgo MP, Aguilar MI. Exploring Molecular-Biomembrane Interactions with Surface Plasmon Resonance and Dual Polarization Interferometry Technology: Expanding the Spotlight onto Biomembrane Structure. Chem Rev 2018; 118:5392-5487. [PMID: 29793341 DOI: 10.1021/acs.chemrev.7b00729] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The molecular analysis of biomolecular-membrane interactions is central to understanding most cellular systems but has emerged as a complex technical challenge given the complexities of membrane structure and composition across all living cells. We present a review of the application of surface plasmon resonance and dual polarization interferometry-based biosensors to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. We first describe the optical principals and instrumentation of surface plasmon resonance, including both linear and extraordinary transmission modes and dual polarization interferometry. We then describe the wide range of model membrane systems that have been developed for deposition on the chips surfaces that include planar, polymer cushioned, tethered bilayers, and liposomes. This is followed by a description of the different chemical immobilization or physisorption techniques. The application of this broad range of engineered membrane surfaces to biomolecular-membrane interactions is then overviewed and how the information obtained using these techniques enhance our molecular understanding of membrane-mediated peptide and protein function. We first discuss experiments where SPR alone has been used to characterize membrane binding and describe how these studies yielded novel insight into the molecular events associated with membrane interactions and how they provided a significant impetus to more recent studies that focus on coincident membrane structure changes during binding of peptides and proteins. We then discuss the emerging limitations of not monitoring the effects on membrane structure and how SPR data can be combined with DPI to provide significant new information on how a membrane responds to the binding of peptides and proteins.
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Affiliation(s)
- Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Daniel J Hirst
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Mark P Del Borgo
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
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18
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Birkholz O, Burns JR, Richter CP, Psathaki OE, Howorka S, Piehler J. Multi-functional DNA nanostructures that puncture and remodel lipid membranes into hybrid materials. Nat Commun 2018; 9:1521. [PMID: 29670084 PMCID: PMC5906680 DOI: 10.1038/s41467-018-02905-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 01/08/2018] [Indexed: 02/06/2023] Open
Abstract
Synthetically replicating key biological processes requires the ability to puncture lipid bilayer membranes and to remodel their shape. Recently developed artificial DNA nanopores are one possible synthetic route due to their ease of fabrication. However, an unresolved fundamental question is how DNA nanopores bind to and dynamically interact with lipid bilayers. Here we use single-molecule fluorescence microscopy to establish that DNA nanopores carrying cholesterol anchors insert via a two-step mechanism into membranes. Nanopores are furthermore shown to locally cluster and remodel membranes into nanoscale protrusions. Most strikingly, the DNA pores can function as cytoskeletal components by stabilizing autonomously formed lipid nanotubes. The combination of membrane puncturing and remodeling activity can be attributed to the DNA pores’ tunable transition between two orientations to either span or co-align with the lipid bilayer. This insight is expected to catalyze the development of future functional nanodevices relevant in synthetic biology and nanobiotechnology. DNA nanopores can span lipid bilayers but how they interact with lipids is not known. Here the authors establish at single-molecule level the insertion mechanism and show that DNA nanopores can locally cluster and remodel membranes, and stabilize autonomously formed lipid nanotubes.
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19
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Struntz P, Weiss M. The hitchhiker's guide to quantitative diffusion measurements. Phys Chem Chem Phys 2018; 20:28910-28919. [DOI: 10.1039/c8cp06158k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quantitative comparison of three widely used techniques for diffusion measurements, implemented on a light sheet microscope.
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Affiliation(s)
- Philipp Struntz
- Experimental Physics I
- University of Bayreuth
- D-95447 Bayreuth
- Germany
| | - Matthias Weiss
- Experimental Physics I
- University of Bayreuth
- D-95447 Bayreuth
- Germany
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20
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Ligand-induced type II interleukin-4 receptor dimers are sustained by rapid re-association within plasma membrane microcompartments. Nat Commun 2017; 8:15976. [PMID: 28706306 PMCID: PMC5519985 DOI: 10.1038/ncomms15976] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 05/16/2017] [Indexed: 12/14/2022] Open
Abstract
The spatiotemporal organization of cytokine receptors in the plasma membrane is still debated with models ranging from ligand-independent receptor pre-dimerization to ligand-induced receptor dimerization occurring only after receptor uptake into endosomes. Here, we explore the molecular and cellular determinants governing the assembly of the type II interleukin-4 receptor, taking advantage of various agonists binding the receptor subunits with different affinities and rate constants. Quantitative kinetic studies using artificial membranes confirm that receptor dimerization is governed by the two-dimensional ligand–receptor interactions and identify a critical role of the transmembrane domain in receptor dimerization. Single molecule localization microscopy at physiological cell surface expression levels, however, reveals efficient ligand-induced receptor dimerization by all ligands, largely independent of receptor binding affinities, in line with the similar STAT6 activation potencies observed for all IL-4 variants. Detailed spatiotemporal analyses suggest that kinetic trapping of receptor dimers in actin-dependent microcompartments sustains robust receptor dimerization and signalling. The contribution of ligands for cytokine receptor dimerization is still not fully understood. Here, the authors show the efficient ligand-induced dimerization of type II interleukin-4 receptor at the plasma membrane and the kinetic trapping of signalling complexes by actin-dependent membrane microdomains.
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21
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Nishimura T, Tamura F, Kobayashi S, Tanimoto Y, Hayashi F, Sudo Y, Iwasaki Y, Morigaki K. Hybrid Model Membrane Combining Micropatterned Lipid Bilayer and Hydrophilic Polymer Brush. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:5752-5759. [PMID: 28514175 DOI: 10.1021/acs.langmuir.7b00463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Substrate-supported planar lipid bilayers (SPBs) are being utilized as a versatile model system of the biological membrane. However, the proximity between the solid support and membrane limits utility of SPBs for the functional analyses of membrane proteins. Here, we present a model membrane that can enlarge the distance between the substrate surface and the membrane by combining a stable scaffold of polymerized lipid bilayer with a hydrophilic polymer brush. A micropatterned SPB was generated by the lithographic polymerization of diacetylene lipids and subsequent incorporation of natural (fluid) lipid bilayers. Hydrophilic polymer brush of poly-2-methacryloyloxyethyl phosphorylcholine (poly(MPC)) was formed on the surface of polymeric bilayer by the in situ atom transfer radical polymerization (ATRP) in aqueous solution, in the presence of embedded fluid lipid bilayers. A model membrane protein (Haloquadratum walsbyi bacteriorhodopsin: HwBR) could be reconstituted into the polymer brush-supported bilayers with significantly reduced immobile molecules. Furthermore, the polymer brush terminals could be functionalized by successively polymerizing MPC and 2-aminoethyl methacrylate (AMA). The reactive amine moiety of poly(AMA) enables to conjugate a wide range of biological molecules and surfaces to the membrane. The combination of micropatterned bilayer and polymer brush mimics the two- and three-dimensional structures of the biological membrane, providing a platform to assay membrane proteins in a truly biomimetic environment.
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Affiliation(s)
| | | | | | | | | | - Yuki Sudo
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University , 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Yasuhiko Iwasaki
- Faculty of Chemistry, Materials and Bioengineering, Kansai University , 3-3-35 Yamatecho, Suita 564-8680, Japan
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22
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Bronder AM, Bieker A, Elter S, Etzkorn M, Häussinger D, Oesterhelt F. Oriented Membrane Protein Reconstitution into Tethered Lipid Membranes for AFM Force Spectroscopy. Biophys J 2016; 111:1925-1934. [PMID: 27806274 PMCID: PMC5103026 DOI: 10.1016/j.bpj.2016.08.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 12/11/2022] Open
Abstract
Membrane proteins act as a central interface between the extracellular environment and the intracellular response and as such represent one of the most important classes of drug targets. The characterization of the molecular properties of integral membrane proteins, such as topology and interdomain interaction, is key to a fundamental understanding of their function. Atomic force microscopy (AFM) and force spectroscopy have the intrinsic capabilities of investigating these properties in a near-native setting. However, atomic force spectroscopy of membrane proteins is traditionally carried out in a crystalline setup. Alternatively, model membrane systems, such as tethered bilayer membranes, have been developed for surface-dependent techniques. While these setups can provide a more native environment, data analysis may be complicated by the normally found statistical orientation of the reconstituted protein in the model membrane. We have developed a model membrane system that enables the study of membrane proteins in a defined orientation by single-molecule force spectroscopy. Our approach is demonstrated using cell-free expressed bacteriorhodopsin coupled to a quartz glass surface in a defined orientation through a protein anchor and reconstituted inside an artificial membrane system. This approach offers an effective way to study membrane proteins in a planar lipid bilayer. It can be easily transferred to all membrane proteins that possess a suitable tag and can be reconstituted into a lipid bilayer. In this respect, we anticipate that this technique may contribute important information on structure, topology, and intra- and intermolecular interactions of other seven-transmembrane helical receptors.
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Affiliation(s)
- Anna M Bronder
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany.
| | - Adeline Bieker
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Shantha Elter
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Manuel Etzkorn
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology and Infectiology, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Filipp Oesterhelt
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany; Department for Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
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23
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Garni M, Thamboo S, Schoenenberger CA, Palivan CG. Biopores/membrane proteins in synthetic polymer membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:619-638. [PMID: 27984019 DOI: 10.1016/j.bbamem.2016.10.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Mimicking cell membranes by simple models based on the reconstitution of membrane proteins in lipid bilayers represents a straightforward approach to understand biological function of these proteins. This biomimetic strategy has been extended to synthetic membranes that have advantages in terms of chemical and mechanical stability, thus providing more robust hybrid membranes. SCOPE OF THE REVIEW We present here how membrane proteins and biopores have been inserted both in the membrane of nanosized and microsized compartments, and in planar membranes under various conditions. Such bio-hybrid membranes have new properties (as for example, permeability to ions/molecules), and functionality depending on the specificity of the inserted biomolecules. Interestingly, membrane proteins can be functionally inserted in synthetic membranes provided these have appropriate properties to overcome the high hydrophobic mismatch between the size of the biomolecule and the membrane thickness. MAJOR CONCLUSION Functional insertion of membrane proteins and biopores in synthetic membranes of compartments or in planar membranes is possible by an appropriate selection of the amphiphilic copolymers, and conditions of the self-assembly process. These hybrid membranes have new properties and functionality based on the specificity of the biomolecules and the nature of the synthetic membranes. GENERAL SIGNIFICANCE Bio-hybrid membranes represent new solutions for the development of nanoreactors, artificial organelles or active surfaces/membranes that, by further gaining in complexity and functionality, will promote translational applications. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Martina Garni
- Chemistry Department, University of Basel, Klingelbergstrasse 80, Switzerland
| | - Sagana Thamboo
- Chemistry Department, University of Basel, Klingelbergstrasse 80, Switzerland
| | | | - Cornelia G Palivan
- Chemistry Department, University of Basel, Klingelbergstrasse 80, Switzerland.
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24
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Palivan CG, Goers R, Najer A, Zhang X, Car A, Meier W. Bioinspired polymer vesicles and membranes for biological and medical applications. Chem Soc Rev 2016; 45:377-411. [DOI: 10.1039/c5cs00569h] [Citation(s) in RCA: 413] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Biological membranes play an essential role in living organisms by providing stable and functional compartments, supporting signalling and selective transport. Combining synthetic polymer membranes with biological molecules promises to be an effective strategy to mimic the functions of cell membranes and apply them in artificial systems.
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Affiliation(s)
| | - Roland Goers
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
- Department of Biosystems Science and Engineering
| | - Adrian Najer
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | - Xiaoyan Zhang
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | - Anja Car
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | - Wolfgang Meier
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
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25
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Beutel O, Roder F, Birkholz O, Rickert C, Steinhoff HJ, Grzybek M, Coskun Ü, Piehler J. Two-Dimensional Trap for Ultrasensitive Quantification of Transient Protein Interactions. ACS NANO 2015; 9:9783-9791. [PMID: 26331529 DOI: 10.1021/acsnano.5b02696] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present an ultrasensitive technique for quantitative protein-protein interaction analysis in a two-dimensional format based on phase-separated, micropatterned membranes. Interactions between proteins captured to lipid probes via an affinity tag trigger partitioning into the liquid-ordered phase, which is readily quantified by fluorescence imaging. Based on a calibration with well-defined low-affinity protein-protein interactions, equilibrium dissociation constants >1 mM were quantified. Direct capturing of proteins from mammalian cell lysates enabled us to detect homo- and heterodimerization of signal transducer and activator of transcription proteins. Using the epidermal growth factor receptor (EGFR) as a model system, quantification of low-affinity interactions between different receptor domains contributing to EGFR dimerization was achieved. By exploitation of specific features of the membrane-based assay, the regulation of EGFR dimerization by lipids was demonstrated.
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Affiliation(s)
- Oliver Beutel
- Department of Biology, University of Osnabrück , 49074 Osnabrück, Germany
| | - Friedrich Roder
- Department of Biology, University of Osnabrück , 49074 Osnabrück, Germany
| | - Oliver Birkholz
- Department of Biology, University of Osnabrück , 49074 Osnabrück, Germany
| | - Christian Rickert
- Department of Physics, University of Osnabrück , 49076 Osnabrück, Germany
| | | | - Michał Grzybek
- Paul Langerhans Institute Dresden of the Helmholtz Centre Munich at the University Clinic Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
- German Center for Diabetes Research (DZD) , 85764 Neuherberg, Germany
| | - Ünal Coskun
- Paul Langerhans Institute Dresden of the Helmholtz Centre Munich at the University Clinic Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
- German Center for Diabetes Research (DZD) , 85764 Neuherberg, Germany
| | - Jacob Piehler
- Department of Biology, University of Osnabrück , 49074 Osnabrück, Germany
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26
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Pace H, Simonsson Nyström L, Gunnarsson A, Eck E, Monson C, Geschwindner S, Snijder A, Höök F. Preserved transmembrane protein mobility in polymer-supported lipid bilayers derived from cell membranes. Anal Chem 2015; 87:9194-203. [PMID: 26268463 DOI: 10.1021/acs.analchem.5b01449] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Supported lipid bilayers (SLBs) have contributed invaluable information about the physiochemical properties of cell membranes, but their compositional simplicity often limits the level of knowledge that can be gained about the structure and function of transmembrane proteins in their native environment. Herein, we demonstrate a generic protocol for producing polymer-supported lipid bilayers on glass surfaces that contain essentially all naturally occurring cell-membrane components of a cell line while still retaining transmembrane protein mobility and activity. This was achieved by merging vesicles made from synthetic lipids (PEGylated lipids and POPC lipids) with native cell-membrane vesicles to generate hybrid vesicles which readily rupture into a continuous polymer-supported lipid bilayer. To investigate the properties of these complex hybrid SLBs and particularly the behavior of their integral membrane-proteins, we used total internal reflection fluorescence imaging to study a transmembrane protease, β-secretase 1 (BACE1), whose ectoplasmic and cytoplasmic domains could both be specifically targeted with fluorescent reporters. By selectively probing the two different orientations of BACE1 in the resulting hybrid SLBs, the role of the PEG-cushion on transmembrane protein lateral mobility was investigated. The results reveal the necessity of having the PEGylated lipids present during vesicle adsorption to prevent immobilization of transmembrane proteins with protruding domains. The proteolytic activity of BACE1 was unadulterated by the sonication process used to merge the synthetic and native membrane vesicles; importantly it was also conserved in the SLB. The presented strategy could thus serve both fundamental studies of membrane biophysics and the production of surface-based bioanalytical sensor platforms.
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Affiliation(s)
- Hudson Pace
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
| | - Lisa Simonsson Nyström
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
| | - Anders Gunnarsson
- Discovery Sciences, AstraZeneca R&D Mölndal , SE-43183 Mölndal, Sweden
| | - Elizabeth Eck
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
| | - Christopher Monson
- Department of Physical Science, Southern Utah University , Cedar City, Utah 84720 United States
| | | | - Arjan Snijder
- Discovery Sciences, AstraZeneca R&D Mölndal , SE-43183 Mölndal, Sweden
| | - Fredrik Höök
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
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27
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Peel MJ, Cross SJ, Birkholz O, Aladağ A, Piehler J, Peel S. Rupture of Stochastically Occurring Vesicle Clusters Limits Bilayer Formation on Alkane-PEG-Type Supports: Uncoupling Clustering from Surface Coverage. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:8830-40. [PMID: 26176185 DOI: 10.1021/acs.langmuir.5b00925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Polymer-supported bilayers (PSBs) are a recognized tool for drug discovery through function-interaction analysis of membrane proteins. While silica-supported bilayers (SSBs) spontaneously form from surface-adsorbed vesicles, successful PSB formation via a similar method has thus far been limited by an insufficient understanding of the underlying vesicle-remodelling processes. Here, we generated a polymer support through the incubation of poly-L-lysine conjugated to alkyl-chain-terminated poly(ethylene)glycol on silica. This polymer-coated silica substrate yielded efficient vesicle adsorption and spontaneous bilayer formation, thereby providing a rare opportunity to address the mechanism of PSB formation and compare it to that of SSB. The combined use of super-resolution imaging, kinetics, and simulations indicates that the rupture of stochastically formed vesicle clusters is the rate-limiting step, which is an order of magnitude higher for silica than for polymer-coated silica. This was confirmed by directly demonstrating increased rupture rates for surface adsorbed multivesicle assemblies formed by vesicle cross-linking in solution. On the basis of this key insight we surmised that a low propensity of cluster rupture can be compensated for by an increase in the number density of clusters: the deposition of a mixture of oppositely charged vesicles resulted in bilayer formation on another alkane-PEG type of interface, which despite efficient vesicle adsorption otherwise fails to support spontaneous bilayer formation. This potentially provides a universal strategy for promoting bilayer formation on resistant surfaces without resorting to modifying the surface itself. Therefore, multivesicle assemblies with tailored geometries not only could facilitate bilayer formation on polymers with interesting functional properties but also could instigate the exploration of vesicle architecture for other processes involving vesicle remodelling such as drug delivery.
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Affiliation(s)
| | | | - Oliver Birkholz
- §Department of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | | | - Jacob Piehler
- §Department of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
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28
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Meyer RA, Sunshine JC, Green JJ. Biomimetic particles as therapeutics. Trends Biotechnol 2015; 33:514-524. [PMID: 26277289 DOI: 10.1016/j.tibtech.2015.07.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/03/2015] [Accepted: 07/07/2015] [Indexed: 11/28/2022]
Abstract
In recent years, there have been major advances in the development of novel nanoparticle- and microparticle-based therapeutics. An emerging paradigm is the incorporation of biomimetic features into these synthetic therapeutic constructs to enable them to better interface with biological systems. Through the control of size, shape, and material consistency, particle cores have been generated that better mimic natural cells and viruses. In addition, there have been significant advances in biomimetic surface functionalization of particles through the integration of bio-inspired artificial cell membranes and naturally derived cell membranes. Biomimetic technologies enable therapeutic particles to have increased potency to benefit human health.
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Affiliation(s)
- Randall A Meyer
- Department of Biomedical Engineering, Translational Tissue Engineering Center, and Institute for Nanobiotechnology, Johns Hopkins School of Medicine, 400 N Broadway, Smith 5017, Baltimore MD, 21231, USA
| | - Joel C Sunshine
- Department of Biomedical Engineering, Translational Tissue Engineering Center, and Institute for Nanobiotechnology, Johns Hopkins School of Medicine, 400 N Broadway, Smith 5017, Baltimore MD, 21231, USA
| | - Jordan J Green
- Department of Biomedical Engineering, Translational Tissue Engineering Center, and Institute for Nanobiotechnology, Johns Hopkins School of Medicine, 400 N Broadway, Smith 5017, Baltimore MD, 21231, USA.,Departments of Materials Science and Engineering, Oncology, Ophthalmology, and Neurosurgery, Johns Hopkins School of Medicine, 400 N Broadway, Smith 5017, Baltimore MD, 21231, USA
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29
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Rassam P, Copeland NA, Birkholz O, Tóth C, Chavent M, Duncan AL, Cross SJ, Housden NG, Kaminska R, Seger U, Quinn DM, Garrod TJ, Sansom MSP, Piehler J, Baumann CG, Kleanthous C. Supramolecular assemblies underpin turnover of outer membrane proteins in bacteria. Nature 2015; 523:333-6. [PMID: 26061769 PMCID: PMC4905513 DOI: 10.1038/nature14461] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 04/08/2015] [Indexed: 12/24/2022]
Abstract
Gram-negative bacteria inhabit a broad range of ecological niches. For Escherichia coli, this includes river water as well as humans and animals, where it can be both a commensal and a pathogen. Intricate regulatory mechanisms ensure that bacteria have the right complement of β-barrel outer membrane proteins (OMPs) to enable adaptation to a particular habitat. Yet no mechanism is known for replacing OMPs in the outer membrane, an issue that is further confounded by the lack of an energy source and the high stability and abundance of OMPs. Here we uncover the process underpinning OMP turnover in E. coli and show it to be passive and binary in nature, in which old OMPs are displaced to the poles of growing cells as new OMPs take their place. Using fluorescent colicins as OMP-specific probes, in combination with ensemble and single-molecule fluorescence microscopy in vivo and in vitro, as well as molecular dynamics simulations, we established the mechanism for binary OMP partitioning. OMPs clustered to form ∼0.5-μm diameter islands, where their diffusion is restricted by promiscuous interactions with other OMPs. OMP islands were distributed throughout the cell and contained the Bam complex, which catalyses the insertion of OMPs in the outer membrane. However, OMP biogenesis occurred as a gradient that was highest at mid-cell but largely absent at cell poles. The cumulative effect is to push old OMP islands towards the poles of growing cells, leading to a binary distribution when cells divide. Hence, the outer membrane of a Gram-negative bacterium is a spatially and temporally organized structure, and this organization lies at the heart of how OMPs are turned over in the membrane.
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Affiliation(s)
- Patrice Rassam
- 1] Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK [2] Department of Biology, University of York, York YO10 5DD, UK
| | | | - Oliver Birkholz
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Csaba Tóth
- Department of Biology, University of York, York YO10 5DD, UK
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Stephen J Cross
- Department of Biology, University of York, York YO10 5DD, UK
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Urban Seger
- Department of Biology, University of York, York YO10 5DD, UK
| | - Diana M Quinn
- Department of Biology, University of York, York YO10 5DD, UK
| | - Tamsin J Garrod
- Department of Biology, University of York, York YO10 5DD, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | | | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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30
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Wang L, Roth JS, Han X, Evans SD. Photosynthetic Proteins in Supported Lipid Bilayers: Towards a Biokleptic Approach for Energy Capture. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:3306-3318. [PMID: 25727786 DOI: 10.1002/smll.201403469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/11/2015] [Indexed: 06/04/2023]
Abstract
In nature, plants and some bacteria have evolved an ability to convert solar energy into chemical energy usable by the organism. This process involves several proteins and the creation of a chemical gradient across the cell membrane. To transfer this process to a laboratory environment, several conditions have to be met: i) proteins need to be reconstituted into a lipid membrane, ii) the proteins need to be correctly oriented and functional and, finally, iii) the lipid membrane should be capable of maintaining chemical and electrical gradients. Investigating the processes of photosynthesis and energy generation in vivo is a difficult task due to the complexity of the membrane and its associated proteins. Solid, supported lipid bilayers provide a good model system for the systematic investigation of the different components involved in the photosynthetic pathway. In this review, the progress made to date in the development of supported lipid bilayer systems suitable for the investigation of membrane proteins is described; in particular, there is a focus on those used for the reconstitution of proteins involved in light capture.
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Affiliation(s)
- Lei Wang
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
- State Key Laboratory of Urban Water Resource and Environment, School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Johannes S Roth
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Stephen D Evans
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
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31
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Tran-Ba KH, Higgins DA, Ito T. Fluorescence Recovery after Photobleaching and Single-Molecule Tracking Measurements of Anisotropic Diffusion within Identical Regions of a Cylinder-Forming Diblock Copolymer Film. Anal Chem 2015; 87:5802-9. [PMID: 25923826 DOI: 10.1021/acs.analchem.5b01041] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This work demonstrates ensemble and single-molecule diffusion measurements within identical regions of a cylinder-forming polystyrene-poly(ethylene oxide) diblock copolymer (PS-b-PEO) film using fluorescence recovery after photobleaching (FRAP) and single-molecule tracking (SMT). A PS-b-PEO film (∼4 μm thick) with aligned cylindrical PEO microdomains containing 10 μM sulforhodamine B (SRB) was prepared by directional solvent-vapor penetration (SVP) of 1,4-dioxane. The ensemble diffusion behavior of SRB in the microdomains was assessed in FRAP studies of circular photobleached regions (∼7 μm in diameter). The SRB concentration was subsequently reduced by additional photobleaching, and the diffusion of individual SRB molecules was explored using SMT in the identical area (∼16 × 16 μm(2)). The FRAP data showed anisotropic fluorescence recovery, yielding the average microdomain orientation. The extent of fluorescence recovery observed (∼90%) demonstrated long-range microdomain connectivity, while the recovery time dependence provided an ensemble measurement of the SRB diffusion coefficient within the cylindrical microdomains. The SMT data exhibited one-dimensional diffusion of individual SRB molecules along the SVP direction across the entire film thickness, as consistent with the FRAP results. Importantly, the average of the single-molecule diffusion coefficients was close to the value obtained from FRAP in the identical area. In some cases, SMT offered smaller diffusion coefficients than FRAP, possibly due to contributions from SRB molecules confined within short PEO microdomains. The implementation of FRAP and SMT measurements in identical areas provides complementary information on molecular diffusion with minimal influence of sample heterogeneity, permitting direct comparison of ensemble and single-molecule diffusion behavior.
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Affiliation(s)
- Khanh-Hoa Tran-Ba
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506-0401, United States
| | - Daniel A Higgins
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506-0401, United States
| | - Takashi Ito
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506-0401, United States
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32
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Hydrophobic mismatch sorts SNARE proteins into distinct membrane domains. Nat Commun 2015; 6:5984. [PMID: 25635869 PMCID: PMC4313621 DOI: 10.1038/ncomms6984] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 11/28/2014] [Indexed: 12/12/2022] Open
Abstract
The clustering of proteins and lipids in distinct microdomains is emerging as an important principle for the spatial patterning of biological membranes. Such domain formation can be the result of hydrophobic and ionic interactions with membrane lipids as well as of specific protein–protein interactions. Here using plasma membrane-resident SNARE proteins as model, we show that hydrophobic mismatch between the length of transmembrane domains (TMDs) and the thickness of the lipid membrane suffices to induce clustering of proteins. Even when the TMDs differ in length by only a single residue, hydrophobic mismatch can segregate structurally closely homologous membrane proteins in distinct membrane domains. Domain formation is further fine-tuned by interactions with polyanionic phosphoinositides and homo and heterotypic protein interactions. Our findings demonstrate that hydrophobic mismatch contributes to the structural organization of membranes. Clustering of proteins in the plasma membrane plays an important role in the regulation of both cellular signalling and membrane remodelling. Milovanovic et al. demonstrate that mismatch between transmembrane domain length and the lipid bilayer thickness is sufficient to drive clustering of SNARE proteins.
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33
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Roder F, Wilmes S, Richter CP, Piehler J. Rapid transfer of transmembrane proteins for single molecule dimerization assays in polymer-supported membranes. ACS Chem Biol 2014; 9:2479-84. [PMID: 25203456 DOI: 10.1021/cb5005806] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Dimerization of transmembrane receptors is a key regulatory factor in cellular communication, which has remained challenging to study under well-defined conditions in vitro. We developed a novel strategy to explore membrane protein interactions in a controlled lipid environment requiring minute sample quantities. By rapid transfer of transmembrane proteins from mammalian cells into polymer-supported membranes, membrane proteins could be efficiently fluorescence labeled and reconstituted with very low background. Thus, differential ligand-induced dimerization of the type I interferon (IFN) receptor subunits IFNAR1 and IFNAR2 could be probed quantitatively at physiologically relevant concentrations by single molecule imaging. These measurements clearly support a regulatory role of the affinity of IFNs toward IFNAR1 for controlling the level of receptor dimerization.
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Affiliation(s)
- Friedrich Roder
- Division
of Biophysics, Department
of Biology, University of Osnabrück, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Stephan Wilmes
- Division
of Biophysics, Department
of Biology, University of Osnabrück, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Christian P. Richter
- Division
of Biophysics, Department
of Biology, University of Osnabrück, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Division
of Biophysics, Department
of Biology, University of Osnabrück, Barbarastr. 11, 49076 Osnabrück, Germany
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34
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Mashaghi S, van Oijen AM. A versatile approach to the generation of fluid supported lipid bilayers and its applications. Biotechnol Bioeng 2014; 111:2076-81. [PMID: 24771312 DOI: 10.1002/bit.25273] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/01/2014] [Accepted: 04/15/2014] [Indexed: 12/26/2022]
Abstract
Establishing supported lipid bilayers with biologically relevant composition, including transmembrane proteins and various classes of lipids, presents a significant challenge. We describe a generic and facile approach to the production of fluid polymer-supported lipid bilayers that allows for the incorporation of a wide variety of lipids and transmembrane proteins. The method is based on the formation of a polymer brush displaying lipid groups, followed by spin-coating of membrane lipids. Subsequentially, transmembrane proteins are incorporated by the fusion of proteoliposomes with the bilayer. Several applications, including the incorporation and single-molecule tracking of transmembrane proteins in a bilayer and the visualization of the fusion of individual, membrane-enveloped viruses with a supported membrane, are demonstrated. Our results suggest that the membrane properties are consistent with those found in physiologically relevant conditions and underscore the wide applicability of our approach to synthetic biology, lab-on-a-chip applications, biophysical and pharmaceutical studies.
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Affiliation(s)
- Samaneh Mashaghi
- Zernike Institute for Advanced Materials, Center for Synthetic Biology, University of Groningen, Groningen, the Netherlands
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35
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de Groot GW, Demarche S, Santonicola MG, Tiefenauer L, Vancso GJ. Smart polymer brush nanostructures guide the self-assembly of pore-spanning lipid bilayers with integrated membrane proteins. NANOSCALE 2014; 6:2228-37. [PMID: 24425208 DOI: 10.1039/c3nr05356c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nanopores in arrays on silicon chips are functionalized with pH-responsive poly(methacrylic acid) (PMAA) brushes and used as supports for pore-spanning lipid bilayers with integrated membrane proteins. Robust platforms are created by the covalent grafting of polymer brushes using surface-initiated atom transfer radical polymerization (ATRP), resulting in sensor chips that can be successfully reused over several assays. His-tagged proteins are selectively and reversibly bound to the nitrilotriacetic acid (NTA) functionalization of the PMAA brush, and consequently lipid bilayer membranes are formed. The enhanced membrane resistance as determined by electrochemical impedance spectroscopy and free diffusion of dyed lipids observed as fluorescence recovery after photobleaching confirmed the presence of lipid bilayers. Immobilization of the His-tagged membrane proteins on the NTA-modified PMAA brush near the pore edges is characterized by fluorescence microscopy. This system allows us to adjust the protein density in free-standing bilayers, which are stabilized by the polymer brush underneath. The potential application of the integrated platform for ion channel protein assays is demonstrated.
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Affiliation(s)
- G Wilhelmina de Groot
- Materials Science and Technology of Polymers, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands.
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36
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Czogalla A, Grzybek M, Jones W, Coskun U. Validity and applicability of membrane model systems for studying interactions of peripheral membrane proteins with lipids. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:1049-59. [PMID: 24374254 DOI: 10.1016/j.bbalip.2013.12.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/12/2013] [Accepted: 12/17/2013] [Indexed: 12/11/2022]
Abstract
The cell membrane serves, at the same time, both as a barrier that segregates as well as a functional layer that facilitates selective communication. It is characterized as much by the complexity of its components as by the myriad of signaling process that it supports. And, herein lays the problems in its study and understanding of its behavior - it has a complex and dynamic nature that is further entangled by the fact that many events are both temporal and transient in their nature. Model membrane systems that bypass cellular complexity and compositional diversity have tremendously accelerated our understanding of the mechanisms and biological consequences of lipid-lipid and protein-lipid interactions. Concurrently, in some cases, the validity and applicability of model membrane systems are tarnished by inherent methodical limitations as well as undefined quality criteria. In this review we introduce membrane model systems widely used to study protein-lipid interactions in the context of key parameters of the membrane that govern lipid availability for peripheral membrane proteins. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Aleksander Czogalla
- Laboratory of Membrane Biochemistry, Paul Langerhans Institute Dresden, Faculty of Medicine Carl Gustav Carus at the TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), Germany.
| | - Michał Grzybek
- Laboratory of Membrane Biochemistry, Paul Langerhans Institute Dresden, Faculty of Medicine Carl Gustav Carus at the TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), Germany
| | - Walis Jones
- Laboratory of Membrane Biochemistry, Paul Langerhans Institute Dresden, Faculty of Medicine Carl Gustav Carus at the TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), Germany
| | - Unal Coskun
- Laboratory of Membrane Biochemistry, Paul Langerhans Institute Dresden, Faculty of Medicine Carl Gustav Carus at the TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), Germany.
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37
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Waichman S, Roder F, Richter CP, Birkholz O, Piehler J. Diffusion and interaction dynamics of individual membrane protein complexes confined in micropatterned polymer-supported membranes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:570-577. [PMID: 23109503 DOI: 10.1002/smll.201201530] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/12/2012] [Indexed: 06/01/2023]
Abstract
Micropatterned polymer-supported membranes (PSM) are established as a tool for confining the diffusion of transmembrane proteins for single molecule studies. To this end, a photochemical surface modification with hydrophobic tethers on a PEG polymer brush is implemented for capturing of lipid vesicles and subsequent fusion. Formation of contiguous membranes within micropatterns is confirmed by scanning force microscopy, fluorescence recovery after photobleaching (FRAP), and super-resolved single-molecule tracking and localization microscopy. Free diffusion of transmembrane proteins reconstituted into micropatterned PSM is demonstrated by FRAP and by single-molecule tracking. By exploiting the confinement of diffusion within micropatterned PSM, the diffusion and interaction dynamics of individual transmembrane receptors are quantitatively resolved.
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Affiliation(s)
- Sharon Waichman
- Department of Biology, University of Osnabrück, Osnabrück, Germany
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38
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Otterstrom J, van Oijen AM. Visualization of membrane fusion, one particle at a time. Biochemistry 2013; 52:1654-68. [PMID: 23421412 DOI: 10.1021/bi301573w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein-mediated fusion between phospholipid bilayers is a fundamental and necessary mechanism for many cellular processes. The short-lived nature of the intermediate states visited during fusion makes it challenging to capture precise kinetic information using classical, ensemble-averaging biophysical techniques. Recently, a number of single-particle fluorescence microscopy-based assays that allow researchers to obtain highly quantitative data about the fusion process by observing individual fusion events in real time have been developed. These assays depend upon changes in the acquired fluorescence signal to provide a direct readout for transitions between the various fusion intermediates. The resulting data yield meaningful and detailed kinetic information about the transitory states en route to productive membrane fusion. In this review, we highlight recent in vitro and in vivo studies of membrane fusion at the single-particle level in the contexts of viral membrane fusion and SNARE-mediated synaptic vesicle fusion. These studies afford insight into mechanisms of coordination between fusion-mediating proteins as well as coordination of the overall fusion process with other cellular processes. The development of single-particle approaches to investigate membrane fusion and their successful application to a number of model systems have resulted in a new experimental paradigm and open up considerable opportunities to extend these methods to other biological processes that involve membrane fusion.
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Affiliation(s)
- Jason Otterstrom
- Harvard Biophysics Program, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
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39
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de Groot GW, Santonicola MG, Sugihara K, Zambelli T, Reimhult E, Vörös J, Vancso GJ. Switching transport through nanopores with pH-responsive polymer brushes for controlled ion permeability. ACS APPLIED MATERIALS & INTERFACES 2013; 5:1400-1407. [PMID: 23360664 DOI: 10.1021/am302820y] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Several nanoporous platforms were functionalized with pH-responsive poly(methacrylic acid) (PMAA) brushes using surface-initiated atom transfer radical polymerization (SI-ATRP). The growth of the PMAA brush and its pH-responsive behavior from the nanoporous platforms were confirmed by scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The swelling behavior of the pH-responsive PMAA brushes grafted only from the nanopore walls was investigated by AFM in aqueous liquid environment with pH values of 4 and 8. AFM images displayed open nanopores at pH 4 and closed ones at pH 8, which rationalizes their use as gating platforms. Ion conductivity across the nanopores was investigated with current-voltage measurements at various pH values. Enhanced higher resistance across the nanopores was observed in a neutral polymer brush state (lower pH values) and lower resistance when the brush was charged (higher pH values). By adding a fluorescent dye in an environment of pH 4 or pH 8 at one side of the PMAA-brush functionalized nanopore array chips, diffusion across the nanopores was followed. These experiments displayed faster diffusion rates of the fluorescent molecules at pH 4 (PMAA neutral state, open pores) and slower diffusion at pH 8 (PMAA charged state, closed pores) showing the potential of this technology toward nanoscale valve applications.
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Affiliation(s)
- G Wilhelmina de Groot
- Materials Science and Technology of Polymers, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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40
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Roder F, Birkholz O, Beutel O, Paterok D, Piehler J. Spatial organization of lipid phases in micropatterned polymer-supported membranes. J Am Chem Soc 2013; 135:1189-92. [PMID: 23289715 DOI: 10.1021/ja310186g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have established an approach for the spatial control of lipid phase separation in tethered polymer-supported membranes (PSMs), which were obtained by vesicle fusion on a poly(ethylene glycol) polymer brush functionalized with fatty acid moieties. Phase separation of ternary lipid mixtures (1,2-dioleoyl-sn-glycero-3-phosphocholine/sphingomyelin/cholesterol) into liquid-disordered (l(d)) and liquid-ordered (l(o)) phases within both leaflets was obtained with palmitic acid as the anchoring group. In contrast, tethering of the PSM with oleic acid interfered with the phase separation in the surface-proximal leaflet. We exploited this feature for the assembly of l(o) domains within PSMs into defined structures by binary micropatterning of palmitic and oleic acid into complementary areas. Ternary lipid mixtures spontaneously separated into l(o) and l(d) phases controlled by the geometry of the underlying tethers. Transmembrane proteins reconstituted in these phase-separated PSMs strictly partitioned into the l(d) phase. Hence, the l(o) phase could be used for confining transmembrane proteins into microscopic and submicroscopic domains.
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Affiliation(s)
- Friedrich Roder
- Division of Biophysics, Department of Biology, University of Osnabrück, 49069 Osnabrück, Germany
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Sanguigno L, Cosenza C, Causa F, Netti PA. Accounting for misalignments and thermal fluctuations in fluorescence correlation spectroscopy experiments on membranes. Analyst 2013; 138:1674-81. [DOI: 10.1039/c2an36681a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Gözen I, Jesorka A. Instrumental Methods to Characterize Molecular Phospholipid Films on Solid Supports. Anal Chem 2012; 84:822-38. [DOI: 10.1021/ac203126f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Irep Gözen
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden
| | - Aldo Jesorka
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden
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