ABSTRACT
The D2 dopamine receptor (DRD2) is a therapeutic target for Parkinson's disease1 and antipsychotic drugs2. DRD2 is activated by the endogenous neurotransmitter dopamine and synthetic agonist drugs such as bromocriptine3, leading to stimulation of Gi and inhibition of adenylyl cyclase. Here we used cryo-electron microscopy to elucidate the structure of an agonist-bound activated DRD2-Gi complex reconstituted into a phospholipid membrane. The extracellular ligand-binding site of DRD2 is remodelled in response to agonist binding, with conformational changes in extracellular loop 2, transmembrane domain 5 (TM5), TM6 and TM7, propagating to opening of the intracellular Gi-binding site. The DRD2-Gi structure represents, to our knowledge, the first experimental model of a G-protein-coupled receptor-G-protein complex embedded in a phospholipid bilayer, which serves as a benchmark to validate the interactions seen in previous detergent-bound structures. The structure also reveals interactions that are unique to the membrane-embedded complex, including helix 8 burial in the inner leaflet, ordered lysine and arginine side chains in the membrane interfacial regions, and lipid anchoring of the G protein in the membrane. Our model of the activated DRD2 will help to inform the design of subtype-selective DRD2 ligands for multiple human central nervous system disorders.
Subject(s)
Cryoelectron Microscopy , GTP-Binding Protein alpha Subunits, Gi-Go/chemistry , GTP-Binding Protein alpha Subunits, Gi-Go/ultrastructure , Membrane Lipids/metabolism , Membranes, Artificial , Receptors, Dopamine D2/chemistry , Receptors, Dopamine D2/ultrastructure , Bromocriptine/chemistry , Bromocriptine/metabolism , Dopamine/chemistry , Dopamine/metabolism , GTP-Binding Protein alpha Subunits, Gi-Go/metabolism , Humans , Membrane Lipids/chemistry , Models, Molecular , Protein Conformation , Receptors, Dopamine D2/agonists , Receptors, Dopamine D2/metabolism , Signal TransductionABSTRACT
Permeabilization of the outer mitochondrial membrane by pore-forming Bcl2 proteins is a crucial step for the induction of apoptosis. Despite a large set of data suggesting global conformational changes within pro-apoptotic Bak during pore formation, high-resolution structural details in a membrane environment remain sparse. Here, we used NMR and HDX-MS (Hydrogen deuterium exchange mass spectrometry) in lipid nanodiscs to gain important high-resolution structural insights into the conformational changes of Bak at the membrane that are dependent on a direct activation by BH3-only proteins. Furthermore, we determined the first high-resolution structure of the Bak transmembrane helix. Upon activation, α-helix 1 in the soluble domain of Bak dissociates from the protein and adopts an unfolded and dynamic potentially membrane-bound state. In line with this finding, comparative protein folding experiments with Bak and anti-apoptotic BclxL suggest that α-helix 1 in Bak is a metastable structural element contributing to its pro-apoptotic features. Consequently, mutagenesis experiments aimed at stabilizing α-helix 1 yielded Bak variants with delayed pore-forming activity. These insights will contribute to a better mechanistic understanding of Bak-mediated membrane permeabilization.
Subject(s)
Liposomes/chemistry , Membrane Lipids/chemistry , Proto-Oncogene Proteins c-bcl-2/chemistry , bcl-2 Homologous Antagonist-Killer Protein/chemistry , bcl-X Protein/chemistry , Binding Sites , Cloning, Molecular , Deuterium Exchange Measurement , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Humans , Kinetics , Liposomes/metabolism , Membrane Lipids/metabolism , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Folding , Protein Interaction Domains and Motifs , Protein Multimerization , Proto-Oncogene Proteins c-bcl-2/genetics , Proto-Oncogene Proteins c-bcl-2/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Thermodynamics , bcl-2 Homologous Antagonist-Killer Protein/genetics , bcl-2 Homologous Antagonist-Killer Protein/metabolism , bcl-X Protein/genetics , bcl-X Protein/metabolismABSTRACT
BAK and BAX, the effectors of intrinsic apoptosis, each undergo major reconfiguration to an activated conformer that self-associates to damage mitochondria and cause cell death. However, the dynamic structural mechanisms of this reconfiguration in the presence of a membrane have yet to be fully elucidated. To explore the metamorphosis of membrane-bound BAK, we employed hydrogen-deuterium exchange mass spectrometry (HDX-MS). The HDX-MS profile of BAK on liposomes comprising mitochondrial lipids was consistent with known solution structures of inactive BAK. Following activation, HDX-MS resolved major reconfigurations in BAK. Mutagenesis guided by our HDX-MS profiling revealed that the BCL-2 homology (BH) 4 domain maintains the inactive conformation of BAK, and disrupting this domain is sufficient for constitutive BAK activation. Moreover, the entire N-terminal region preceding the BAK oligomerisation domains became disordered post-activation and remained disordered in the activated oligomer. Removal of the disordered N-terminus did not impair, but rather slightly potentiated, BAK-mediated membrane permeabilisation of liposomes and mitochondria. Together, our HDX-MS analyses reveal new insights into the dynamic nature of BAK activation on a membrane, which may provide new opportunities for therapeutic targeting.
Subject(s)
Liposomes/chemistry , Membrane Lipids/chemistry , Proto-Oncogene Proteins c-bcl-2/chemistry , bcl-2 Homologous Antagonist-Killer Protein/chemistry , Animals , Binding Sites , Cloning, Molecular , Deuterium Exchange Measurement , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Humans , Kinetics , Liposomes/metabolism , Membrane Lipids/metabolism , Mice , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Folding , Protein Interaction Domains and Motifs , Protein Multimerization , Proto-Oncogene Proteins c-bcl-2/genetics , Proto-Oncogene Proteins c-bcl-2/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Thermodynamics , bcl-2 Homologous Antagonist-Killer Protein/genetics , bcl-2 Homologous Antagonist-Killer Protein/metabolismABSTRACT
Enveloped viruses are enclosed by a lipid membrane inside of which are all of the components necessary for the virus life cycle; viral proteins, the viral genome and metabolites. Viral envelopes are lipid bilayers that adopt morphologies ranging from spheres to tubes. The envelope is derived from the host cell during viral replication. Thus, the composition of the bilayer depends on the complex constitution of lipids from the host-cell's organelle(s) where assembly and/or budding of the viral particle occurs. Here, molecular dynamics (MD) simulations of authentic, asymmetric HIV-1 liposomes are used to derive a unique level of resolution of its full-scale structure, mechanics and dynamics. Analysis of the structural properties reveal the distribution of thicknesses of the bilayers over the entire liposome as well as its global fluctuations. Moreover, full-scale mechanical analyses are employed to derive the global bending rigidity of HIV-1 liposomes. Finally, dynamical properties of the lipid molecules reveal important relationships between their 3D diffusion, the location of lipid-rafts and the asymmetrical composition of the envelope. Overall, our simulations reveal complex relationships between the rich lipid composition of the HIV-1 liposome and its structural, mechanical and dynamical properties with critical consequences to different stages of HIV-1's life cycle.
Subject(s)
HIV-1 , Liposomes , Membrane Lipids , Diffusion , HIV-1/chemistry , HIV-1/metabolism , Liposomes/chemistry , Liposomes/metabolism , Membrane Lipids/chemistry , Membrane Lipids/metabolism , Membrane Microdomains/chemistry , Membrane Microdomains/metabolism , Molecular Dynamics SimulationABSTRACT
Within cell membranes numerous protein assemblies reside. Among their many functions, these assemblies regulate the movement of molecules between membranes, facilitate signaling into and out of cells, allow movement of cells by cell-matrix attachment, and regulate the electric potential of the membrane. With such critical roles, membrane protein complexes are of considerable interest for human health, yet they pose an enduring challenge for structural biologists because it is difficult to study these protein structures at atomic resolution in in situ environments. To advance structural and functional insights for these protein assemblies, membrane mimetics are typically employed to recapitulate some of the physical and chemical properties of the lipid bilayer membrane. However, extraction from native membranes can sometimes change the structure and lipid-binding properties of these complexes, leading to conflicting results and fueling a drive to study complexes directly from native membranes. Here we consider the co-development of membrane mimetics with technological breakthroughs in both cryo-electron microscopy (cryo-EM) and native mass spectrometry (nMS). Together, these developments are leading to a plethora of high-resolution protein structures, as well as new knowledge of their lipid interactions, from different membrane-like environments.
Subject(s)
Cell Membrane/chemistry , Eukaryotic Cells/metabolism , Membrane Lipids/chemistry , Membrane Proteins/chemistry , Animals , Biological Transport , Cell Membrane/metabolism , Cell Membrane/ultrastructure , Cryoelectron Microscopy , Detergents/chemistry , Eukaryotic Cells/cytology , Humans , Membrane Lipids/classification , Membrane Lipids/metabolism , Membrane Proteins/genetics , Membrane Proteins/metabolism , Membranes, Artificial , Micelles , Models, Molecular , Protein Structure, Secondary , Signal Transduction , Thermus thermophilus/metabolism , Thermus thermophilus/ultrastructureABSTRACT
In this article, it is hypothesized that a fundamental chemical reactivity exists between some non-lipid constituents of cellular membranes and ester-based lipids, the significance of which is not generally recognized. Many peptides and smaller organic molecules have now been shown to undergo lipidation reactions in model membranes in circumstances where direct reaction with the lipid is the only viable route for acyl transfer. Crucially, drugs like propranolol are lipidated in vivo with product profiles that are comparable to those produced in vitro. Some compounds have also been found to promote lipid hydrolysis. Drugs with high lytic activity in vivo tend to have higher toxicity in vitro. Deacylases and lipases are proposed as key enzymes that protect cells against the effects of intrinsic lipidation. The toxic effects of intrinsic lipidation are hypothesized to include a route by which nucleation can occur during the formation of amyloid fibrils.
Subject(s)
Cell Membrane/chemistry , Cell Membrane/metabolism , Membrane Lipids/chemistry , Membrane Lipids/metabolism , Acetyl-CoA Hydrolase/chemistry , Acetyl-CoA Hydrolase/metabolism , Acyl Coenzyme A/chemistry , Acyl Coenzyme A/metabolism , Alzheimer Disease/metabolism , Amyloid beta-Peptides/chemistry , Amyloid beta-Peptides/metabolism , Animals , Humans , Hydrolysis , Lipase/chemistry , Lipase/metabolism , Liposomes/chemistry , Liposomes/metabolism , Parkinson Disease/metabolism , Protein Aggregation, Pathological/metabolism , Protein Binding , Protein Conformation, beta-Strand , Signal TransductionABSTRACT
In the twelve years since styrene maleic acid (SMA) was first used to extract and purify a membrane protein within a native lipid bilayer, this technological breakthrough has provided insight into the structural and functional details of protein-lipid interactions. Most recently, advances in cryo-EM have demonstrated that SMA-extracted membrane proteins are a rich-source of structural data. For example, it has been possible to resolve the details of annular lipids and protein-protein interactions within complexes, the nature of lipids within central cavities and binding pockets, regions involved in stabilising multimers, details of terminal residues that would otherwise remain unresolved and the identification of physiologically relevant states. Functionally, SMA extraction has allowed the analysis of membrane proteins that are unstable in detergents, the characterization of an ultrafast component in the kinetics of electron transfer that was not possible in detergent-solubilised samples and quantitative, real-time measurement of binding assays with low concentrations of purified protein. While the use of SMA comes with limitations such as its sensitivity to low pH and divalent cations, its major advantage is maintenance of a protein's lipid bilayer. This has enabled researchers to view and assay proteins in an environment close to their native ones, leading to new structural and mechanistic insights.
Subject(s)
Lipid Bilayers/chemistry , Maleates/chemistry , Membrane Proteins/chemistry , Membrane Proteins/isolation & purification , Polystyrenes/chemistry , Cryoelectron Microscopy/methods , Membrane Lipids/chemistry , Membrane Proteins/ultrastructure , Protein Binding , Protein Conformation , Protein StabilityABSTRACT
Membrane proteins play vital roles in living organisms, serving as targets for most currently prescribed drugs. Membrane protein structural biology aims to provide accurate structural information to understand their mechanisms of action. The advance of membrane protein structural biology has primarily relied on detergent-based methods over the past several decades. However, detergent-based approaches have significant drawbacks because detergents often damage the native protein-lipid interactions, which are often crucial for maintaining the natural structure and function of membrane proteins. Detergent-free methods recently have emerged as alternatives with a great promise, e.g. for high-resolution structure determinations of membrane proteins in their native cell membrane lipid environments. This minireview critically examines the current status of detergent-free methods by a comparative analysis of five groups of membrane protein structures determined using detergent-free and detergent-based methods. This analysis reveals that current detergent-free systems, such as the styrene-maleic acid lipid particles (SMALP), the diisobutyl maleic acid lipid particles (DIBMALP), and the cycloalkane-modified amphiphile polymer (CyclAPol) technologies are not better than detergent-based approaches in terms of maintenance of native cell membrane lipids on the transmembrane domain and high-resolution structure determination. However, another detergent-free technology, the native cell membrane nanoparticles (NCMN) system, demonstrated improved maintenance of native cell membrane lipids with the studied membrane proteins, and produced particles that were suitable for high-resolution structural analysis. The ongoing development of new membrane-active polymers and their optimization will facilitate the maturation of these new detergent-free systems.
Subject(s)
Cell Membrane/chemistry , Lipid Bilayers/chemistry , Membrane Lipids/chemistry , Membrane Proteins/chemistry , Nanoparticles/chemistry , Polymers/chemistry , Cryoelectron Microscopy/methods , Detergents/chemistry , Membrane Proteins/isolation & purification , Membrane Proteins/ultrastructure , Protein Binding , Protein ConformationABSTRACT
Success rates in drug discovery are extremely low, and the imbalance between new drugs entering clinical research and their approval is steadily widening. Among the causes of the failure of new therapeutic agents are the lack of safety and insufficient efficacy. On the other hand, timely disease diagnosis may enable an early management of the disease, generally leading to better and less costly outcomes. Several strategies have been explored to overcome the barriers for drug development and facilitate diagnosis. Using lipid membranes as platforms for drug delivery or as biosensors are promising strategies, due to their biocompatibility and unique physicochemical properties. We examine some of the lipid membrane-based strategies for drug delivery and diagnostics, including their advantages and shortcomings. Regarding synthetic lipid membrane-based strategies for drug delivery, liposomes are the archetypic example of a successful approach, already with a long period of well-succeeded clinical application. The use of lipid membrane-based structures from biological sources as drug carriers, currently under clinical evaluation, is also discussed. These biomimetic strategies can enhance the in vivo lifetime of drug and delivery system by avoiding fast clearance, consequently increasing their therapeutic window. The strategies under development using lipid membranes for diagnostic purposes are also reviewed.
Subject(s)
Biomimetic Materials , Biosensing Techniques , Membrane Lipids , Biomimetic Materials/chemistry , Biomimetic Materials/therapeutic use , Humans , Liposomes , Membrane Lipids/chemistry , Membrane Lipids/metabolism , Membrane Lipids/therapeutic useABSTRACT
The aggregation and deposition of amyloid ß (Aß) peptide onto neuronal cells, with consequent cellular membrane perturbation, are central to the pathogenesis of Alzheimer's disease (AD). Substantial evidence reveals that biological membranes play a key role in this process. Thus, elucidating the mechanisms by which Aß interacts with biomembranes and becomes neurotoxic is fundamental to developing effective therapies for this devastating progressive disease. However, the structural basis behind such interactions is not fully understood, largely due to the complexity of natural membranes. In this context, lipid biomembrane models provide a simplified way to mimic the characteristics and composition of membranes. Aß-biomembrane interactions have been extensively investigated applying artificial membrane models to elucidate the molecular mechanisms underlying the AD pathogenesis. This review summarizes the latest findings on this field using liposomes as biomembrane model, as they are considered the most promising 3D model. The current challenges and future directions are discussed.
Subject(s)
Alzheimer Disease/pathology , Amyloid beta-Peptides/metabolism , Cell Membrane/metabolism , Liposomes/metabolism , Alzheimer Disease/metabolism , Amyloid beta-Peptides/chemistry , Cell Membrane/chemistry , Cell Membrane/pathology , Cell Membrane Permeability , Humans , Liposomes/chemistry , Membrane Lipids/chemistry , Membrane Lipids/metabolism , Oxidative StressABSTRACT
BACKGROUND: The molecular mechanisms of abnormal palatogenesis were investigated in this study. A key regulator, miR-106a-5p, and its target pathway were analyzed. OBJECTIVES: This research is trying to clarify the underlying mechanism of the modulation of miRNA transcription during the formation of cleft palate by 7T and 9.4T NMR metabolomic platforms. METHOD: Differentially expressed miRNAs and mRNAs were analyzed by microarray analysis and verified by qRT-PCR. The protein expression in TGFß signaling pathways were analyzed by Western Blotting. The relationship between miR-106a-5p and TGFß were analyzed by luciferase reporter assay. Cell apoptosis were analyzed by flow cytometer. And finally, the metabonomics were analyzed by NMR and multivariate data analysis models (MVDA). RESULTS: The expression of miR-106a-5p increased in cleft palatal tissue and negatively correlated with the protein level of Tgfbr2. The luciferase assay further proved that the tgfbr2 was a direct target of miR-106a-5p. In another aspect, miR-106a-5p increased apoptosis level in palatal mesenchymal cells, possibly because its inhibition of TGFß signaling pathway. Moreover, low cholesterol and choline levels with high citric acid and lipid levels were observed by 7T and 9.4T NMR metabonomic analysis, which inferred the disorder of cell membrane synthesis in cleft palate formation. Furthermore, transformation from choline to phosphatidylcholine regulated by miR-106a-5p was also disrupted, resulting in phosphatidic choline synthesis disorder and reduced cell membrane synthesis. CONCLUSIONS: The regulatory mechanism of cleft palate was studied at transcriptional and metabolomics levels, which may provide important information in understanding the primary cause of this abnormality.
Subject(s)
Cleft Palate/genetics , Mesenchymal Stem Cells/metabolism , MicroRNAs/genetics , Palate/drug effects , Smad2 Protein/genetics , Transforming Growth Factor beta/genetics , Animals , Apoptosis/drug effects , Apoptosis/genetics , Cell Membrane/chemistry , Cell Membrane/drug effects , Cell Membrane/metabolism , Citric Acid/metabolism , Cleft Palate/chemically induced , Cleft Palate/metabolism , Cleft Palate/pathology , Disease Models, Animal , Embryo, Mammalian , Female , Gene Expression Regulation, Developmental , Humans , Male , Membrane Lipids/chemistry , Membrane Lipids/metabolism , Mesenchymal Stem Cells/drug effects , Mesenchymal Stem Cells/pathology , Metabolome/genetics , Mice , MicroRNAs/classification , MicroRNAs/metabolism , Palate/growth & development , Palate/metabolism , Palate/pathology , Receptor, Transforming Growth Factor-beta Type II/genetics , Receptor, Transforming Growth Factor-beta Type II/metabolism , Signal Transduction , Smad2 Protein/metabolism , Smad3 Protein/genetics , Smad3 Protein/metabolism , Transcriptome , Transforming Growth Factor beta/metabolism , Tretinoin/toxicityABSTRACT
The molecular details of the passive water flux across the hydrophobic membrane interior are still a matter of debate. One of the postulated mechanisms is the spontaneous, water-filled pore opening, which facilitates the hydrophilic connection between aqueous phases separated by the membrane. In the paper, we provide experimental evidence showing that the spontaneous lipid pore formation correlates with the membrane mechanics; hence, it depends on the composition of the lipid bilayer and the concentration of the osmotically active compound. Using liposomes as an experimental membrane model, osmotically induced water efflux was measured with the stopped-flow technique. Shapes of kinetic curves obtained at low osmotic pressure differences are interpreted in terms of two events: the lipid pore opening and water flow across the aqueous channel. The biological significance of the dependence of the lipid pore formation on the concentration difference of an osmotically active compound was illustrated by the demonstration that osmotically driven water flow can be accompanied by the dissipation of the pH gradient. The application of the Helfrich model to describe the probability of lipid pore opening was validated by demonstrating that the probability of pore opening correlates with the membrane bending rigidity. The correlation was determined by experimentally derived bending rigidity coefficients and probabilities of lipid pores opening.
Subject(s)
Cell Membrane/chemistry , Lipid Bilayers/chemistry , Lipid Bilayers/metabolism , Water/metabolism , Eggs , Hydrogen-Ion Concentration , Kinetics , Light , Liposomes/chemistry , Lysophosphatidylcholines/chemistry , Membrane Lipids/chemistry , Models, Chemical , Osmotic Pressure , Phosphatidylcholines/chemistry , Phosphatidylethanolamines/chemistry , Protons , Water/chemistryABSTRACT
The ability of sodium caprylate and l-menthol to fluidize phospholipid bilayers composed of lipids simulating the buccal epithelium was investigated using electron spin resonance (ESR) to evaluate the action of these agents as permeation enhancers. 5-Doxyl stearic acid (5-DSA) and 16-doxyl stearic acid (16-DSA) were used as spin labels to identify alterations in membrane fluidity near the polar head groups or inner acyl regions of the lipid bilayer, respectively. The molecular motion of both 5-DSA and 16-DSA showed increased disorder near the polar and inner hydrophobic regions of the bilayer in the presence of sodium caprylate suggesting fluidization in both the regions, which contributes to its permeation enhancing effects. L-menthol decreased the order parameter for 16-DSA, showing membrane fluidization only in the inner acyl regions of the bilayer, which also corresponded to its weaker permeation enhancing effects. The rapid evaluation of changes in fluidity of the bilayer in the presence of potential permeation enhancers using ESR enables improved selection of effective permeation enhancers and enhancer combinations based on their effect on membrane fluidization.
Subject(s)
Caprylates/pharmacology , Electron Spin Resonance Spectroscopy , Membrane Fluidity/drug effects , Menthol/pharmacology , Mouth Mucosa/drug effects , Mouth Mucosa/metabolism , Cell Membrane Permeability/drug effects , Cyclic N-Oxides/chemistry , Cyclic N-Oxides/pharmacology , Electron Spin Resonance Spectroscopy/methods , Lipid Bilayers , Liposomes , Membrane Lipids/chemistry , Membrane Lipids/metabolism , Phospholipids/chemistry , Phospholipids/metabolismABSTRACT
Caveolin-1 (CAV1), a membrane protein that is necessary for the formation and maintenance of caveolae, is a promising drug target for the therapy of various diseases, such as cancer, diabetes, and liver fibrosis. The biology and pathology of caveolae have been widely investigated; however, very little information about the structural features of full-length CAV1 is available, as well as its biophysical role in reshaping the cellular membrane. Here, we established a method, with high reliability and reproducibility, for the expression and purification of CAV1. Amyloid-like properties of CAV1 and its C-terminal peptide CAV1(168-178) suggest a structural basis for the short linear CAV1 assemblies that have been recently observed in caveolin polyhedral cages in Escherichia coli (E. coli). Reconstitution of CAV1 into artificial lipid membranes induces a caveolae-like membrane curvature. Structural characterization of CAV1 in the membrane by solid-state nuclear magnetic resonance (ssNMR) indicate that it is largely α-helical, with very little ß-sheet content. Its scaffolding domain adopts a α-helical structure as identified by chemical shift analysis of threonine (Thr). Taken together, an in vitro model was developed for the CAV1 structural study, which will further provide meaningful evidences for the design and screening of bioactive compounds targeting CAV1.
Subject(s)
Caveolin 1/chemistry , Amino Acid Sequence , Caveolin 1/genetics , Caveolin 1/ultrastructure , Humans , Magnetic Resonance Spectroscopy , Membrane Lipids/chemistry , Membranes, Artificial , Microscopy, Electron, Transmission , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Structure, Quaternary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/ultrastructureABSTRACT
Specific intracellular localization of RAB GTPases has been reported to be dependent on protein factors, but the contribution of the membrane physicochemical properties to this process has been poorly described. Here, we show that three RAB proteins (RAB1/RAB5/RAB6) preferentially bind in vitro to disordered and curved membranes, and that this feature is uniquely dependent on their prenyl group. Our results imply that the addition of a prenyl group confers to RAB proteins, and most probably also to other prenylated proteins, the ability to sense lipid packing defects induced by unsaturated conical-shaped lipids and curvature. Consistently, RAB recruitment increases with the amount of lipid packing defects, further indicating that these defects drive RAB membrane targeting. Membrane binding of RAB35 is also modulated by lipid packing defects but primarily dependent on negatively charged lipids. Our results suggest that a balance between hydrophobic insertion of the prenyl group into lipid packing defects and electrostatic interactions of the RAB C-terminal region with charged membranes tunes the specific intracellular localization of RAB proteins.
Subject(s)
Membrane Lipids/metabolism , Unilamellar Liposomes/chemistry , rab GTP-Binding Proteins/metabolism , Humans , Membrane Lipids/chemistry , Protein Binding , Protein Prenylation , Static Electricity , Unilamellar Liposomes/metabolism , rab GTP-Binding Proteins/chemistryABSTRACT
Membrane tethering is a highly regulated event occurring during the initial physical contact between membrane-bounded transport carriers and their target subcellular membrane compartments, thereby ensuring the spatiotemporal specificity of intracellular membrane trafficking. Although Rab-family small GTPases and specific Rab-interacting effectors, such as coiled-coil tethering proteins and multisubunit tethering complexes, are known to be involved in membrane tethering, how these protein components directly act upon the tethering event remains enigmatic. Here, using a chemically defined reconstitution system, we investigated the molecular basis of membrane tethering by comprehensively and quantitatively evaluating the intrinsic capacities of 10 representative human Rab-family proteins (Rab1a, -3a, -4a, -5a, -6a, -7a, -9a, -11a, -27a, and -33b) to physically tether two distinct membranes via homotypic and heterotypic Rab-Rab assembly. All of the Rabs tested, except Rab27a, specifically caused homotypic membrane tethering at physiologically relevant Rab densities on membrane surfaces (e.g. Rab/lipid molar ratios of 1:100-1:3,000). Notably, endosomal Rab5a retained its intrinsic potency to drive efficient homotypic tethering even at concentrations below the Rab/lipid ratio of 1:3,000. Comprehensive reconstitution experiments further uncovered that heterotypic combinations of human Rab-family isoforms, including Rab1a/6a, Rab1a/9a, and Rab1a/33b, can directly and selectively mediate membrane tethering. Rab1a and Rab9a in particular synergistically triggered very rapid and efficient membrane tethering reactions through their heterotypic trans-assembly on two opposing membranes. In conclusion, our findings establish that, in the physiological context, homotypic and heterotypic trans-assemblies of Rab-family small GTPases can provide the essential molecular machinery necessary to drive membrane tethering in eukaryotic endomembrane systems.
Subject(s)
Membrane Lipids/chemistry , Membranes, Artificial , rab GTP-Binding Proteins/chemistry , Humans , Membrane Lipids/metabolism , rab GTP-Binding Proteins/metabolismABSTRACT
The lipid bilayer, together with embedded proteins, is the central structure in biomembranes. While artificial lipid bilayers are useful to model natural membranes, they are generally symmetric, with the same membrane lipid composition in each lipid monolayer (leaflet). In contrast, natural membranes are often asymmetric, with different lipids in each leaflet. To prepare asymmetric lipid vesicles, we developed cyclodextrin-catalyzed phospholipid exchange procedures. The basic method is that an excess of vesicles with one set of lipids (the donor vesicles) is mixed with a second set of vesicles (acceptor vesicles) with a different set of lipids. Cyclodextrin is introduced into the external aqueous solution, so that lipids in the outer leaflet of the vesicles bind to it and are shuttled between the vesicles. At equilibrium, the lipids in the outer leaflet of the acceptor vesicles are replaced by those from the donor vesicles. The exchanged acceptor vesicles are then isolated. Asymmetric vesicles are versatile in terms of vesicle sizes and lipid compositions that can be prepared. Measuring asymmetry is often difficult. A variety of assays can be used to measure the extent of asymmetry, but most are specific for one particular membrane lipid type or class, and there are none that can be used in all situations. Studies using asymmetric vesicles have begun to explore how asymmetry influences lipid movement across the bilayer, the formation of ordered lipid domains, coupling between the physical properties in each leaflet, and membrane protein conformation. Lipid domain formation stands out as one of the most important properties in which asymmetry is likely to be crucial. Lipid bilayers can exist in both liquidlike and solid/ordered-like states depending on lipid structure, and in lipid vesicles with a mixture of lipids highly ordered and disordered domains can coexist. However, until very recently, such studies only had been carried out in symmetric artificial membranes. Whether ordered domains (often called lipid rafts) and disordered lipid domains coexist in asymmetric cell membranes remains controversial partly because lipids favoring the formation of an ordered state are largely restricted to the leaflet facing the external environment. Studies using asymmetric vesicles have recently shown that each leaflet can influence the physical behavior of the other, i.e., that the domain forming properties in each leaflet tend to be coupled, with consequences highly dependent upon the details of lipid structure. Future studies investigating the dependence of coupling and properties upon the details of lipid composition should clarify the potential of natural membranes to form lipid domains. In addition, we recently extended the exchange method to living mammalian cells, using exchange to efficiently replace virtually the entire phospholipid and sphingolipid population of the plasma membrane outer leaflet with exogenous lipids without harming cells. This should allow detailed studies of the functional impact of lipid structure, asymmetry, domain organization, and interactions with membrane proteins in living cells.
Subject(s)
Lipid Bilayers/chemistry , Liposomes/chemistry , Diffusion , Membrane Lipids/chemistry , Membrane Microdomains/chemistryABSTRACT
Quantitative MRI (qMRI) is a method for the non-invasive study of brain-structure-associated changes expressed with measurable units. The qMRI-derived parameters have been shown to reflect brain tissue composition such as myelin content. Nevertheless, it remains a major challenge to identify and quantify the contributions of specific molecular components to the MRI signal. Here, we describe a phantom system that can be used to evaluate the contribution of membrane lipids to qMRI-derived parameters. We used a hydration-dehydration dry film technique to formulate liposomes that can be used as a model of the bilayer lipid membrane. The liposomes were comprised of the most abundant types of lipid found in the human brain. We then applied clinically available qMRI techniques with adjusted bias corrections in order to test the ability of the phantom system to estimate multiple qMRI parameters such as proton density (PD), T1 , T2 , T2 * and magnetization transfer. In addition, we accurately measured the phantom sample water fraction (normalized PD). A similar protocol was also applied to the human brain in vivo. The phantom system allows for a reliable estimation of qMRI parameters for phantoms composed of various lipid types using a clinical MRI scanner. We also found a comparable reproducibility between the phantom and in vivo human brain qMRI estimations. To conclude, we have successfully created a biologically relevant liposome phantom system whose lipid composition can be fully controlled. Our lipid system and analysis can be used to measure the contributions to qMRI parameters of membrane lipids found in the human brain under scanning conditions that are relevant to in vivo human brain scans. Such a model system can be used to test the contributions of lipidomic changes in normal and pathological brain states.
Subject(s)
Membrane Lipids/chemistry , Phantoms, Imaging , Protons , Water/chemistry , Adult , Diffusion , Humans , Lipids/chemistry , Liposomes , Magnetic Resonance Imaging , Reproducibility of Results , Young AdultABSTRACT
We analyze the nonequilibrium shape fluctuations of giant unilamellar vesicles encapsulating motile bacteria. Owing to bacteria-membrane collisions, we experimentally observe a significant increase in the magnitude of membrane fluctuations at low wave numbers, compared to the well-known thermal fluctuation spectrum. We interrogate these results by numerically simulating membrane height fluctuations via a modified Langevin equation, which includes bacteria-membrane contact forces. Taking advantage of the lengthscale and timescale separation of these contact forces and thermal noise, we further corroborate our results with an approximate theoretical solution to the dynamical membrane equations. Our theory and simulations demonstrate excellent agreement with nonequilibrium fluctuations observed in experiments. Moreover, our theory reveals that the fluctuation-dissipation theorem is not broken by the bacteria; rather, membrane fluctuations can be decomposed into thermal and active components.
Subject(s)
Cytoplasmic Vesicles/chemistry , Membrane Lipids/chemistry , Models, Biological , Models, Chemical , Bacillus subtilis/chemistry , Bacillus subtilis/cytology , Bacillus subtilis/metabolism , Cytoplasmic Vesicles/metabolism , Locomotion , Membrane Lipids/metabolism , Phosphatidylethanolamines/chemistry , Rhodamines/chemistry , Thermodynamics , Unilamellar Liposomes/chemistry , Unilamellar Liposomes/metabolismABSTRACT
Ion pairing between the major phospholipids of the Staphylococcus aureus plasma membrane (phosphatidylglycerol - PG and lysyl-phosphatidylglycerol - LPG) confers resistance to antimicrobial peptides and other antibiotics. We developed 3adLPG, a stable synthetic analogue which can substitute for the highy-labile native LPG, in biophysical experiments examining the membrane-protecting role of lipid ion pairing, in S. aureus and other important bacteria. Here we examine the surface charge and lipid packing characteristics of synthetic biomimetic mixtures of DPPG and DP3adLPG in Langmuir monolayers, using a combination of complementary surface-probing techniques such as infrared reflection-absorption spectroscopy and grazing-incidence x-ray diffraction. The resultant phase diagram for the ion paired lipids sheds light on the mixing behavior of lipids in monolayer models of resistant phenotype bacterial membranes, and provides a platform for future biophysical studies.