1
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Maremonti MI, Panzetta V, Netti PA, Causa F. HiViPore: a highly viable in-flow compression for a one-step cell mechanoporation in microfluidics to induce a free delivery of nano- macro-cargoes. J Nanobiotechnology 2024; 22:441. [PMID: 39068464 PMCID: PMC11282774 DOI: 10.1186/s12951-024-02730-y] [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: 04/04/2024] [Accepted: 07/21/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Among mechanoporation techniques for intracellular delivery, microfluidic approaches succeed in high delivery efficiency and throughput. However, especially the entry of large cargoes (e.g. DNA origami, mRNAs, organic/inorganic nanoparticles) is currently impaired since it requires large cell membrane pores with the need to apply multi-step processes and high forces, dramatically reducing cell viability. RESULTS Here, HiViPore presents as a microfluidic viscoelastic contactless compression for one-step cell mechanoporation to produce large pores while preserving high cell viability. Inducing an increase of curvature at the equatorial region of cells, formation of a pore with a size of ~ 1 μm is obtained. The poration is coupled to an increase of membrane tension, measured as a raised fluorescence lifetime of 12% of a planarizable push-pull fluorescent probe (Flipper-TR) labelling the cell plasma membrane. Importantly, the local disruptions of cell membrane are transient and non-invasive, with a complete recovery of cell integrity and functions in ~ 10 min. As result, HiViPore guarantees cell viability as high as ~ 90%. In such conditions, an endocytic-free diffusion of large nanoparticles is obtained with typical size up to 500 nm and with a delivery efficiency up to 12 times higher than not-treated cells. CONCLUSIONS The proposed one-step contactless mechanoporation results in an efficient and safe approach for advancing intracellular delivery strategies. In detail, HiViPore solves the issues of low cell viability when multiple steps of poration are required to obtain large pores across the cell plasma membrane. Moreover, the compression uses a versatile, low-cost, biocompatible viscoelastic fluid, thus also optimizing the operational costs. With HiViPore, we aim to propose an easy-to-use microfluidic device to a wide range of users, involved in biomedical research, imaging techniques and nanotechnology for intracellular delivery applications in cell engineering.
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Affiliation(s)
- Maria Isabella Maremonti
- Interdisciplinary Research Centre on Biomaterials (CRIB), Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, University of Naples "Federico II", Naples, 80125, Italy
| | - Valeria Panzetta
- Interdisciplinary Research Centre on Biomaterials (CRIB), Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, University of Naples "Federico II", Naples, 80125, Italy
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia, Naples, 80125, Italy
| | - Paolo Antonio Netti
- Interdisciplinary Research Centre on Biomaterials (CRIB), Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, University of Naples "Federico II", Naples, 80125, Italy
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia, Naples, 80125, Italy
| | - Filippo Causa
- Interdisciplinary Research Centre on Biomaterials (CRIB), Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, University of Naples "Federico II", Naples, 80125, Italy.
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2
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Jimah JR, Kundu N, Stanton AE, Sochacki KA, Canagarajah B, Chan L, Strub MP, Wang H, Taraska JW, Hinshaw JE. Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission. Dev Cell 2024; 59:1783-1793.e5. [PMID: 38663399 PMCID: PMC11265984 DOI: 10.1016/j.devcel.2024.04.008] [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: 06/08/2023] [Revised: 12/29/2023] [Accepted: 04/04/2024] [Indexed: 07/25/2024]
Abstract
Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the plasma membrane. Although atomic models of the dynamin helical polymer bound to guanosine triphosphate (GTP) analogs define earlier stages of membrane constriction, there are no atomic models of the assembled state post-GTP hydrolysis. Here, we used cryo-EM methods to determine atomic structures of the dynamin helical polymer assembled on lipid tubules, akin to necks of budding endocytic vesicles, in a guanosine diphosphate (GDP)-bound, super-constricted state. In this state, dynamin is assembled as a 2-start helix with an inner lumen of 3.4 nm, primed for spontaneous fission. Additionally, by cryo-electron tomography, we trapped dynamin helical assemblies within HeLa cells using the GTPase-defective dynamin K44A mutant and observed diverse dynamin helices, demonstrating that dynamin can accommodate a range of assembled complexes in cells that likely precede membrane fission.
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Affiliation(s)
- John R Jimah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Nidhi Kundu
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abigail E Stanton
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kem A Sochacki
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bertram Canagarajah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lieza Chan
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jenny E Hinshaw
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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3
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Swaminathan U, Pucadyil TJ. Reconstituting membrane fission using a high content and throughput assay. Biochem Soc Trans 2024; 52:1449-1457. [PMID: 38747723 DOI: 10.1042/bst20231325] [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: 03/13/2024] [Revised: 04/21/2024] [Accepted: 05/01/2024] [Indexed: 06/27/2024]
Abstract
Protein-mediated membrane fission has been analyzed both in bulk and at the single event resolution. Studies on membrane fission in vitro using tethers have provided fundamental insights into the process but are low in throughput. In recent years, supported membrane template (SMrT) have emerged as a facile and convenient assay system for membrane fission. SMrTs provide useful information on intermediates in the pathway to fission and are therefore high in content. They are also high in throughput because numerous fission events can be monitored in a single experiment. This review discusses the utility of SMrTs in providing insights into fission pathways and its adaptation to annotate membrane fission functions in proteins.
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Affiliation(s)
- Uma Swaminathan
- Indian Institute of Science Education and Research, Pune, India
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4
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Bussoletti M, Gallo M, Bottacchiari M, Abbondanza D, Casciola CM. Mesoscopic elasticity controls dynamin-driven fission of lipid tubules. Sci Rep 2024; 14:14003. [PMID: 38890460 PMCID: PMC11189461 DOI: 10.1038/s41598-024-64685-2] [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: 03/09/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
Mesoscale physics bridges the gap between the microscopic degrees of freedom of a system and its large-scale continuous behavior and highlights the role of a few key quantities in complex and multiscale phenomena, like dynamin-driven fission of lipid membranes. The dynamin protein wraps the neck formed during clathrin-mediated endocytosis, for instance, and constricts it until severing occurs. Although ubiquitous and fundamental for life, the cooperation between the GTP-consuming conformational changes within the protein and the full-scale response of the underlying lipid substrate is yet to be unraveled. In this work, we build an effective mesoscopic model from constriction to fission of lipid tubules based on continuum membrane elasticity and implicitly accounting for ratchet-like power strokes of dynamins. Localization of the fission event, the overall geometry, and the energy expenditure we predict comply with the major experimental findings. This bolsters the idea that a continuous picture emerges soon enough to relate dynamin polymerization length and membrane rigidity and tension with the optimal pathway to fission. We therefore suggest that dynamins found in in vivo processes may optimize their structure accordingly. Ultimately, we shed light on real-time conductance measurements available in literature and predict the fission time dependency on elastic parameters.
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Affiliation(s)
- Marco Bussoletti
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
| | - Mirko Gallo
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
| | - Matteo Bottacchiari
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Rome, Italy
| | - Dario Abbondanza
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
| | - Carlo Massimo Casciola
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy.
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5
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Schumann W, Loschwitz J, Reiners J, Degrandi D, Legewie L, Stühler K, Pfeffer K, Poschmann G, Smits SHJ, Strodel B. Integrative modeling of guanylate binding protein dimers. Protein Sci 2023; 32:e4818. [PMID: 37916607 PMCID: PMC10683561 DOI: 10.1002/pro.4818] [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: 05/12/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 11/03/2023]
Abstract
Guanylate-binding proteins (GBPs) are essential interferon-γ-activated large GTPases that play a crucial role in host defense against intracellular bacteria and parasites. While their protective functions rely on protein polymerization, our understanding of the structural intricacies of these multimerized states remains limited. To bridge this knowledge gap, we present dimer models for human GBP1 (hGBP1) and murine GBP2 and 7 (mGBP2 and mGBP7) using an integrative approach, incorporating the crystal structure of hGBP1's GTPase domain dimer, crosslinking mass spectrometry, small-angle X-ray scattering, protein-protein docking, and molecular dynamics simulations. Our investigation begins by comparing the protein dynamics of hGBP1, mGBP2, and mGBP7. We observe that the M/E domain in all three proteins exhibits significant mobility and hinge motion, with mGBP7 displaying a slightly less pronounced motion but greater flexibility in its GTPase domain. These dynamic distinctions can be attributed to variations in the sequences of mGBP7 and hGBP1/mGBP2, resulting in different dimerization modes. Unlike hGBP1 and its close ortholog mGBP2, which exclusively dimerize through their GTPase domains, we find that mGBP7 exhibits three equally probable alternative dimer structures. The GTPase domain of mGBP7 is only partially involved in its dimerization, primarily due to an accumulation of negative charge, allowing mGBP7 to dimerize independently of GTP. Instead, mGBP7 exhibits a strong tendency to dimerize in an antiparallel arrangement across its stalks. The results of this work go beyond the sequence-structure-function relationship, as the sequence differences in mGBP7 and mGBP2/hGBP1 do not lead to different structures, but to different protein dynamics and dimerization. The distinct GBP dimer structures are expected to encode specific functions crucial for disrupting pathogen membranes.
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Affiliation(s)
- Wibke Schumann
- Institute of Theoretical and Computational ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Biological Information Processing: Structural BiochemistryForschungszentrum JülichJülichGermany
| | - Jennifer Loschwitz
- Institute of Theoretical and Computational ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Biological Information Processing: Structural BiochemistryForschungszentrum JülichJülichGermany
| | - Jens Reiners
- Center for Structural StudiesHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Daniel Degrandi
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine UniversityDüsseldorfGermany
| | - Larissa Legewie
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine UniversityDüsseldorfGermany
| | - Kai Stühler
- Institute of Molecular Medicine, Proteome ResearchMedical Faculty and University Hospital Düsseldorf, Heinrich Heine University DüsseldorfDüsseldorfGermany
- Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ)Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine UniversityDüsseldorfGermany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome ResearchMedical Faculty and University Hospital Düsseldorf, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Sander H. J. Smits
- Center for Structural StudiesHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute for BiochemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Birgit Strodel
- Institute of Theoretical and Computational ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Biological Information Processing: Structural BiochemistryForschungszentrum JülichJülichGermany
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6
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Gallen AF, Romero-Arias JR, Barrio RA, Hernandez-Machado A. Vesicle formation induced by thermal fluctuations. SOFT MATTER 2023; 19:2908-2918. [PMID: 37006200 DOI: 10.1039/d2sm01167k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The process of fission and vesicle formation depends on the geometry of the membrane that will split. For instance, a flat surface finds it difficult to form vesicles because of the lack of curved regions where to start the process. Here we show that vesicle formation can be promoted by temperature, by using a membrane phase field model with Gaussian curvature. We find a phase transition between fluctuating and vesiculation phases that depends on temperature, spontaneous curvature, and the ratio between bending and Gaussian moduli. We analysed the energy dynamical behaviour of these processes and found that the main driving ingredient is the Gaussian energy term, although the curvature energy term usually helps with the process as well. We also found that the chemical potential can be used to investigate the temperature of the system. Finally we address how temperature changes the condition for spontaneous vesiculation for all geometries, making it happen in a wider range of values of the Gaussian modulus.
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Affiliation(s)
- Andreu F Gallen
- Departament Fisica de la Materia Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain.
| | - J Roberto Romero-Arias
- Instituto de Investigaciones en Matematicas Aplicadas y en Sistemas, Universidad Nacional Autonoma de Mexico, 01000 Ciudad de Mexico, Mexico
| | - Rafael A Barrio
- Instituto de Fisica, U.N.A.M., 01000, Ap. Postal 101000, Mexico D.F, Mexico
| | - Aurora Hernandez-Machado
- Departament Fisica de la Materia Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain.
- Institute of Nanoscience and Nanotechnology (IN2UB), 08028 Barcelona, Spain
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7
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Tiwari A, Pradhan S, Sannigrahi A, Mahakud AK, Jha S, Chattopadhyay K, Biswas M, Saleem M. “Interplay of lipid-head group and packing defects in driving Amyloid-beta mediated myelin-like model membrane deformation”. J Biol Chem 2023; 299:104653. [PMID: 36990217 PMCID: PMC10148160 DOI: 10.1016/j.jbc.2023.104653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/24/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Accumulating evidence suggests that amyloid plaque associated myelin lipid loss as a result of elevated amyloid burden might also contribute to Alzheimer's disease. The amyloid fibrils though closely associated with lipids under physiological conditions, however, the progression of membrane remodeling events leading to lipid-fibril assembly remains unknown. Here we first reconstitute the interaction of Aβ-40 with myelin-like model membrane and show that the binding of Aβ-40 induces extensive tubulation. To look into the mechanism of membrane tubulation we chose a set of membrane conditions varying in lipid packing density and net charge that allows us to dissect the contribution of lipid specificity of Aβ-40 binding, aggregation kinetics, and subsequent changes in membrane parameters such as fluidity, diffusion, and compressibility modulus. We show that the binding of Aβ-40 depends predominantly on the lipid packing defect densities and electrostatic interactions and results in rigidification of the myelin-like model membrane during the early phase of amyloid aggregation. Furthermore, elongation of Aβ-40 into higher oligomeric and fibrillar species leads to eventual fluidization of the model membrane followed by extensive lipid membrane tubulation observed in the late phase. Taken together, our results capture mechanistic insights into snapshots of temporal dynamics of Aβ-40 - myelin-like model membrane interaction and demonstrate how short timescale, local phenomena of binding, and fibril-mediated load generation results in the consequent association of lipids with growing amyloid fibrils.
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8
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Wu X, Qiu H, Zhang M. Interactions between Membraneless Condensates and Membranous Organelles at the Presynapse: A Phase Separation View of Synaptic Vesicle Cycle. J Mol Biol 2023; 435:167629. [PMID: 35595170 DOI: 10.1016/j.jmb.2022.167629] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023]
Abstract
Action potential-induced neurotransmitter release in presynaptic boutons involves coordinated actions of a large list of proteins that are associated directly or indirectly with membrane structures including synaptic vesicles and plasma membranes. These proteins are often highly abundant in different synaptic bouton sub-compartments, and they rarely act alone. Instead, these proteins interact with each other forming intricate and distinct molecular complexes. Many of these complexes form condensed clusters on membrane surfaces. This review summarizes findings in recent years showing that many of presynaptic protein complex assemblies are formed via phase separation. These protein condensates extensively interact with lipid membranes via distinct modes, forming various mesoscale structures by different mode of organizations between membraneless condensates and membranous organelles. We discuss that such mesoscale interactions could have deep implications on mobilization, exocytosis, and retrieval of synaptic vesicles.
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Affiliation(s)
- Xiandeng Wu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Hua Qiu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Mingjie Zhang
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen 518036, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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9
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Remodeling of the Plasma Membrane by Surface-Bound Protein Monomers and Oligomers: The Critical Role of Intrinsically Disordered Regions. J Membr Biol 2022; 255:651-663. [PMID: 35930019 PMCID: PMC9718270 DOI: 10.1007/s00232-022-00256-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/07/2022] [Indexed: 12/24/2022]
Abstract
The plasma membrane (PM) of cells is a dynamic structure whose morphology and composition is in constant flux. PM morphologic changes are particularly relevant for the assembly and disassembly of signaling platforms involving surface-bound signaling proteins, as well as for many other mechanochemical processes that occur at the PM surface. Surface-bound membrane proteins (SBMP) require efficient association with the PM for their function, which is often achieved by the coordinated interactions of intrinsically disordered regions (IDRs) and globular domains with membrane lipids. This review focuses on the role of IDR-containing SBMPs in remodeling the composition and curvature of the PM. The ability of IDR-bearing SBMPs to remodel the Gaussian and mean curvature energies of the PM is intimately linked to their ability to sort subsets of phospholipids into nanoclusters. We therefore discuss how IDRs of many SBMPs encode lipid-binding specificity or facilitate cluster formation, both of which increase their membrane remodeling capacity, and how SBMP oligomers alter membrane shape by monolayer surface area expansion and molecular crowding.
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10
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Jiang X, Harker-Kirschneck L, Vanhille-Campos C, Pfitzner AK, Lominadze E, Roux A, Baum B, Šarić A. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLoS Comput Biol 2022; 18:e1010586. [PMID: 36251703 PMCID: PMC9612822 DOI: 10.1371/journal.pcbi.1010586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 10/27/2022] [Accepted: 09/19/2022] [Indexed: 12/24/2022] Open
Abstract
ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.
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Affiliation(s)
- Xiuyun Jiang
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Lena Harker-Kirschneck
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Christian Vanhille-Campos
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Elene Lominadze
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Buzz Baum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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11
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Cail RC, Drubin DG. Membrane curvature as a signal to ensure robustness of diverse cellular processes. Trends Cell Biol 2022; 33:427-441. [PMID: 36244874 DOI: 10.1016/j.tcb.2022.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/05/2022]
Abstract
An increasing corpus of research has demonstrated that membrane shape, generated either by the external environment of the cell or by intrinsic mechanisms such as cytokinesis and vesicle or organelle formation, is an important parameter in the control of diverse cellular processes. In this review we discuss recent findings that demonstrate how membrane curvature (from nanometer to micron length-scales) alters protein function. We describe an expanding toolkit for experimentally modulating membrane curvature to reveal effects on protein function, and discuss how membrane curvature - far from being a passive consequence of the physical environment and the internal protein activity of a cell - is an important signal that controls protein affinity and enzymatic activity to ensure robust forward progression of key processes within the cell.
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12
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Baker JR, O'Brien NS, Prichard KL, Robinson PJ, McCluskey A, Russell CC. Dynole 34-2 and Acrylo-Dyn 2-30, Novel Dynamin GTPase Chemical Biology Probes. Methods Mol Biol 2022; 2417:221-238. [PMID: 35099803 DOI: 10.1007/978-1-0716-1916-2_17] [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] [Indexed: 06/14/2023]
Abstract
This protocol describes the chemical synthesis of the dynamin inhibitors Dynole 34-2 and Acrylo-Dyn 2-30, and their chemical scaffold matched partner inactive compounds. The chosen active and inactive paired compounds represent potent dynamin inhibitors and very closely related dynamin-inactive compounds, with the synthesis of three of the four compounds readily possible via a common intermediate. Combined with the assay data provided, this allows the interrogation of dynamin in vitro and potentially in vivo.
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Affiliation(s)
- Jennifer R Baker
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Nicholas S O'Brien
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Kate L Prichard
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Phillip J Robinson
- Cell Signaling Unit, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Adam McCluskey
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Cecilia C Russell
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia.
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13
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Anderson RH, Sochacki KA, Vuppula H, Scott BL, Bailey EM, Schultz MM, Kerkvliet JG, Taraska JW, Hoppe AD, Francis KR. Sterols lower energetic barriers of membrane bending and fission necessary for efficient clathrin-mediated endocytosis. Cell Rep 2021; 37:110008. [PMID: 34788623 PMCID: PMC8620193 DOI: 10.1016/j.celrep.2021.110008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/03/2021] [Accepted: 10/26/2021] [Indexed: 01/16/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) is critical for cellular signal transduction, receptor recycling, and membrane homeostasis in mammalian cells. Acute depletion of cholesterol disrupts CME, motivating analysis of CME dynamics in the context of human disorders of cholesterol metabolism. We report that inhibition of post-squalene cholesterol biosynthesis impairs CME. Imaging of membrane bending dynamics and the CME pit ultrastructure reveals prolonged clathrin pit lifetimes and shallow clathrin-coated structures, suggesting progressive impairment of curvature generation correlates with diminishing sterol abundance. Sterol structural requirements for efficient CME include 3′ polar head group and B-ring conformation, resembling the sterol structural prerequisites for tight lipid packing and polarity. Furthermore, Smith-Lemli-Opitz fibroblasts with low cholesterol abundance exhibit deficits in CME-mediated transferrin internalization. We conclude that sterols lower the energetic costs of membrane bending during pit formation and vesicular scission during CME and suggest that reduced CME activity may contribute to cellular phenotypes observed within disorders of cholesterol metabolism. Anderson et al. demonstrate that sterol abundance and identity play a dominant role in facilitating clathrin-mediated endocytosis. Detailed analyses of clathrin-coated pits under sterol depletion support a requirement for sterol-mediated membrane bending during multiple stages of endocytosis, implicating endocytic dysfunction within the pathogenesis of disorders of cholesterol metabolism.
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Affiliation(s)
- Ruthellen H Anderson
- Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA; Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Kem A Sochacki
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Harika Vuppula
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA
| | - Brandon L Scott
- Nanoscience and Nanoengineering, South Dakota School of Mines & Technology, Rapid City, SD 57701, USA
| | - Elizabeth M Bailey
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA
| | - Maycie M Schultz
- Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Jason G Kerkvliet
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA
| | - Justin W Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Adam D Hoppe
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA.
| | - Kevin R Francis
- Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD 57104, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA.
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14
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Sadeghi M, Noé F. Thermodynamics and Kinetics of Aggregation of Flexible Peripheral Membrane Proteins. J Phys Chem Lett 2021; 12:10497-10504. [PMID: 34677984 DOI: 10.1021/acs.jpclett.1c02954] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biomembrane remodeling is essential for cellular trafficking, with membrane-binding peripheral proteins playing a key role in it. Significant membrane remodeling as in endo- and exocytosis is often due to aggregates of many proteins with direct or membrane-mediated interactions. Understanding this process via computer simulations is extremely challenging: protein-membrane systems involve time and length scales that make atomistic simulations impractical, while most coarse-grained models fall short in resolving dynamics and physical effects of protein and membrane flexibility. Here, we develop a coarse-grained model of the bilayer membrane bestrewed with rotationally symmetric flexible proteins, parametrized to reflect local curvatures and lateral dynamics of proteins. We investigate the kinetics, equilibrium distributions, and the free energy landscape governing the formation and breakup of protein clusters on the surface of the membrane. We demonstrate how the flexibility of the proteins as well as their surface concentration play deciding roles in highly selective macroscopic aggregation behavior.
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Affiliation(s)
- Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 12, 14195 Berlin, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 12, 14195 Berlin, Germany
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15
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Auddya D, Zhang X, Gulati R, Vasan R, Garikipati K, Rangamani P, Rudraraju S. Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematicsand revealed by a three-dimensional computational framework. Proc Math Phys Eng Sci 2021; 477:20210246. [PMID: 35153593 PMCID: PMC8580429 DOI: 10.1098/rspa.2021.0246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/11/2021] [Indexed: 01/10/2023] Open
Abstract
Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging and transport of nutrients, transmission of nerve impulses, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo significant morphological changes through deformation, scission, and fusion. Modelling the underlying mechanics of such morphological changes has traditionally relied on reduced order axisymmetric representations of membrane geometry and deformation. Axisymmetric representations, while robust and extensively deployed, suffer from their inability to model-symmetry breaking deformations and structural bifurcations. To address this limitation, a three-dimensional computational mechanics framework for high fidelity modelling of biomembrane deformation is presented. The proposed framework brings together Kirchhoff–Love thin-shell kinematics, Helfrich-energy-based mechanics, and state-of-the-art numerical techniques for modelling deformation of surface geometries. Lipid bilayers are represented as spline-based surface discretizations immersed in a three-dimensional space; this enables modelling of a wide spectrum of membrane geometries, boundary conditions, and deformations that are physically admissible in a three-dimensional space. The mathematical basis of the framework and its numerical machinery are presented, and their utility is demonstrated by modelling three classical, yet non-trivial, membrane deformation problems: formation of tubular shapes and their lateral constriction, Piezo1-induced membrane footprint generation and gating response, and the budding of membranes by protein coats during endocytosis. For each problem, the full three-dimensional membrane deformation is captured, potential symmetry-breaking deformation paths identified, and various case studies of boundary and load conditions are presented. Using the endocytic vesicle budding as a case study, we also present a ‘phase diagram’ for its symmetric and broken-symmetry states.
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Affiliation(s)
- Debabrata Auddya
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiaoxuan Zhang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Gulati
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ritvik Vasan
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Krishna Garikipati
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA.,Michigan Institute for Computational Discovery and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Shiva Rudraraju
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
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16
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Recent developments in membrane curvature sensing and induction by proteins. Biochim Biophys Acta Gen Subj 2021; 1865:129971. [PMID: 34333084 DOI: 10.1016/j.bbagen.2021.129971] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/11/2021] [Accepted: 07/25/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Membrane-bound intracellular organelles have characteristic shapes attributed to different local membrane curvatures, and these attributes are conserved across species. Over the past decade, it has been confirmed that specific proteins control the large curvatures of the membrane, whereas many others due to their specific structural features can sense the curvatures and bind to the specific geometrical cues. Elucidating the interplay between sensing and induction is indispensable to understand the mechanisms behind various biological processes such as vesicular trafficking and budding. SCOPE OF REVIEW We provide an overview of major classes of membrane proteins and the mechanisms of curvature sensing and induction. We then discuss the importance of membrane elastic characteristics to induce the membrane shapes similar to intracellular organelles. Finally, we survey recently available assays developed for studying the curvature sensing and induction by many proteins. MAJOR CONCLUSIONS Recent theoretical/computational modeling along with experimental studies have uncovered fascinating connections between lipid membrane and protein interactions. However, the phenomena of protein localization and synchronization to generate spatiotemporal dynamics in membrane morphology are yet to be fully understood. GENERAL SIGNIFICANCE The understanding of protein-membrane interactions is essential to shed light on various biological processes. This further enables the technological applications of many natural proteins/peptides in therapeutic treatments. The studies of membrane dynamic shapes help to understand the fundamental functions of membranes, while the medicinal roles of various macromolecules (such as proteins, peptides, etc.) are being increasingly investigated.
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17
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Trochet D, Bitoun M. A review of Dynamin 2 involvement in cancers highlights a promising therapeutic target. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:238. [PMID: 34294140 PMCID: PMC8296698 DOI: 10.1186/s13046-021-02045-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/15/2021] [Indexed: 12/23/2022]
Abstract
Dynamin 2 (DNM2) is an ubiquitously expressed large GTPase well known for its role in vesicle formation in endocytosis and intracellular membrane trafficking also acting as a regulator of cytoskeletons. During the last two decades, DNM2 involvement, through mutations or overexpression, emerged in an increasing number of cancers and often associated with poor prognosis. A wide panel of DNM2-dependent processes was described in cancer cells which explains DNM2 contribution to cancer pathomechanisms. First, DNM2 dysfunction may promote cell migration, invasion and metastasis. Second, DNM2 acts on intracellular signaling pathways fostering tumor cell proliferation and survival. Relative to these roles, DNM2 was demonstrated as a therapeutic target able to reduce cell proliferation, induce apoptosis, and reduce the invasive phenotype in a wide range of cancer cells in vitro. Moreover, proofs of concept of therapy by modulation of DNM2 expression was also achieved in vivo in several animal models. Consequently, DNM2 appears as a promising molecular target for the development of anti-invasive agents and the already provided proofs of concept in animal models represent an important step of preclinical development.
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Affiliation(s)
- Delphine Trochet
- Centre de Recherche en Myologie, Sorbonne Université, Inserm, UMRS 974, Institut de Myologie, F-75013, Paris, France
| | - Marc Bitoun
- Centre de Recherche en Myologie, Sorbonne Université, Inserm, UMRS 974, Institut de Myologie, F-75013, Paris, France.
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18
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Ganichkin OM, Vancraenenbroeck R, Rosenblum G, Hofmann H, Mikhailov AS, Daumke O, Noel JK. Quantification and demonstration of the collective constriction-by-ratchet mechanism in the dynamin molecular motor. Proc Natl Acad Sci U S A 2021; 118:e2101144118. [PMID: 34244431 PMCID: PMC8285958 DOI: 10.1073/pnas.2101144118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Dynamin oligomerizes into helical filaments on tubular membrane templates and, through constriction, cleaves them in a GTPase-driven way. Structural observations of GTP-dependent cross-bridges between neighboring filament turns have led to the suggestion that dynamin operates as a molecular ratchet motor. However, the proof of such mechanism remains absent. Particularly, it is not known whether a powerful enough stroke is produced and how the motor modules would cooperate in the constriction process. Here, we characterized the dynamin motor modules by single-molecule Förster resonance energy transfer (smFRET) and found strong nucleotide-dependent conformational preferences. Integrating smFRET with molecular dynamics simulations allowed us to estimate the forces generated in a power stroke. Subsequently, the quantitative force data and the measured kinetics of the GTPase cycle were incorporated into a model including both a dynamin filament, with explicit motor cross-bridges, and a realistic deformable membrane template. In our simulations, collective constriction of the membrane by dynamin motor modules, based on the ratchet mechanism, is directly reproduced and analyzed. Functional parallels between the dynamin system and actomyosin in the muscle are seen. Through concerted action of the motors, tight membrane constriction to the hemifission radius can be reached. Our experimental and computational study provides an example of how collective motor action in megadalton molecular assemblies can be approached and explicitly resolved.
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Affiliation(s)
- Oleg M Ganichkin
- Crystallography, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Renee Vancraenenbroeck
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Gabriel Rosenblum
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Hagen Hofmann
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Alexander S Mikhailov
- Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
- Computational Molecular Biophysics, Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Oliver Daumke
- Crystallography, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany;
- Institute for Chemistry and Biochemistry, Free University of Berlin, 14195 Berlin, Germany
| | - Jeffrey K Noel
- Crystallography, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany;
- Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
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19
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Cheng X, Chen K, Dong B, Yang M, Filbrun SL, Myoung Y, Huang TX, Gu Y, Wang G, Fang N. Dynamin-dependent vesicle twist at the final stage of clathrin-mediated endocytosis. Nat Cell Biol 2021; 23:859-869. [PMID: 34253896 PMCID: PMC8355216 DOI: 10.1038/s41556-021-00713-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/09/2021] [Indexed: 12/11/2022]
Abstract
Dynamin plays an important role in clathrin-mediated endocytosis (CME) by cutting the neck of nascent vesicles from the cell membrane. Here through using gold nanorods as cargos to image dynamin action during live CME, we show that near the peak of dynamin accumulation, the cargo-containing vesicles always exhibit abrupt, right-handed rotations that finish in a short time (~0.28 s). The large and quick twist, herein named the super twist, is the result of the coordinated dynamin helix action upon GTP hydrolysis. After the super twist, the rotational freedom of the vesicle drastically increases, accompanied with simultaneous or delayed translational movement, indicating that it detaches from the cell membrane. These observations suggest that dynamin-mediated scission involves a large torque generated by coordinated actions of multiple dynamins in the helix, which is the main driving force for vesicle scission.
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Affiliation(s)
- Xiaodong Cheng
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.,State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Kuangcai Chen
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Bin Dong
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Meek Yang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Seth L Filbrun
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Yong Myoung
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Teng-Xiang Huang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Yan Gu
- The Bristol-Myers Squibb Company, Devens, MA, USA
| | - Gufeng Wang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
| | - Ning Fang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA. .,State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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20
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Binotti B, Jahn R, Pérez-Lara Á. An overview of the synaptic vesicle lipid composition. Arch Biochem Biophys 2021; 709:108966. [PMID: 34139199 DOI: 10.1016/j.abb.2021.108966] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 11/29/2022]
Abstract
Chemical neurotransmission is the major mechanism of neuronal communication. Neurotransmitters are released from secretory organelles, the synaptic vesicles (SVs) via exocytosis into the synaptic cleft. Fusion of SVs with the presynaptic plasma membrane is balanced by endocytosis, thus maintaining the presynaptic membrane at steady-state levels. The protein machineries responsible for exo- and endocytosis have been extensively investigated. In contrast, less is known about the role of lipids in synaptic transmission and how the lipid composition of SVs is affected by dynamic exo-endocytotic cycling. Here we summarize the current knowledge about the composition, organization, and function of SV membrane lipids. We also cover lipid biogenesis and maintenance during the synaptic vesicle cycle.
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Affiliation(s)
- Beyenech Binotti
- Department of Biochemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Reinhard Jahn
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
| | - Ángel Pérez-Lara
- Department of Physical Chemistry, University of Granada, Campus Universitario de Cartuja, 18071, Granada, Spain.
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21
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Abstract
Lipid membranes in cells are fluid structures that undergo constant synthesis, remodeling, fission, and fusion. The dynamic nature of lipid membranes enables their use as adaptive compartments, making them indispensable for all life on Earth. Efforts to create life-like artificial cells will likely involve mimicking the structure and function of lipid membranes to recapitulate fundamental cellular processes such as growth and division. As such, there is considerable interest in chemistry that mimics the functional properties of membranes, with the express intent of recapitulating biological phenomena. We suggest expanding the definition of membrane mimetic chemistry to capture these efforts. In this Perspective, we discuss how membrane mimetic chemistry serves the development of artificial cells. By leveraging recent advances in chemical biology and systems chemistry, we have an opportunity to use simplified chemical and biochemical systems to mimic the remarkable properties of living membranes.
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Affiliation(s)
- Jacob A Vance
- Chemistry and Biochemistry, University of California San Diego, California 92093, United States
| | - Neal K Devaraj
- Chemistry and Biochemistry, University of California San Diego, California 92093, United States
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22
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Baratam K, Jha K, Srivastava A. Flexible pivoting of dynamin pleckstrin homology domain catalyzes fission: insights into molecular degrees of freedom. Mol Biol Cell 2021; 32:1306-1319. [PMID: 33979205 PMCID: PMC8351549 DOI: 10.1091/mbc.e20-12-0794] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The neuronal dynamin1 functions in the release of synaptic vesicles by orchestrating the process of GTPase-dependent membrane fission. Dynamin1 associates with the plasma membrane–localized phosphatidylinositol-4,5-bisphosphate (PIP2) through the centrally located pleckstrin homology domain (PHD). The PHD is dispensable as fission (in model membranes) can be managed, even when the PHD-PIP2 interaction is replaced by a generic polyhistidine- or polylysine-lipid interaction. However, the absence of the PHD renders a dramatic dampening of the rate of fission. These observations suggest that the PHD-PIP2–containing membrane interaction could have evolved to expedite fission to fulfill the requirement of rapid kinetics of synaptic vesicle recycling. Here, we use a suite of multiscale modeling approaches to explore PHD–membrane interactions. Our results reveal that 1) the binding of PHD to PIP2-containing membranes modulates the lipids toward fission-favoring conformations and softens the membrane, and 2) PHD associates with membrane in multiple orientations using variable loops as pivots. We identify a new loop (VL4), which acts as an auxiliary pivot and modulates the orientation flexibility of PHD on the membrane—a mechanism that we believe may be important for high-fidelity dynamin collar assembly. Together, these insights provide a molecular-level understanding of the catalytic role of PHD in dynamin-mediated membrane fission.
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Affiliation(s)
| | - Kirtika Jha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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23
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Allard A, Lopes Dos Santos R, Campillo C. Remodelling of membrane tubules by the actin cytoskeleton. Biol Cell 2021; 113:329-343. [PMID: 33826772 DOI: 10.1111/boc.202000148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 12/14/2022]
Abstract
Inside living cells, the remodelling of membrane tubules by actomyosin networks is crucial for processes such as intracellular trafficking or organelle reshaping. In this review, we first present various in vivo situations in which actin affects membrane tubule remodelling, then we recall some results on force production by actin dynamics and on membrane tubules physics. Finally, we show that our knowledge of the underlying mechanisms by which actomyosin dynamics affect tubule morphology has recently been moved forward. This is thanks to in vitro experiments that mimic cellular membranes and actin dynamics and allow deciphering the physics of tubule remodelling in biochemically controlled conditions, and shed new light on tubule shape regulation.
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Affiliation(s)
- Antoine Allard
- LAMBE, Université d'Évry, CNRS, CEA, Université Paris-Saclay, Évry-Courcouronnes, 91025, France.,Sorbonne Université, UPMC, Paris 06, Paris, France.,Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France.,Department of Physics, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | | | - Clément Campillo
- LAMBE, Université d'Évry, CNRS, CEA, Université Paris-Saclay, Évry-Courcouronnes, 91025, France
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24
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Johnston ST, Faria M, Crampin EJ. Understanding nano-engineered particle-cell interactions: biological insights from mathematical models. NANOSCALE ADVANCES 2021; 3:2139-2156. [PMID: 36133772 PMCID: PMC9417320 DOI: 10.1039/d0na00774a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/08/2021] [Indexed: 05/02/2023]
Abstract
Understanding the interactions between nano-engineered particles and cells is necessary for the rational design of particles for therapeutic, diagnostic and imaging purposes. In particular, the informed design of particles relies on the quantification of the relationship between the physicochemical properties of the particles and the rate at which cells interact with, and subsequently internalise, particles. Quantitative models, both mathematical and computational, provide a powerful tool for elucidating this relationship, as well as for understanding the mechanisms governing the intertwined processes of interaction and internalisation. Here we review the different types of mathematical and computational models that have been used to examine particle-cell interactions and particle internalisation. We detail the mathematical methodology for each type of model, the benefits and limitations associated with the different types of models, and highlight the advances in understanding gleaned from the application of these models to experimental observations of particle internalisation. We discuss the recent proposal and ongoing community adoption of standardised experimental reporting, and how this adoption is an important step toward unlocking the full potential of modelling approaches. Finally, we consider future directions in quantitative models of particle-cell interactions and highlight the need for hybrid experimental and theoretical investigations to address hitherto unanswered questions.
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Affiliation(s)
- Stuart T Johnston
- School of Mathematics and Statistics, University of Melbourne Parkville Victoria 3010 Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Melbourne School of Engineering, University of Melbourne Parkville Victoria 3010 Australia
- Systems Biology Laboratory, School of Mathematics and Statistics, Department of Biomedical Engineering, University of Melbourne Parkville Victoria 3010 Australia
| | - Matthew Faria
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Melbourne School of Engineering, University of Melbourne Parkville Victoria 3010 Australia
- Systems Biology Laboratory, School of Mathematics and Statistics, Department of Biomedical Engineering, University of Melbourne Parkville Victoria 3010 Australia
- Department of Biomedical Engineering, University of Melbourne Parkville Victoria 3010 Australia
| | - Edmund J Crampin
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Melbourne School of Engineering, University of Melbourne Parkville Victoria 3010 Australia
- Systems Biology Laboratory, School of Mathematics and Statistics, Department of Biomedical Engineering, University of Melbourne Parkville Victoria 3010 Australia
- School of Medicine, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne Parkville Victoria 3010 Australia
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25
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Mahecic D, Carlini L, Kleele T, Colom A, Goujon A, Matile S, Roux A, Manley S. Mitochondrial membrane tension governs fission. Cell Rep 2021; 35:108947. [PMID: 33852852 DOI: 10.1016/j.celrep.2021.108947] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/15/2020] [Accepted: 03/14/2021] [Indexed: 01/03/2023] Open
Abstract
During mitochondrial fission, key molecular and cellular factors assemble on the outer mitochondrial membrane, where they coordinate to generate constriction. Constriction sites can eventually divide or reverse upon disassembly of the machinery. However, a role for membrane tension in mitochondrial fission, although speculated, has remained undefined. We capture the dynamics of constricting mitochondria in mammalian cells using live-cell structured illumination microscopy (SIM). By analyzing the diameters of tubules that emerge from mitochondria and implementing a fluorescence lifetime-based mitochondrial membrane tension sensor, we discover that mitochondria are indeed under tension. Under perturbations that reduce mitochondrial tension, constrictions initiate at the same rate, but are less likely to divide. We propose a model based on our estimates of mitochondrial membrane tension and bending energy in living cells which accounts for the observed probability distribution for mitochondrial constrictions to divide.
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Affiliation(s)
- Dora Mahecic
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015 Lausanne, Switzerland; National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
| | - Lina Carlini
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015 Lausanne, Switzerland; National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
| | - Tatjana Kleele
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015 Lausanne, Switzerland; National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
| | - Adai Colom
- National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland; Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland; Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Antoine Goujon
- National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Stefan Matile
- National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Aurélien Roux
- National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland; Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Suliana Manley
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015 Lausanne, Switzerland; National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland.
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26
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Matthaeus C, Taraska JW. Energy and Dynamics of Caveolae Trafficking. Front Cell Dev Biol 2021; 8:614472. [PMID: 33692993 PMCID: PMC7939723 DOI: 10.3389/fcell.2020.614472] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Caveolae are 70–100 nm diameter plasma membrane invaginations found in abundance in adipocytes, endothelial cells, myocytes, and fibroblasts. Their bulb-shaped membrane domain is characterized and formed by specific lipid binding proteins including Caveolins, Cavins, Pacsin2, and EHD2. Likewise, an enrichment of cholesterol and other lipids makes caveolae a distinct membrane environment that supports proteins involved in cell-type specific signaling pathways. Their ability to detach from the plasma membrane and move through the cytosol has been shown to be important for lipid trafficking and metabolism. Here, we review recent concepts in caveolae trafficking and dynamics. Second, we discuss how ATP and GTP-regulated proteins including dynamin and EHD2 control caveolae behavior. Throughout, we summarize the potential physiological and cell biological roles of caveolae internalization and trafficking and highlight open questions in the field and future directions for study.
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Affiliation(s)
- Claudia Matthaeus
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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27
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Allard A, Valentino F, Sykes C, Betz T, Campillo C. Fluctuations of a membrane nanotube covered with an actin sleeve. Phys Rev E 2020; 102:052402. [PMID: 33327147 DOI: 10.1103/physreve.102.052402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/11/2020] [Indexed: 06/12/2023]
Abstract
Many biological functions rely on the reshaping of cell membranes, in particular into nanotubes, which are covered in vivo by dynamic actin networks. Nanotubes are subject to thermal fluctuations, but the effect of these on cell functions is unknown. Here, we form nanotubes from liposomes using an optically trapped bead adhering to the liposome membrane. From the power spectral density of this bead, we study the nanotube fluctuations in the range of membrane tensions measured in vivo. We show that an actin sleeve covering the nanotube damps its high-frequency fluctuations because of the network viscoelasticity. Our work paves the way for further studies of the effect of nanotube fluctuations on cellular functions.
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Affiliation(s)
- A Allard
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Université, UPMC, Paris 06, Paris, France
- LAMBE, Université d'Évry, CNRS, CEA, Université Paris-Saclay, 91025 Évry-Courcouronnes, France
| | - F Valentino
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Université, UPMC, Paris 06, Paris, France
| | - C Sykes
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Université, UPMC, Paris 06, Paris, France
| | - T Betz
- Institute of Cell Biology, Cells in Motion Interfaculty Center, Centre for Molecular Biology of Inflammation, 48149 Münster, Germany
| | - C Campillo
- LAMBE, Université d'Évry, CNRS, CEA, Université Paris-Saclay, 91025 Évry-Courcouronnes, France
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28
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Pfitzner AK, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux A. An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission. Cell 2020; 182:1140-1155.e18. [PMID: 32814015 PMCID: PMC7479521 DOI: 10.1016/j.cell.2020.07.021] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 05/04/2020] [Accepted: 07/15/2020] [Indexed: 01/02/2023]
Abstract
The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity.
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Affiliation(s)
| | - Vincent Mercier
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland; National Center of Competence in Research in Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Xiuyun Jiang
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK; Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK; MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Buzz Baum
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK; MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK; Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK; MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland; National Center of Competence in Research in Chemical Biology, University of Geneva, 1211 Geneva, Switzerland.
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29
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Endosomal membrane tension regulates ESCRT-III-dependent intra-lumenal vesicle formation. Nat Cell Biol 2020; 22:947-959. [PMID: 32753669 PMCID: PMC7612185 DOI: 10.1038/s41556-020-0546-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 06/22/2020] [Indexed: 12/15/2022]
Abstract
Plasma membrane tension strongly affects cell surface processes, such as migration, endocytosis and signalling. However, it is not known whether membrane tension of organelles regulates their functions, notably intracellular traffic. The ESCRT-III complex is the major membrane remodelling complex that drives Intra-Lumenal Vesicle (ILV) formation on endosomal membranes. Here, we made use of a fluorescent membrane tension probe to show that ESCRT-III subunits are recruited onto endosomal membranes when membrane tension is reduced. We find that tension-dependent recruitment is associated with ESCRT-III polymerization and membrane deformation in vitro, and correlates with increased ILV formation in ESCRT-III decorated endosomes in vivo. Finally, we find that endosomal membrane tension decreases when ILV formation is triggered by EGF under physiological conditions. These results indicate that membrane tension is a major regulator of ILV formation and of endosome trafficking, leading us to conclude that membrane tension can control organelle functions.
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30
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Al-Izzi SC, Sens P, Turner MS. Shear-Driven Instabilities of Membrane Tubes and Dynamin-Induced Scission. PHYSICAL REVIEW LETTERS 2020; 125:018101. [PMID: 32678660 DOI: 10.1103/physrevlett.125.018101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 10/21/2019] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
Motivated by the mechanics of dynamin-mediated membrane tube fission, we analyze the stability of fluid membrane tubes subjected to shear flow in azimuthal direction. We find a novel helical instability driven by the membrane shear flow which results in a nonequilibrium steady state for the tube fluctuations. This instability has its onset at shear rates that may be physiologically accessible under the action of dynamin and could also be probed using in vitro experiments on membrane nanotubes, e.g., using magnetic tweezers. We discuss how such an instability may play a role in the mechanism for dynamin-mediated membrane tube fission.
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Affiliation(s)
- Sami C Al-Izzi
- Department of Mathematics, University of Warwick, Coventry CV4 7AL, United Kingdom
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
- Institut Curie, PSL Research University, CNRS, Physical Chemistry Curie, F-75005, Paris, France
- Sorbonne Université, CNRS, UMR 168, F-75005, Paris, France
| | - Pierre Sens
- Institut Curie, PSL Research University, CNRS, Physical Chemistry Curie, F-75005, Paris, France
- Sorbonne Université, CNRS, UMR 168, F-75005, Paris, France
| | - Matthew S Turner
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
- Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom
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31
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Jaumouillé V, Waterman CM. Physical Constraints and Forces Involved in Phagocytosis. Front Immunol 2020; 11:1097. [PMID: 32595635 PMCID: PMC7304309 DOI: 10.3389/fimmu.2020.01097] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023] Open
Abstract
Phagocytosis is a specialized process that enables cellular ingestion and clearance of microbes, dead cells and tissue debris that are too large for other endocytic routes. As such, it is an essential component of tissue homeostasis and the innate immune response, and also provides a link to the adaptive immune response. However, ingestion of large particulate materials represents a monumental task for phagocytic cells. It requires profound reorganization of the cell morphology around the target in a controlled manner, which is limited by biophysical constraints. Experimental and theoretical studies have identified critical aspects associated with the interconnected biophysical properties of the receptors, the membrane, and the actin cytoskeleton that can determine the success of large particle internalization. In this review, we will discuss the major physical constraints involved in the formation of a phagosome. Focusing on two of the most-studied types of phagocytic receptors, the Fcγ receptors and the complement receptor 3 (αMβ2 integrin), we will describe the complex molecular mechanisms employed by phagocytes to overcome these physical constraints.
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Affiliation(s)
- Valentin Jaumouillé
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Clare M Waterman
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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32
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Kalia R, Frost A. Open and cut: allosteric motion and membrane fission by dynamin superfamily proteins. Mol Biol Cell 2020; 30:2097-2104. [PMID: 31365329 PMCID: PMC6743466 DOI: 10.1091/mbc.e16-10-0709] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cells have evolved diverse protein-based machinery to reshape, cut, or fuse their membrane-delimited compartments. Dynamin superfamily proteins are principal components of this machinery and use their ability to hydrolyze GTP and to polymerize into helices and rings to achieve these goals. Nucleotide-binding, hydrolysis, and exchange reactions drive significant conformational changes across the dynamin family, and these changes alter the shape and stability of supramolecular dynamin oligomers, as well as the ability of dynamins to bind receptors and membranes. Mutations that interfere with the conformational repertoire of these enzymes, and hence with membrane fission, exist in several inherited human diseases. Here, we discuss insights from new x-ray crystal structures and cryo-EM reconstructions that have enabled us to infer some of the allosteric dynamics for these proteins. Together, these studies help us to understand how dynamins perform mechanical work, as well as how specific mutants of dynamin family proteins exhibit pathogenic properties.
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Affiliation(s)
- Raghav Kalia
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158.,Department of Biochemistry, University of Utah, Salt Lake City, UT 84132
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158.,Department of Biochemistry, University of Utah, Salt Lake City, UT 84132.,Chan-Zuckerberg Biohub, San Francisco, CA 94158
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33
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Joseph JG, Liu AP. Mechanical Regulation of Endocytosis: New Insights and Recent Advances. ACTA ACUST UNITED AC 2020; 4:e1900278. [PMID: 32402120 DOI: 10.1002/adbi.201900278] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/23/2022]
Abstract
Endocytosis is a mechanosensitive process. It involves remodeling of the plasma membrane from a flat shape to a budded morphology, often at the sub-micrometer scale. This remodeling process is energy-intensive and is influenced by mechanical factors such as membrane tension, membrane rigidity, and physical properties of cargo and extracellular surroundings. The cellular responses to a variety of mechanical factors by distinct endocytic pathways are important for cells to counteract rapid and extreme disruptions in the mechanohomeostasis of cells. Recent advances in microscopy and mechanical manipulation at the cellular scale have led to new discoveries of mechanoregulation of endocytosis by the aforementioned factors. While factors such as membrane tension and membrane rigidity are generally shown to inhibit endocytosis, other mechanical stimuli have complex relationships with endocytic pathways. At this juncture, it is now possible to utilize experimental techniques to interrogate theoretical predictions on mechanoregulation of endocytosis in cells and even living organisms.
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Affiliation(s)
- Jophin G Joseph
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA
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34
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Miele Y, Medveczky Z, Holló G, Tegze B, Derényi I, Hórvölgyi Z, Altamura E, Lagzi I, Rossi F. Self-division of giant vesicles driven by an internal enzymatic reaction. Chem Sci 2020; 11:3228-3235. [PMID: 34122829 PMCID: PMC8157745 DOI: 10.1039/c9sc05195c] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/08/2020] [Indexed: 12/16/2022] Open
Abstract
Self-division is one of the most common phenomena in living systems and one of the most important properties of life driven by internal mechanisms of cells. Design and engineering of synthetic cells from abiotic components can recreate a life-like function thus contributing to the understanding of the origin of life. Existing methods to induce the self-division of vesicles require external and non-autonomous triggers (temperature change and the addition of membrane precursors). Here we show that pH-responsive giant unilamellar vesicles on the micrometer scale can undergo self-division triggered by an internal autonomous chemical stimulus driven by an enzymatic (urea-urease) reaction coupled to a cross-membrane transport of the substrate, urea. The bilayer of the artificial cells is composed of a mixture of phospholipids (POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine) and oleic acid molecules. The enzymatic reaction increases the pH in the lumen of the vesicles, which concomitantly changes the protonation state of the oleic acid in the inner leaflet of the bilayer causing the removal of the membrane building blocks into the lumen of the vesicles thus decreasing the inner membrane area with respect to the outer one. This process coupled to the osmotic stress (responsible for the volume loss of the vesicles) leads to the division of a mother vesicle into two smaller daughter vesicles. These two processes must act in synergy; none of them alone can induce the division. Overall, our self-dividing system represents a step forward in the design and engineering of a complex autonomous model of synthetic cells.
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Affiliation(s)
- Ylenia Miele
- Department of Chemistry and Biology "A. Zambelli", University of Salerno Via Giovanni Paolo II 132, 84084 - Fisciano SA Italy
| | - Zsófia Medveczky
- Department of Physics, Budapest University of Technology and Economics H-1111, Budafoki ut 8 Budapest Hungary
| | - Gábor Holló
- MTA-BME Condensed Matter Research Group, Budapest University of Technology and Economics H-1111, Budafoki út 8 Budapest Hungary
| | - Borbála Tegze
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics H-1111 Budafoki ut 8 Budapest Hungary
| | - Imre Derényi
- Department of Biological Physics, Eötvös Loránd University H-1117 Pázmány Péter sétány 1/A Budapest Hungary
- MTA-ELTE Statistical and Biological Physics Research Group, Eötvös Loránd University H-1117 Pázmány Péter sétány 1/A Budapest Hungary
| | - Zoltán Hórvölgyi
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics H-1111 Budafoki ut 8 Budapest Hungary
| | - Emiliano Altamura
- Department of Chemistry, University of Bari, "Aldo Moro" Via Orabona 4 I-70125 Bari Italy
| | - István Lagzi
- Department of Physics, Budapest University of Technology and Economics H-1111, Budafoki ut 8 Budapest Hungary
- MTA-BME Condensed Matter Research Group, Budapest University of Technology and Economics H-1111, Budafoki út 8 Budapest Hungary
| | - Federico Rossi
- Department of Chemistry and Biology "A. Zambelli", University of Salerno Via Giovanni Paolo II 132, 84084 - Fisciano SA Italy
- Department of Earth, Environmental and Physical Sciences - DEEP Sciences, University of Siena Pian dei Mantellini 44 53100 - Siena Italy
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35
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Tiberti ML, Antonny B, Gautier R. The transbilayer distribution of polyunsaturated phospholipids determines their facilitating effect on membrane deformation. SOFT MATTER 2020; 16:1722-1730. [PMID: 31916552 DOI: 10.1039/c9sm02107h] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the cell, membrane deformation and fission (collectively referred to as 'budding') is driven by specific protein machineries but is also influenced by lipid composition. We previously reported that phospholipids with polyunsaturated acyl chains facilitate membrane budding because they adapt their shape to membrane curvature, thereby decreasing membrane bending rigidity. The facilitating effect of polyunsaturated lipids was observed in experiments and simulations performed on membranes where the two bilayer leaflets had the same lipid composition. However, biological membranes are generally asymmetric. Here, we present coarse-grained molecular dynamics simulations on asymmetric phospholipid bilayers undergoing deformation via a pulling force along the bilayer normal. One leaflet contains monounsaturated C18:0-C18:1-phospholipids, whereas the opposite leaflet contains polyunsaturated C18:0-C22:6-phospholipids. When present in the monolayer orientated towards the pulling force and thereby in the convex face of the forming tube, C18:0-C22:6-phospholipids facilitate membrane tubulation. In contrast, C18:0-C22:6-phospholipids in the concave face of the tube have no effect. Analysis of lipid shape indicates that these contrasting effects arise from the superior ability of polyunsaturated phospholipids to swell in the convex leaflet, whereas mono and polyunsaturated phospholipids behave similarly in the concave leaflet. The leaflet-dependent effect of polyunsaturated phospholipids matches well their asymmetric distribution in biological membranes, notably in synaptic vesicles, which are produced by the fastest budding event in the body.
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Affiliation(s)
- Marion L Tiberti
- Université Côte d'Azur et CNRS, IPMC, 660 route des lucioles, 06560 Valbonne, France.
| | - Bruno Antonny
- Université Côte d'Azur et CNRS, IPMC, 660 route des lucioles, 06560 Valbonne, France.
| | - Romain Gautier
- Université Côte d'Azur et CNRS, IPMC, 660 route des lucioles, 06560 Valbonne, France.
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36
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Vasan R, Rudraraju S, Akamatsu M, Garikipati K, Rangamani P. A mechanical model reveals that non-axisymmetric buckling lowers the energy barrier associated with membrane neck constriction. SOFT MATTER 2020; 16:784-797. [PMID: 31830191 DOI: 10.1039/c9sm01494b] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Membrane neck formation is essential for scission, which, as recent experiments on tubules have demonstrated, can be location dependent. The diversity of biological machinery that can constrict a neck such as dynamin, actin, ESCRTs and BAR proteins, and the range of forces and deflection over which they operate, suggest that the constriction process is functionally mechanical and robust to changes in biological environment. In this study, we used a mechanical model of the lipid bilayer to systematically investigate the influence of location, symmetry constraints, and helical forces on membrane neck constriction. Simulations from our model demonstrated that the energy barriers associated with constriction of a membrane neck are location-dependent. Importantly, if symmetry restrictions are relaxed, then the energy barrier for constriction is dramatically lowered and the membrane buckles at lower values of forcing parameters. Our simulations also show that constriction due to helical proteins further reduces the energy barrier for neck formation when compared to cylindrical proteins. These studies establish that despite different molecular mechanisms of neck formation in cells, the mechanics of constriction naturally leads to a loss of symmetry that can lower the energy barrier to constriction.
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Affiliation(s)
- R Vasan
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093, USA.
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37
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Abstract
Phagocytosis is a specialized process that enables cellular ingestion and clearance of microbes, dead cells and tissue debris that are too large for other endocytic routes. As such, it is an essential component of tissue homeostasis and the innate immune response, and also provides a link to the adaptive immune response. However, ingestion of large particulate materials represents a monumental task for phagocytic cells. It requires profound reorganization of the cell morphology around the target in a controlled manner, which is limited by biophysical constraints. Experimental and theoretical studies have identified critical aspects associated with the interconnected biophysical properties of the receptors, the membrane, and the actin cytoskeleton that can determine the success of large particle internalization. In this review, we will discuss the major physical constraints involved in the formation of a phagosome. Focusing on two of the most-studied types of phagocytic receptors, the Fcγ receptors and the complement receptor 3 (αMβ2 integrin), we will describe the complex molecular mechanisms employed by phagocytes to overcome these physical constraints.
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Affiliation(s)
- Valentin Jaumouillé
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Clare M Waterman
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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38
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Piontek MC, Lira RB, Roos WH. Active probing of the mechanical properties of biological and synthetic vesicles. Biochim Biophys Acta Gen Subj 2019; 1865:129486. [PMID: 31734458 DOI: 10.1016/j.bbagen.2019.129486] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/05/2019] [Accepted: 11/09/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND The interest in mechanics of synthetic and biological vesicles has been continuously growing during the last decades. Liposomes serve as model systems for investigating fundamental membrane processes and properties. More recently, extracellular vesicles (EVs) have been investigated mechanically as well. EVs are widely studied in fundamental and applied sciences, but their material properties remained elusive until recently. Elucidating the mechanical properties of vesicles is essential to unveil the mechanisms behind a variety of biological processes, e.g. budding, vesiculation and cellular uptake mechanisms. SCOPE OF REVIEW The importance of mechanobiology for studies of vesicles and membranes is discussed, as well as the different available techniques to probe their mechanical properties. In particular, the mechanics of vesicles and membranes as obtained by nanoindentation, micropipette aspiration, optical tweezers, electrodeformation and electroporation experiments is addressed. MAJOR CONCLUSIONS EVs and liposomes possess an astonishing rich, diverse behavior. To better understand their properties, and for optimization of their applications in nanotechnology, an improved understanding of their mechanical properties is needed. Depending on the size of the vesicles and the specific scientific question, different techniques can be chosen for their mechanical characterization. GENERAL SIGNIFICANCE Understanding the mechanical properties of vesicles is necessary to gain deeper insight in the fundamental biological mechanisms involved in vesicle generation and cellular uptake. This furthermore facilitates technological applications such as using vesicles as targeted drug delivery vehicles. Liposome studies provide insight into fundamental membrane processes and properties, whereas the role and functioning of EVs in biology and medicine are increasingly elucidated.
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Affiliation(s)
- Melissa C Piontek
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
| | - Rafael B Lira
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
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39
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Polymer-like Model to Study the Dynamics of Dynamin Filaments on Deformable Membrane Tubes. Biophys J 2019; 117:1870-1891. [PMID: 31672269 DOI: 10.1016/j.bpj.2019.09.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/08/2019] [Accepted: 09/24/2019] [Indexed: 01/30/2023] Open
Abstract
Peripheral membrane proteins with intrinsic curvature can act both as sensors of membrane curvature and shape modulators of the underlying membranes. A well-studied example of such proteins is the mechanochemical GTPase dynamin, which assembles into helical filaments around membrane tubes and catalyzes their scission in a GTPase-dependent manner. It is known that the dynamin coat alone, without GTP, can constrict membrane tubes to radii of ∼10 nm, indicating that the intrinsic shape and elasticity of dynamin filaments should play an important role in membrane remodeling. However, molecular and dynamic understanding of the process is lacking. Here, we develop a dynamical polymer-chain model for a helical elastic filament bound on a deformable membrane tube of conserved mass, accounting for thermal fluctuations in the filament and lipid flows in the membrane. The model is based on the locally cylindrical helix approximation for dynamin. We obtain the elastic parameters of the dynamin filament by molecular dynamics simulations of its tetrameric building block and also from coarse-grained structure-based simulations of a 17-dimer filament. The results show that the stiffness of dynamin is comparable to that of the membrane. We determine equilibrium shapes of the filament and the membrane and find that mostly the pitch of the filament, not its radius, is sensitive to variations in membrane tension and stiffness. The close correspondence between experimental estimates of the inner tube radius and those predicted by the model suggests that dynamin's "stalk" region is responsible for its GTP-independent membrane-shaping ability. The model paves the way for future mesoscopic modeling of dynamin with explicit motor function.
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40
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Ford MGJ, Chappie JS. The structural biology of the dynamin-related proteins: New insights into a diverse, multitalented family. Traffic 2019; 20:717-740. [PMID: 31298797 DOI: 10.1111/tra.12676] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 12/13/2022]
Abstract
Dynamin-related proteins are multidomain, mechanochemical GTPases that self-assemble and orchestrate a wide array of cellular processes. Over the past decade, structural insights from X-ray crystallography and cryo-electron microscopy have reshaped our mechanistic understanding of these proteins. Here, we provide a historical perspective on these advances that highlights the structural attributes of different dynamin family members and explores how these characteristics affect GTP hydrolysis, conformational coupling and oligomerization. We also discuss a number of lingering challenges remaining in the field that suggest future directions of study.
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Affiliation(s)
- Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, New York
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41
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Shurer CR, Kuo JCH, Roberts LM, Gandhi JG, Colville MJ, Enoki TA, Pan H, Su J, Noble JM, Hollander MJ, O'Donnell JP, Yin R, Pedram K, Möckl L, Kourkoutis LF, Moerner WE, Bertozzi CR, Feigenson GW, Reesink HL, Paszek MJ. Physical Principles of Membrane Shape Regulation by the Glycocalyx. Cell 2019; 177:1757-1770.e21. [PMID: 31056282 PMCID: PMC6768631 DOI: 10.1016/j.cell.2019.04.017] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 02/19/2019] [Accepted: 04/09/2019] [Indexed: 12/12/2022]
Abstract
Cells bend their plasma membranes into highly curved forms to interact with the local environment, but how shape generation is regulated is not fully resolved. Here, we report a synergy between shape-generating processes in the cell interior and the external organization and composition of the cell-surface glycocalyx. Mucin biopolymers and long-chain polysaccharides within the glycocalyx can generate entropic forces that favor or disfavor the projection of spherical and finger-like extensions from the cell surface. A polymer brush model of the glycocalyx successfully predicts the effects of polymer size and cell-surface density on membrane morphologies. Specific glycocalyx compositions can also induce plasma membrane instabilities to generate more exotic undulating and pearled membrane structures and drive secretion of extracellular vesicles. Together, our results suggest a fundamental role for the glycocalyx in regulating curved membrane features that serve in communication between cells and with the extracellular matrix.
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Affiliation(s)
- Carolyn R Shurer
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Joe Chin-Hun Kuo
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | | | - Jay G Gandhi
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | | | - Thais A Enoki
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Hao Pan
- Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
| | - Jin Su
- Department of Clinical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Jade M Noble
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Hollander
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - John P O'Donnell
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Rose Yin
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Kayvon Pedram
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Leonhard Möckl
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Lena F Kourkoutis
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA; Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY 14853, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Gerald W Feigenson
- Field of Biophysics, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Heidi L Reesink
- Department of Clinical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Matthew J Paszek
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA; Field of Biophysics, Cornell University, Ithaca, NY 14853, USA; Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY 14853, USA.
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42
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Abstract
Dynamin proteins assemble into characteristic helical structures around necks of clathrin-coated membrane buds. Hydrolysis of dynamin-bound GTP results in both fission of the membrane neck and partial disruption of the dynamin oligomer. Imaging by atomic force microscopy reveals that, on GTP hydrolysis, dynamin oligomers undergo a dynamic remodeling and lose their distinctive helical shape. While breakup of the dynamin helix is a critical stage in clathrin-mediated endocytosis, the mechanism for this remodeling of the oligomer has not been resolved. In this paper, we formulate an analytical, elasticity-based model for the reshaping and disassembly of the dynamin scaffold. We predict that the shape of the oligomer is modulated by the orientation of dynamin's pleckstrin homology (PH) domain relative to the underlying membrane. Our results indicate that tilt of the PH domain drives deformation and fragmentation of the oligomer, in agreement with experimental observations. This model motivated the introduction of the tilted helix: a curve that maintains a fixed angle between its normal and the normal of the embedding surface. Our findings highlight the importance of tilt as a key regulator of size and morphology of membrane-bound oligomers.
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43
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Zhang X, Huang W, Fan Y, Sun Y, Ge X. Role of GTPases in the regulation of mitochondrial dynamics in Parkinson's disease. Exp Cell Res 2019; 382:111460. [PMID: 31194975 DOI: 10.1016/j.yexcr.2019.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/27/2019] [Accepted: 06/08/2019] [Indexed: 12/11/2022]
Abstract
Mitochondria are highly dynamic organelle that undergo frequent fusion and division, and the balance of these opposing processes regulates mitochondrial morphology, distribution, and function. Mitochondrial fission facilitates the replication and distribution of mitochondria during cell division, whereas the fusion process including inner and outer mitochondrial membrane fusion allows the exchange of intramitochondrial material between adjacent mitochondria. Despite several GTPase family proteins have been implicated as key modulators of mitochondrial dynamics, the mechanisms by which these proteins regulate mitochondrial homeostasis and function remain not clearly understood. Neuronal function and survival are closely related to mitochondria dynamics, and disturbed mitochondrial fission/fusion may influence neurotransmission, synaptic maintenance, neuronal survival and function. Recent studies have shown that mitochondrial dysfunction caused by aberrant mitochondrial dynamics plays an essential role in the pathogenesis of both sporadic and familial Parkinson's disease (PD). Collectively, we review the molecular mechanism of known GTPase proteins in regulating mitochondrial fission and fusion, but also highlight the causal role for mitochondrial dynamics in PD pathogenesis.
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Affiliation(s)
- Xiaoling Zhang
- Department of Pharmacology, Medical College, Yangzhou University, Yangzhou, 225009, China; Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225009, China
| | - Wenmin Huang
- Department of Pharmacology, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Yiyun Fan
- Department of Pharmacology, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Ying Sun
- Department of Pharmacology, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoqun Ge
- Department of Pharmacology, Medical College, Yangzhou University, Yangzhou, 225009, China; Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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44
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Riggi M, Bourgoint C, Macchione M, Matile S, Loewith R, Roux A. TORC2 controls endocytosis through plasma membrane tension. J Cell Biol 2019; 218:2265-2276. [PMID: 31123183 PMCID: PMC6605812 DOI: 10.1083/jcb.201901096] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/11/2019] [Accepted: 05/06/2019] [Indexed: 12/27/2022] Open
Abstract
Target of rapamycin complex 2 (TORC2) is a conserved protein kinase that regulates multiple plasma membrane (PM)-related processes, including endocytosis. Direct, chemical inhibition of TORC2 arrests endocytosis but with kinetics that is relatively slow and therefore inconsistent with signaling being mediated solely through simple phosphorylation cascades. Here, we show that in addition to and independently from regulation of the phosphorylation of endocytic proteins, TORC2 also controls endocytosis by modulating PM tension. Elevated PM tension, upon TORC2 inhibition, impinges on endocytosis at two different levels by (1) severing the bonds between the PM adaptor proteins Sla2 and Ent1 and the actin cytoskeleton and (2) hindering recruitment of Rvs167, an N-BAR-containing protein important for vesicle fission to endocytosis sites. These results underline the importance of biophysical cues in the regulation of cellular and molecular processes.
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Affiliation(s)
- Margot Riggi
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland.,Department of Biochemistry, University of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.,Swiss National Centre for Competence in Research Program Chemical Biology, Geneva, Switzerland
| | - Clélia Bourgoint
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Mariano Macchione
- Swiss National Centre for Competence in Research Program Chemical Biology, Geneva, Switzerland.,Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Swiss National Centre for Competence in Research Program Chemical Biology, Geneva, Switzerland.,Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland .,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.,Swiss National Centre for Competence in Research Program Chemical Biology, Geneva, Switzerland
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, Switzerland .,Swiss National Centre for Competence in Research Program Chemical Biology, Geneva, Switzerland
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45
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Viplav A, Saha T, Huertas J, Selenschik P, Ebrahimkutty MP, Grill D, Lehrich J, Hentschel A, Biasizzo M, Mengoni S, Ahrends R, Gerke V, Cojocaru V, Klingauf J, Galic M. ArhGEF37 assists dynamin 2 during clathrin-mediated endocytosis. J Cell Sci 2019; 132:jcs.226530. [PMID: 30926623 PMCID: PMC6526708 DOI: 10.1242/jcs.226530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/22/2019] [Indexed: 12/20/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) engages over 30 proteins to secure efficient cargo and membrane uptake. While the function of most core CME components is well established, auxiliary mechanisms crucial for fine-tuning and adaptation remain largely elusive. In this study, we identify ArhGEF37, a currently uncharacterized protein, as a constituent of CME. Structure prediction together with quantitative cellular and biochemical studies present a unique BAR domain and PI(4,5)P2-dependent protein–membrane interactions. Functional characterization yields accumulation of ArhGEF37 at dynamin 2-rich late endocytic sites and increased endocytosis rates in the presence of ArhGEF37. Together, these results introduce ArhGEF37 as a regulatory protein involved in endocytosis. Summary: Accumulation of ArhGEF37 at dynamin 2-rich late endocytic sites yields increased rates of endocytosis.
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Affiliation(s)
- Abhiyan Viplav
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany.,Institute of Medical Physics and Biophysics, University of Muenster, 48149 Muenster, Germany
| | - Tanumoy Saha
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany.,Institute of Medical Physics and Biophysics, University of Muenster, 48149 Muenster, Germany
| | - Jan Huertas
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany.,Computational Structural Biology Group, Dept. of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149 Muenster, Germany
| | - Philipp Selenschik
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany.,Institute of Medical Physics and Biophysics, University of Muenster, 48149 Muenster, Germany
| | - Mirsana P Ebrahimkutty
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany.,Institute of Medical Physics and Biophysics, University of Muenster, 48149 Muenster, Germany
| | - David Grill
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany.,Institute for Medical Biochemistry, ZMBE, University of Muenster, 48149 Muenster, Germany
| | - Julia Lehrich
- Institute of Medical Physics and Biophysics, University of Muenster, 48149 Muenster, Germany
| | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften, ISAS, 44139 Dortmund, Germany
| | - Monika Biasizzo
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany.,Institute of Medical Physics and Biophysics, University of Muenster, 48149 Muenster, Germany
| | - Simone Mengoni
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany.,Institute of Medical Physics and Biophysics, University of Muenster, 48149 Muenster, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften, ISAS, 44139 Dortmund, Germany
| | - Volker Gerke
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany.,Institute for Medical Biochemistry, ZMBE, University of Muenster, 48149 Muenster, Germany
| | - Vlad Cojocaru
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany.,Computational Structural Biology Group, Dept. of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149 Muenster, Germany
| | - Jürgen Klingauf
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany.,Institute of Medical Physics and Biophysics, University of Muenster, 48149 Muenster, Germany
| | - Milos Galic
- DFG Cluster of Excellence 'Cells in Motion', University of Muenster, 48149 Muenster, Germany .,Institute of Medical Physics and Biophysics, University of Muenster, 48149 Muenster, Germany
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46
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Chuang MC, Lin SS, Ohniwa RL, Lee GH, Su YA, Chang YC, Tang MJ, Liu YW. Tks5 and Dynamin-2 enhance actin bundle rigidity in invadosomes to promote myoblast fusion. J Cell Biol 2019; 218:1670-1685. [PMID: 30894403 PMCID: PMC6504888 DOI: 10.1083/jcb.201809161] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/22/2019] [Accepted: 03/04/2019] [Indexed: 12/12/2022] Open
Abstract
Skeletal muscle development requires the cell-cell fusion of differentiated myoblasts to form muscle fibers. The actin cytoskeleton is known to be the main driving force for myoblast fusion; however, how actin is organized to direct intercellular fusion remains unclear. Here we show that an actin- and dynamin-2-enriched protrusive structure, the invadosome, is required for the fusion process of myogenesis. Upon differentiation, myoblasts acquire the ability to form invadosomes through isoform switching of a critical invadosome scaffold protein, Tks5. Tks5 directly interacts with and recruits dynamin-2 to the invadosome and regulates its assembly around actin filaments to strengthen the stiffness of dynamin-actin bundles and invadosomes. These findings provide a mechanistic framework for the acquisition of myogenic fusion machinery during myogenesis and reveal a novel structural function for Tks5 and dynamin-2 in organizing actin filaments in the invadosome to drive membrane fusion.
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Affiliation(s)
- Mei-Chun Chuang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shan-Shan Lin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ryosuke L Ohniwa
- Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Center for Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Gang-Hui Lee
- International Center of Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - You-An Su
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Chen Chang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Jer Tang
- International Center of Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan.,Department of Physiology, Medical College, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Wen Liu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan .,Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
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47
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Loewith R, Riezman H, Winssinger N. Sphingolipids and membrane targets for therapeutics. Curr Opin Chem Biol 2019; 50:19-28. [PMID: 30897494 DOI: 10.1016/j.cbpa.2019.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/09/2019] [Accepted: 02/13/2019] [Indexed: 12/20/2022]
Abstract
Lipids and membranes are often strongly altered in various diseases and pathologies, but are not often targeted for therapeutic advantage. In particular, the sphingolipids are particularly sensitive to altered physiology and have been implicated as important players in not only several rare hereditary diseases, but also other major pathologies, including cancer. This review discusses some potential targets in the sphingolipid pathway and describes how the initial drug compounds have been evolved to create potentially improved therapeutics. This reveals how lipids and their interactions with proteins can be used for therapeutic advantage. We also discuss the possibility that modification of the physical properties of membranes could also affect intracellular signaling and be of therapeutic interest.
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Affiliation(s)
- Robbie Loewith
- Department of Molecular Biology, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland.
| | - Howard Riezman
- Department of Biochemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland.
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland.
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48
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Gov NS. Guided by curvature: shaping cells by coupling curved membrane proteins and cytoskeletal forces. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0115. [PMID: 29632267 DOI: 10.1098/rstb.2017.0115] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2017] [Indexed: 01/11/2023] Open
Abstract
Eukaryote cells have flexible membranes that allow them to have a variety of dynamical shapes. The shapes of the cells serve important biological functions, both for cells within an intact tissue, and during embryogenesis and cellular motility. How cells control their shapes and the structures that they form on their surface has been a subject of intensive biological research, exposing the building blocks that cells use to deform their membranes. These processes have also drawn the interest of theoretical physicists, aiming to develop models based on physics, chemistry and nonlinear dynamics. Such models explore quantitatively different possible mechanisms that the cells can employ to initiate the spontaneous formation of shapes and patterns on their membranes. We review here theoretical work where one such class of mechanisms was investigated: the coupling between curved membrane proteins, and the cytoskeletal forces that they recruit. Theory indicates that this coupling gives rise to a rich variety of membrane shapes and dynamics, while experiments indicate that this mechanism appears to drive many cellular shape changes.This article is part of the theme issue 'Self-organization in cell biology'.
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Affiliation(s)
- N S Gov
- Department of Chemical Physics, Weizmann Institute of Science, PO Box 26, Rehovot 76100, Israel
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49
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Pannuzzo M, McDargh ZA, Deserno M. The role of scaffold reshaping and disassembly in dynamin driven membrane fission. eLife 2018; 7:39441. [PMID: 30561335 PMCID: PMC6355196 DOI: 10.7554/elife.39441] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 12/13/2018] [Indexed: 12/11/2022] Open
Abstract
The large GTPase dynamin catalyzes membrane fission in eukaryotic cells, but despite three decades of experimental work, competing and partially conflicting models persist regarding some of its most basic actions. Here we investigate the mechanical and functional consequences of dynamin scaffold shape changes and disassembly with the help of a geometrically and elastically realistic simulation model of helical dynamin-membrane complexes. Beyond changes of radius and pitch, we emphasize the crucial role of a third functional motion: an effective rotation of the filament around its longitudinal axis, which reflects alternate tilting of dynamin’s PH binding domains and creates a membrane torque. We also show that helix elongation impedes fission, hemifission is reached via a small transient pore, and coat disassembly assists fission. Our results have several testable structural consequences and help to reconcile mutual conflicting aspects between the two main present models of dynamin fission—the two-stage and the constrictase model. When cells take up material from their surroundings, they must first transport this cargo across their outer membrane, a flexible sheet of tightly organized fat molecules that act as a barrier to the environment. Cells can achieve this by letting their membrane surround the object, pulling it inwards until it is contained in a pouch that bulges into the cell. This bag is then corded up so it splits off from the outer membrane. The ‘cord’ is a protein called dynamin, which is thought to form a tight spiral around the bag’s neck, closing it over and pinching it away. The structure of dynamin is fairly well known, and yet several theories compete to explain how it may snap the bag off the outer membrane. Here, Pannuzzo et al. have created a computer simulation that faithfully replicates the geometry and the elasticity of the membrane and of dynamin, and used it to test different ways the protein could work. The first test featured simple constriction, where the dynamin spiral contracts around the membrane to pinch it; this only separated the bag from the membrane after implausibly tight constriction. The second test added elongation, with the spiral lengthening as well as reducing its diameter, but this further reduced the ability for the protein to snap off the membrane. The final test combined constriction and rotation, whereby dynamin ‘twirls’ as it presses on the neck of the bag: this succeeded in efficiently severing the membrane once the dynamin spiral disassembled. Indeed, the simulations suggested that dynamin might start to dismantle while it constricts, without compromising its role. In fact, getting rid of excess length as the protein contracts helps to dissolve any remnants of a membrane connection. Defects in dynamin are associated with conditions such as centronuclear myopathy and Charcot‐Marie‐Tooth peripheral neuropathy. Recent research also indicates that the protein is involved in a much wider range of neurological disorders that include Alzheimer's, Parkinson's, Huntington's, and amyotrophic lateral sclerosis. The models created by Pannuzzo et al. are useful tools to understand how dynamin and similar proteins work and sometimes fail.
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Affiliation(s)
- Martina Pannuzzo
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States
| | - Zachary A McDargh
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States
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50
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Colom A, Derivery E, Soleimanpour S, Tomba C, Molin MD, Sakai N, González-Gaitán M, Matile S, Roux A. A fluorescent membrane tension probe. Nat Chem 2018; 10:1118-1125. [PMID: 30150727 PMCID: PMC6197433 DOI: 10.1038/s41557-018-0127-3] [Citation(s) in RCA: 288] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/25/2018] [Indexed: 12/24/2022]
Abstract
Cells and organelles are delimited by lipid bilayers in which high deformability is essential to many cell processes, including motility, endocytosis and cell division. Membrane tension is therefore a major regulator of the cell processes that remodel membranes, albeit one that is very hard to measure in vivo. Here we show that a planarizable push-pull fluorescent probe called FliptR (fluorescent lipid tension reporter) can monitor changes in membrane tension by changing its fluorescence lifetime as a function of the twist between its fluorescent groups. The fluorescence lifetime depends linearly on membrane tension within cells, enabling an easy quantification of membrane tension by fluorescence lifetime imaging microscopy. We further show, using model membranes, that this linear dependency between lifetime of the probe and membrane tension relies on a membrane-tension-dependent lipid phase separation. We also provide calibration curves that enable accurate measurement of membrane tension using fluorescence lifetime imaging microscopy.
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Affiliation(s)
- Adai Colom
- Biochemistry Department, University of Geneva, Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Emmanuel Derivery
- Biochemistry Department, University of Geneva, Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Saeideh Soleimanpour
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Caterina Tomba
- Biochemistry Department, University of Geneva, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Marta Dal Molin
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Naomi Sakai
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Marcos González-Gaitán
- Biochemistry Department, University of Geneva, Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Aurélien Roux
- Biochemistry Department, University of Geneva, Geneva, Switzerland.
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland.
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland.
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