The Giant Vesicle Book Dimova, Rumiana; Marques, Carlos
2020, 20191119, 2019, 2019-11-19
eBook
Giant vesicles are widely used as a model membrane system, both for basic biological systems and for their promising applications in the development of smart materials and cell mimetics, as well as ...in driving new technologies in synthetic biology and for the cosmetics and pharmaceutical industry. The reader is guided to use giant vesicles, from the formation of simple membrane platforms to advanced membrane and cell system models. It also includes fundamentals for understanding lipid or polymer membrane structure, properties and behavior. Every chapter includes ideas for further applications and discussions on the implications of the observed phenomena towards understanding membrane-related processes. The Giant Vesicle Book is meant to be a road companion, a trusted guide for those making their first steps in this field as well as a source of information required by experts.
Key Features
• A complete summary of the field, covering fundamental concepts, practical methods, core theory, and the most promising applications
• A start-up package of theoretical and experimental information for newcomers in the field
• Extensive protocols for establishing the required preparations and assays
• Tips and instructions for carefully performing and interpreting measurements with giant vesicles or for observing them, including pitfalls
• Approaches developed for investigating giant vesicles as well as brief overviews of previous studies implementing the described techniques
• Handy tables with data and structures for ready reference
Part I: The making of
Chapter 1 Preparation methods for giant unilamellar vesicles - Rumiana Dimova, Pasquale Stano, Carlos M. Marques and Peter Walde
Chapter 2 Preparation and properties of giant plasma membrane vesicles and giant unilamellar vesicles from natural membranes - Joseph H. Lorent and Ilya Levental
Chapter 3 Protein reconstitution in giant vesicles - Matthias Garten, Daniel Lévy and Patricia Bassereau
Chapter 4 GUVs with cytoskeleton - Tobias Härtel and Petra Schwille
Part II: Giant vesicles theoretically and in silico
Chapter 5 Understanding giant vesicles – a theoretical perspective - Reinhard Lipowsky
Chapter 6 Simulating membranes, vesicles, and cells - Thorsten Auth, Dmitry A. Fedosov and Gerhard Gompper
Chapter 7 Theory of vesicle dynamics in flow and electric fields - Petia M. Vlahovska and Chaouqi Misbah
Chapter 8 Particle-membrane interactions - Jaime Agudo-Canalejo, Reinhard Lipowsky
Chapter 9 Theory of polymer-membrane interactions - Fabrice Thalmann and Carlos M. Marques
Part III: GUV-based techniques and what one can learn from them
Chapter 10 Application of optical microscopy techniques on giant unilamellar vesicles - Luis A. Bagatolli
Chapter 11 Mechanics assays of synthetic lipid membranes based on micropipette aspiration - Elisa Parra and David Needham
Chapter 12 Atomic force microscopy of giant unilamellar vesicles - Andreas Janshoff
Chapter 13 Manipulation and biophysical characterization of GUVs with an optical stretcher - Gheorghe Cojoc, Antoine Girot, Ulysse Delabre and Jochen Guck
Chapter 14 Vesicle fluctuation analysis - John Hjort Ipsen, Allan Grønhøj Hansen and Tripta Bhatia
Chapter 15 Using electric fields to assess membrane material properties in GUVs - Rumiana Dimova and Karin A. Riske
Chapter 16 Creating membrane nanotubes from GUVs - Coline Prévost, Mijo Simunovic and Patricia Bassereau
Chapter 17 Measuring GUV adhesion - Kheya Sengupta and Ana Smith
Chapter 18 Phase diagrams and tie lines in GUVs - Matthew C. Blosser, Caitlin Cornell, Scott P. Rayermann and Sarah L. Keller
Chapter 19 Vesicle dynamics in flow: an experimental approach - Victor Steinberg and Michael Levant
Chapter 20 Membrane permeability measurements - Begoña Ugarte-Uribe, Ana J. García-Sáez and Mireille M. A. E. Claessens
Part IV: GUVs as membrane interaction platforms
Chapter 21 - Lipid and protein mobility in GUVs - Begoña Ugarte-Uribe, Kushal Kumar Das and Ana J. García-Sáez
Chapter 22 Shining light on membranes - Rosangela Itri, Carlos M. Marques and Mauricio S. Baptista
Chapter 23 Protein-membrane interactions - Eva M Schmid and Daniel A Fletcher
Chapter 24 Effects of antimicrobial peptides and detergents on GUVs - Karin A. Riske
Chapter 25 Lipid-polymer interactions: effect on GUVs shapes and behavior - Brigitte Pépin-Donat, François Quemeneur and Clément Campillo
Part V: GUVs as complex membrane containers
Chapter 26 Polymersomes - Praful Nair, David Christian and Dennis E. Discher
Chapter 27 Giant hybrid polymer/lipid vesicles - Thi Phuong Tuyen Dao, Khalid Ferji, Fabio Fernandes, Manuel Prieto, Sébastien Lecommandoux, Emmanuel Ibarboure, Olivier Sandre and Jean-François Le Meins
Chapter 28 Giant unilamellar vesicles: from protocell models to the construction of minimal cells - Masayuki Imai and Peter Walde
Chapter 29 Encapsulation of aqueous two-phase systems and gels within giant lipid vesicles - Allyson M. Marianelli and Christine D. Keating
Chapter 30 Droplet-supported giant lipid vesicles as compartments for synthetic biology - Johannes P. Frohnmayer, Marian Weiss, Lucia T. Benk, Jan-Willi Janiesch, Barbara Haller, Rafael B. Lira, Rumiana Dimova, Ilia Plazman and Joachim P. Spatz
Appendices
Appendix 1 List of lipids and physical constants of lipid bilayers
Appendix 2 List of membrane dyes and fluorescent groups conjugated to lipids
Appendix 3 List of detergents
Appendix 4 List of water-soluble dyes or their fluorescent groups and their structures
Rumiana Dimova leads an experimental lab in biophysics at the Max Planck Institute of Colloids and Interfaces in Potsdam, Germany. She has been working with giant vesicles already from the beginning of her scientific career. After being introduced into the magic of their preparation during her studies as a student in Bulgaria, she remained fascinated by their application and over the years pursued a variety of projects employing giant vesicles as a platform to develop new methods for the biophysical characterization of membranes and processes involving them. Until now, these studies have resulted in more than hundred peer-reviewed publications. Recently, she was also awarded the Emmy Noether distinction for women in physics of the European Physical Society.
Carlos Marques , a CNRS senior scientist, founded the MCube group at the Charles Sadron Institute in Strasbourg, France, where he gears experimental and theoretical research towards the understanding of the physical properties of self-assembled lipid bilayers. Trained as a polymer theoretician, Carlos first got interested in membranes because they interact with polymers and published the first prediction for the membrane changes expected when polymers adsorb on lipid bilayers. He then expanded the scope of his group to include experiments and numerical simulations, and has now published many papers based on research with giant unilamellar vesicles, including the first study of lipid oxidation in GUVs and the discovery of the so-called PVA method for vesicle growth.
A membrane-bound form of Pf1 coat protein reconstituted in magnetically aligned DMPC/DHPC bicelles was used as a molecular probe to quantify for the viscosity of the lipid membrane interior by ...measuring the uniaxial rotational diffusion coefficient of the protein. Orientationally dependent 15N NMR relaxation times in the rotating frame, or T1ρ, were determined by fitting individually the decay of the resolved NMR peaks corresponding to the transmembrane helix of Pf1 coat protein as a function of the spin-lock time incorporated into the 2D SAMPI4 pulse sequence. The T1ρ relaxation mechanism was modeled by uniaxial rotational diffusion on a cone, which yields a linear correlation with respect to the bond factor sin4θB, where θB is the angle that the NH bond forms with respect to the axis of rotation. Importantly, the bond factors can be independently measured from the dipolar couplings in the separated local-field SAMPI4 spectra. From this dependence, the value of the diffusion coefficient D|| = 8.0 × 105 s−1 was inferred from linear regression of the experimental T1ρ data even without any spectroscopic assignment. Alternatively, a close value of D|| = 7.7 × 105 s−1 was obtained by fitting the T1ρ relaxation data for the assigned NMR peaks of the transmembrane domain of Pf1 to a wavelike pattern as a function of residue number. The method illustrates the use of single-helix transmembrane peptides as molecular probes to assess the dynamic parameters of biological membranes by NMR relaxation in oriented lipid bilayers.
Biological membranes are compartmentalized for functional diversity by a variety of specific protein-protein, protein-lipid, and lipid-lipid interactions. A subset of these are the preferential ...interactions between sterols, sphingolipids, and saturated aliphatic lipid tails responsible for liquid-liquid domain coexistence in eukaryotic membranes, which give rise to dynamic, nanoscopic assemblies whose coalescence is regulated by specific biochemical cues. Microscopic phase separation recently observed in isolated plasma membranes (giant plasma membrane vesicles and plasma membrane spheres) (i) confirms the capacity of compositionally complex membranes to phase separate, (ii) reflects the nanoscopic organization of live cell membranes, and (iii) provides a versatile platform for the investigation of the compositions and properties of the phases. Here, we show that the properties of coexisting phases in giant plasma membrane vesicles are dependent on isolation conditions--namely, the chemicals used to induce membrane blebbing. We observe strong correlations between the relative compositions and orders of the coexisting phases, and their resulting miscibility. Chemically unperturbed plasma membranes reflect these properties and validate the observations in chemically induced vesicles. Most importantly, we observe domains with a continuum of varying stabilities, orders, and compositions induced by relatively small differences in isolation conditions. These results show that, based on the principle of preferential association of raft lipids, domains of various properties can be produced in a membrane environment whose complexity is reflective of biological membranes.
Cellular protrusions, invaginations, and many intracellular organelles have strongly curved membrane regions. Transmembrane and peripheral membrane proteins that induce, sense, or stabilize such ...regions cannot be properly fitted into a single flat bilayer. To treat such proteins, we developed a new method and a web tool, PPM 3.0, for positioning proteins in curved or planar, single or multiple membranes. This method determines the energetically optimal spatial position, the hydrophobic thickness, and the radius of intrinsic curvature of a membrane‐deforming protein structure by arranging it in a single or several sphere‐shaped or planar membrane sections. In addition, it can define the lipid‐embedded regions of a protein that simultaneously spans several membranes or determine the optimal position of a peptide in a spherical micelle. The PPM 3.0 web server operates with 17 types of biological membranes and 4 types of artificial bilayers. It is publicly available at https://opm.phar.umich.edu/ppm_server3. PPM 3.0 was applied to identify and characterize arrangements in membranes of 128 proteins with a significant intrinsic curvature, such as BAR domains, annexins, Piezo, and MscS mechanosensitive channels, cation‐chloride cotransporters, as well as mitochondrial ATP synthases, calcium uniporters, and TOM complexes. These proteins form large complexes that are mainly localized in mitochondria, plasma membranes, and endosomes. Structures of bacterial drug efflux pumps, AcrAB‐TolC, MexAB‐OrpM, and MacAB‐TolC, were positioned in both membranes of the bacterial cell envelop, while structures of multimeric gap‐junction channels were arranged in two opposed cellular membranes.
A critical step in cellular-trafficking pathways is the budding of membranes by protein coats, which recent experiments have demonstrated can be inhibited by elevated membrane tension. The robustness ...of processes like clathrin-mediated endocytosis (CME) across a diverse range of organisms and mechanical environments suggests that the protein machinery in this process has evolved to take advantage of some set of physical design principles to ensure robust vesiculation against opposing forces like membrane tension. Using a theoretical model for membrane mechanics and membrane protein interaction, we have systematically investigated the influence of membrane rigidity, curvature induced by the protein coat, area covered by the protein coat, membrane tension, and force from actin polymerization on bud formation. Under low tension, the membrane smoothly evolves from a flat to budded morphology as the coat area or spontaneous curvature increases, whereas the membrane remains essentially flat at high tensions. At intermediate, physiologically relevant, tensions, the membrane undergoes a “snap-through instability” in which small changes in the coat area, spontaneous curvature or membrane tension cause the membrane to “snap” from an open, U-shape to a closed bud. This instability can be smoothed out by increasing the bending rigidity of the coat, allowing for successful budding at higher membrane tensions. Additionally, applied force from actin polymerization can bypass the instability by inducing a smooth transition from an open to a closed bud. Finally, a combination of increased coat rigidity and force from actin polymerization enables robust vesiculation even at high membrane tensions.
A key morphological feature of inflammatory bowel disease (IBD) is the loss of the barrier function of intestinal epithelial cells. The present study investigates endoplasmic reticulum (ER) stress in ...addition to alterations in protein and membrane trafficking in a dextran sulfate sodium (DSS)-induced IBD-like phenotype of intestinal Caco-2 cells in culture. DSS treatment significantly reduced the transepithelial electric resistance (TEER) and increased the epithelial permeability of Caco-2 cells, without affecting their viability. This was associated with an alteration in the expression levels of inflammatory factors in addition to an increase in the expression of the ER stress protein markers, namely immunoglobulin-binding protein (BiP), C/EBP homologous protein (CHOP), activation transcription factor 4 (ATF4), and X-box binding protein (XBP1). The DSS-induced ER-stress resulted in impaired intracellular trafficking and polarized sorting of sucrase-isomaltase (SI) and dipeptidyl peptidase-4 (DPPIV), which are normally sorted to the apical membrane via association with lipid rafts. The observed impaired sorting was caused by reduced cholesterol levels and subsequent distortion of the lipid rafts. The data presented confirm perturbation of ER homeostasis in DSS-treated Caco-2 cells, accompanied by impairment of membrane and protein trafficking resulting in altered membrane integrity, cellular polarity, and hence disrupted barrier function.
Photoreceptors rely on distinct membrane compartments to support their specialized function. Unlike protein localization, identification of critical differences in membrane content has not yet been ...expanded to lipids, due to the difficulty of isolating domain-specific samples. We have overcome this by using SMA to coimmunopurify membrane proteins and their native lipids from two regions of photoreceptor ROS disks. Each sample's copurified lipids were subjected to untargeted lipidomic and fatty acid analysis. Extensive differences between center (rhodopsin) and rim (ABCA4 and PRPH2/ROM1) samples included a lower PC to PE ratio and increased LC- and VLC-PUFAs in the center relative to the rim region, which was enriched in shorter, saturated FAs. The comparatively few differences between the two rim samples likely reflect specific protein-lipid interactions. High-resolution profiling of the ROS disk lipid composition gives new insights into how intricate membrane structure and protein activity are balanced within the ROS, and provides a model for future studies of other complex cellular structures.
Docosahexaenoic acid is an omega-3 polyunsaturated fatty acid that relieves the symptoms of a wide variety of chronic inflammatory disorders. The structural mechanism is not yet completely ...understood. Our focus here is on the plasma membrane as a site of action. We examined the molecular organization of 2H31-N-palmitoylsphingomyelin (PSM-d31) mixed with 1-palmitoyl-2-docosahexaenoylphosphatylcholine (PDPC) or 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), as a monounsaturated control, and cholesterol (chol) (1:1:1 mol) in a model membrane by solid-state 2H NMR. The spectra were analyzed in terms of segregation into ordered SM-rich/chol-rich (raftlike) and disordered PC-rich/chol-poor (nonraft) domains that are nanoscale in size. An increase in the size of domains is revealed when POPC was replaced by PDPC. Spectra that are single-component, attributed to fast exchange between domains (<45 nm), for PSM-d31 mixed with POPC and chol become two-component, attributed to slow exchange between domains (r > 30 nm), for PSM-d31 mixed with PDPC and chol. The resolution of separate signals from PSM-d31, and correspondingly from 3α-2H1cholesterol (chol-d1) and 1-2H31palmitoyl-2-docosahexaenoylphosphatidylcholine (PDPC-d31), in raftlike and nonraft domains enabled us to determine the composition of the domains in the PDPC-containing membrane. Most of the lipid (28% SM, 29% chol, and 23% PDPC with respect to total lipid at 30°C) was found in the raftlike domain. Despite substantial infiltration of PDPC into raftlike domains, there appears to be minimal effect on the order of SM, implying the existence of internal structure that limits contact between SM and PDPC. Our results suggest a significant refinement to the model by which DHA regulates the architecture of ordered, sphingolipid-chol-enriched domains (rafts) in membranes.
Plasma membrane heterogeneity has been tied to a litany of cellular functions and is often explained by analogy to membrane phase separation; however, models based on phase separation alone fall ...short of describing the rich organization available within cell membranes. Here we present comprehensive experimental evidence motivating an updated model of plasma membrane heterogeneity in which membrane domains assemble in response to protein scaffolds. Quantitative super-resolution nanoscopy measurements in live B lymphocytes detect membrane domains that emerge upon clustering B cell receptors (BCRs). These domains enrich and retain membrane proteins based on their preference for the liquid-ordered phase. Unlike phase-separated membranes that consist of binary phases with defined compositions, membrane composition at BCR clusters is modulated through the protein constituents in clusters and the composition of the membrane overall. This tunable domain structure is detected through the variable sorting of membrane probes and impacts the magnitude of BCR activation.
Plastic pollution of the aquatic environment is a major concern considering the disastrous impact on the environment and on human beings. The significant and continuous increase in the production of ...plastics causes an enormous amount of plastic waste on the land entering the aquatic environment. Furthermore, wastewater treatment plants (WWTPs) are reported as the main source of microplastic and nanoplastic in the effluents, since they are not properly designed for this purpose. The application of advanced wastewater treatment technologies is mandatory to avoid effluent contamination by plastics. A concrete solution can be represented by membrane technologies as tertiary treatment of effluents in integrated systems for wastewater treatment, in particular, for the plastic particles with a smaller size (< 100 nm). In this review, a survey of the membrane processes applied in the plastic removal is analyzed and critically discussed. From the literature analysis, it was found that the removal of microplastic by membrane technology is still insufficient, and without the use of specially designed approaches, with the exception of membrane bioreactors (MBRs).
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