1
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Pajtinka P, Vácha R. Amphipathic Helices Can Sense Both Positive and Negative Curvatures of Lipid Membranes. J Phys Chem Lett 2024; 15:175-179. [PMID: 38153203 PMCID: PMC10788957 DOI: 10.1021/acs.jpclett.3c02785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/09/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023]
Abstract
Curvature sensing is an essential ability of biomolecules to preferentially localize to membrane regions of a specific curvature. It has been shown that amphipathic helices (AHs), helical peptides with both hydrophilic and hydrophobic regions, could sense a positive membrane curvature. The origin of this AH sensing has been attributed to their ability to exploit lipid-packing defects that are enhanced in regions of positive curvature. In this study, we revisit an alternative framework where AHs act as sensors of local internal stress within the membrane, suggesting the possibility of an AH sensing a negative membrane curvature. Using molecular dynamics simulations, we gradually tuned the hydrophobicity of AHs, thereby adjusting their insertion depth so that the curvature preference of AHs is switched from positive to negative. This study suggests that highly hydrophobic AHs could preferentially localize proteins to regions of a negative membrane curvature.
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Affiliation(s)
- Peter Pajtinka
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Robert Vácha
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department
of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech
Republic
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2
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Badvaram I, Camley BA. Physical limits to membrane curvature sensing by a single protein. Phys Rev E 2023; 108:064407. [PMID: 38243534 DOI: 10.1103/physreve.108.064407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 09/11/2023] [Indexed: 01/21/2024]
Abstract
Membrane curvature sensing is essential for a diverse range of biological processes. Recent experiments have revealed that a single nanometer-sized septin protein has different binding rates to membrane-coated glass beads of 1-µm and 3-µm diameters, even though the septin is orders of magnitude smaller than the beads. This sensing ability is especially surprising since curvature-sensing proteins must deal with persistent thermal fluctuations of the membrane, leading to discrepancies between the bead's curvature and the local membrane curvature sensed instantaneously by a protein. Using continuum models of fluctuating membranes, we investigate whether it is feasible for a protein acting as a perfect observer of the membrane to sense micron-scale curvature either by measuring local membrane curvature or by using bilayer lipid densities as a proxy. To do this, we develop algorithms to simulate lipid density and membrane shape fluctuations. We derive physical limits to the sensing efficacy of a protein in terms of protein size, membrane thickness, membrane bending modulus, membrane-substrate adhesion strength, and bead size. To explain the experimental protein-bead association rates, we develop two classes of predictive models: (i) for proteins that maximally associate to a preferred curvature and (ii) for proteins with enhanced association rates above a threshold curvature. We find that the experimentally observed sensing efficacy is close to the theoretical sensing limits imposed on a septin-sized protein. Protein-membrane association rates may depend on the curvature of the bead, but the strength of this dependence is limited by the fluctuations in membrane height and density.
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Affiliation(s)
- Indrajit Badvaram
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Brian A Camley
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
- William H. Miller III Department of Physics & Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, USA
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3
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Semeraro EF, Pajtinka P, Marx L, Kabelka I, Leber R, Lohner K, Vácha R, Pabst G. Magainin 2 and PGLa in bacterial membrane mimics IV: Membrane curvature and partitioning. Biophys J 2022; 121:4689-4701. [PMID: 36258677 PMCID: PMC9748257 DOI: 10.1016/j.bpj.2022.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 12/15/2022] Open
Abstract
We previously reported that the synergistically enhanced antimicrobial activity of magainin 2 (MG2a) and PGLa is related to membrane adhesion and fusion. Here, we demonstrate that equimolar mixtures of MG2a and L18W-PGLa induce positive monolayer curvature stress and sense, at the same time, positive mean and Gaussian bilayer curvatures already at low amounts of bound peptide. The combination of both abilities-membrane curvature sensing and inducing-is most likely the base for the synergistically enhanced peptide activity. In addition, our coarse-grained simulations suggest that fusion stalks are promoted by decreasing the free-energy barrier for their formation rather than by stabilizing their shape. We also interrogated peptide partitioning as a function of lipid and peptide concentration using tryptophan fluorescence spectroscopy and peptide-induced leakage of dyes from lipid vesicles. In agreement with a previous report, we find increased membrane partitioning of L18W-PGLa in the presence of MG2a. However, this effect does not prevail to lipid concentrations higher than 1 mM, above which all peptides associate with the lipid bilayers. This implies that synergistic effects of MG2a and L18W-PGLa in previously reported experiments with lipid concentrations >1 mM are due to peptide-induced membrane remodeling and not their specific membrane partitioning.
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Affiliation(s)
- Enrico F Semeraro
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria
| | - Peter Pajtinka
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lisa Marx
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria
| | - Ivo Kabelka
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Regina Leber
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria
| | - Karl Lohner
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria.
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4
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Ivanova KA, Bashkirov PV. Noise in Ultrashort Elastic Membrane Nanotube. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2022. [DOI: 10.1134/s1990747822050063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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5
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Mahata P, Vennamneni L, Chattopadhyay S. A mechanical-thermodynamic model for understanding endocytosis of COVID-19 virus SARS-CoV-2. PROCEEDINGS OF THE INSTITUTION OF MECHANICAL ENGINEERS. PART C. JOURNAL OF MECHANICAL ENGINEERING SCIENCE 2022; 236:9431-9440. [PMID: 38603131 PMCID: PMC9127454 DOI: 10.1177/09544062221098538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 04/11/2022] [Indexed: 04/13/2024]
Abstract
We analyze the endocytosis process of COVID-19 (coronavirus disease 2019) virus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) using a mechanical-thermodynamic model. The virus particle is designed to interface with the cell membrane as a hard sphere. The role of cytoplasmic BAR (Bin/Amphiphysin/RVs) proteins is considered in the endocytosis. Interestingly, the Endophilin N-BAR cytoplasmic proteins show resistance in participating endocytosis, whereas F-BAR, Arfaptin BAR, Amphiphysin N-BAR, and PX-BAR proteins participate in endocytosis. The increase in membrane tension, concentrated force between the cell membrane receptor, and spike glycoprotein present on the surface of virus particle promote the endocytosis. Also, the increase in the bending modulus of membrane leads to the two-phase solution of BAR protein concentration on the interior of cell membrane surface. We observe an unstable region of protein concentration, which may help one to retard the endocytosis process and thus the viral infection. Though the present study is focused on SARS-CoV-2, it can be extended to understand any other viral infections, involving endocytosis process.
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Affiliation(s)
- Paritosh Mahata
- Department of Mechanical Engineering, Birla Institute of Technology, Ranchi, India
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6
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Kluge C, Pöhnl M, Böckmann RA. Spontaneous local membrane curvature induced by transmembrane proteins. Biophys J 2022; 121:671-683. [PMID: 35122737 PMCID: PMC8943716 DOI: 10.1016/j.bpj.2022.01.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/13/2022] [Accepted: 01/28/2022] [Indexed: 11/26/2022] Open
Abstract
The (local) curvature of cellular membranes acts as a driving force for the targeting of membrane-associated proteins to specific membrane domains, as well as a sorting mechanism for transmembrane proteins, e.g., by accumulation in regions of matching spontaneous curvature. The latter measure was previously experimentally employed to study the curvature induced by the potassium channel KvAP and by aquaporin AQP0. However, the direction of the reported spontaneous curvature levels as well as the molecular driving forces governing the membrane curvature induced by these integral transmembrane proteins could not be addressed experimentally. Here, using both coarse-grained and atomistic molecular dynamics (MD) simulations, we report induced spontaneous curvature values for the homologous potassium channel Kv 1.2/2.1 Chimera (KvChim) and AQP0 embedded in unrestrained lipid bicelles that are in very good agreement with experiment. Importantly, the direction of curvature could be directly assessed from our simulations: KvChim induces a strong positive membrane curvature (≈0.036 nm-1) whereas AQP0 causes a comparably small negative curvature (≈-0.019 nm-1). Analyses of protein-lipid interactions within the bicelle revealed that the potassium channel shapes the surrounding membrane via structural determinants. Differences in shape of the protein-lipid interface of the voltage-gating domains between the extracellular and cytosolic membrane leaflets induce membrane stress and thereby promote a protein-proximal membrane curvature. In contrast, the water pore AQP0 displayed a high structural stability and an only faint effect on the surrounding membrane environment that is connected to its wedge-like shape.
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Affiliation(s)
- Christoph Kluge
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Matthias Pöhnl
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany,National Center for High-Performance Computing Erlangen (NHR@FAU), Erlangen, Germany,Corresponding author
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7
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A synergy between mechanosensitive calcium- and membrane-binding mediates tension-sensing by C2-like domains. Proc Natl Acad Sci U S A 2022; 119:2112390119. [PMID: 34969839 PMCID: PMC8740744 DOI: 10.1073/pnas.2112390119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
A cell must be able to measure whether the lipid membranes that surround its insides are stretched. Currently, mechanosensitive ion channels are the best-studied class of membrane tension sensors, but recent work suggests that peripheral membrane enzymes that gauge nuclear confinement or swelling during cell migration or upon tissue injury constitute a second class. The mechanosensitivity of these enzymes derives from their calcium-dependent (“C2-like”) membrane-interaction domains. Although these can be found in many important signaling proteins, they have remained virtually unstudied as mechanotransducers. How membrane tension controls these domains and what features render them mechanosensitive is unclear. Here, we show that membrane tension-sensing by C2-like domains is mediated by a synergy between mechanosensitive calcium-binding and membrane insertion. When nuclear membranes are stretched, the peripheral membrane enzyme cytosolic phospholipase A2 (cPLA2) binds via its calcium-dependent C2 domain (cPLA2-C2) and initiates bioactive lipid signaling and tissue inflammation. More than 150 C2-like domains are encoded in vertebrate genomes. How many of them are mechanosensors and quantitative relationships between tension and membrane recruitment remain unexplored, leaving a knowledge gap in the mechanotransduction field. In this study, we imaged the mechanosensitive adsorption of cPLA2 and its C2 domain to nuclear membranes and artificial lipid bilayers, comparing it to related C2-like motifs. Stretch increased the Ca2+ sensitivity of all tested domains, promoting half-maximal binding of cPLA2 at cytoplasmic resting-Ca2+ concentrations. cPLA2-C2 bound up to 50 times tighter to stretched than to unstretched membranes. Our data suggest that a synergy of mechanosensitive Ca2+ interactions and deep, hydrophobic membrane insertion enables cPLA2-C2 to detect stretched membranes with antibody-like affinity, providing a quantitative basis for understanding mechanotransduction by C2-like domains.
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8
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Fu Y, Zeno WF, Stachowiak JC, Johnson ME. A continuum membrane model can predict curvature sensing by helix insertion. SOFT MATTER 2021; 17:10649-10663. [PMID: 34792524 PMCID: PMC8877990 DOI: 10.1039/d1sm01333e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein domains, such as ENTH (epsin N-terminal homology) and BAR (bin/amphiphysin/rvs), contain amphipathic helices that drive preferential binding to curved membranes. However, predicting how the physical parameters of these domains control this 'curvature sensing' behavior is challenging due to the local membrane deformations generated by the nanoscopic helix on the surface of a large sphere. We here use a deformable continuum model that accounts for the physical properties of the membrane and the helix insertion to predict curvature sensing behavior, with direct validation against multiple experimental datasets. We show that the insertion can be modeled as a local change to the membrane's spontaneous curvature, cins0, producing excellent agreement with the energetics extracted from experiments on ENTH binding to vesicles and cylinders, and of ArfGAP helices to vesicles. For small vesicles with high curvature, the insertion lowers the membrane energy by relieving strain on a membrane that is far from its preferred curvature of zero. For larger vesicles, however, the insertion has the inverse effect, de-stabilizing the membrane by introducing more strain. We formulate here an empirical expression that accurately captures numerically calculated membrane energies as a function of both basic membrane properties (bending modulus κ and radius R) as well as stresses applied by the inserted helix (cins0 and area Ains). We therefore predict how these physical parameters will alter the energetics of helix binding to curved vesicles, which is an essential step in understanding their localization dynamics during membrane remodeling processes.
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Affiliation(s)
- Yiben Fu
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, USA.
| | - Wade F Zeno
- Mork Family Department of Chemical Engineering and Materials Science, The University of Southern California, Los Angeles, California, 90089, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Margaret E Johnson
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, USA.
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9
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Tsai FC, Simunovic M, Sorre B, Bertin A, Manzi J, Callan-Jones A, Bassereau P. Comparing physical mechanisms for membrane curvature-driven sorting of BAR-domain proteins. SOFT MATTER 2021; 17:4254-4265. [PMID: 33870384 DOI: 10.1039/d0sm01573c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Protein enrichment at specific membrane locations in cells is crucial for many cellular functions. It is well-recognized that the ability of some proteins to sense membrane curvature contributes partly to their enrichment in highly curved cellular membranes. In the past, different theoretical models have been developed to reveal the physical mechanisms underlying curvature-driven protein sorting. This review aims to provide a detailed discussion of the two continuous models that are based on the Helfrich elasticity energy, (1) the spontaneous curvature model and (2) the curvature mismatch model. These two models are commonly applied to describe experimental observations of protein sorting. We discuss how they can be used to explain the curvature-induced sorting data of two BAR proteins, amphiphysin and centaurin. We further discuss how membrane rigidity, and consequently the membrane curvature generated by BAR proteins, could influence protein organization on the curved membranes. Finally, we address future directions in extending these models to describe some cellular phenomena involving protein sorting.
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Affiliation(s)
- Feng-Ching Tsai
- Institut Curie, Université PSL, CNRS UMR168, Sorbonne Université, Laboratoire Physico Chimie Curie, 75005 Paris, France.
| | - Mijo Simunovic
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA and Department of Genetics and Development, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, NY 10032, USA
| | - Benoit Sorre
- Institut Curie, Université PSL, CNRS UMR168, Sorbonne Université, Laboratoire Physico Chimie Curie, 75005 Paris, France. and Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS, Université de Paris, Paris, France.
| | - Aurélie Bertin
- Institut Curie, Université PSL, CNRS UMR168, Sorbonne Université, Laboratoire Physico Chimie Curie, 75005 Paris, France.
| | - John Manzi
- Institut Curie, Université PSL, CNRS UMR168, Sorbonne Université, Laboratoire Physico Chimie Curie, 75005 Paris, France.
| | - Andrew Callan-Jones
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS, Université de Paris, Paris, France.
| | - Patricia Bassereau
- Institut Curie, Université PSL, CNRS UMR168, Sorbonne Université, Laboratoire Physico Chimie Curie, 75005 Paris, France.
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10
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Bozelli JC, Aulakh SS, Epand RM. Membrane shape as determinant of protein properties. Biophys Chem 2021; 273:106587. [PMID: 33865153 DOI: 10.1016/j.bpc.2021.106587] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 11/30/2022]
Abstract
Membrane lipids play a role in the modulation of a variety of biological processes. This is often achieved through fine-tuned changes in membrane physical and chemical properties. While some membrane physical properties (e.g., curvature, lipid domains, fluidity) have received increased scientific attention over the years, only recently has membrane shape emerged as an active modulator of protein properties. Biological membranes are mostly found organized into a lipid bilayer arrangement, in which the spontaneous shape is an intrinsically flat, planar morphology (in relation to the size of proteins). However, it is known that many cells and organelles have non-planar morphologies. In addition, perturbations in membrane morphology occur in a variety of biological processes. Recent studies have shown that membrane shape can modulate a variety of biological processes by determining protein properties. While membrane shape generation modulates proteins via changes in membrane mechanical properties, membrane shape recognition regulates proteins by providing the optimal surface for interaction. Hence, membranes have evolved an elegant mechanism to couple mesoscopic perturbations to molecular properties and vice-versa. In this review, the regulation of the enzymatic properties of two isoforms of mammalian diacylglycerol kinase, which play important roles in cellular signal transductions, will be used to exemplify the recent advancements in the field of membrane shape recognition, as well as future challenges and perspectives.
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Affiliation(s)
- José Carlos Bozelli
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, Ontario, Canada.
| | - Sukhvershjit S Aulakh
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, Ontario, Canada
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, Ontario, Canada.
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11
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Abstract
Cellular membranes are anything but flat structures. They display a wide variety of complex and beautiful shapes, most of which have evolved for a particular physiological reason and are adapted to accommodate certain cellular demands. In membrane trafficking events, the dynamic remodelling of cellular membranes is apparent. In clathrin-mediated endocytosis for example, the plasma membrane undergoes heavy deformation to generate and internalize a highly curved clathrin-coated vesicle. This process has become a model system to study proteins with the ability to sense and induce membrane curvature and over the last two decades numerous membrane remodelling molecules and molecular mechanisms have been identified in this process. In this review, we discuss the interaction of epsin1 ENTH domain with membranes, which is one of the best-studied examples of a peripheral and transiently membrane bending protein important for clathrin-mediated endocytosis.
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Affiliation(s)
- Claudia Steinem
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
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12
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Collado J, Kalemanov M, Campelo F, Bourgoint C, Thomas F, Loewith R, Martínez-Sánchez A, Baumeister W, Stefan CJ, Fernández-Busnadiego R. Tricalbin-Mediated Contact Sites Control ER Curvature to Maintain Plasma Membrane Integrity. Dev Cell 2019; 51:476-487.e7. [PMID: 31743662 PMCID: PMC6863395 DOI: 10.1016/j.devcel.2019.10.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 09/23/2019] [Accepted: 10/16/2019] [Indexed: 12/23/2022]
Abstract
Membrane contact sites (MCS) between the endoplasmic reticulum (ER) and the plasma membrane (PM) play fundamental roles in all eukaryotic cells. ER-PM MCS are particularly abundant in Saccharomyces cerevisiae, where approximately half of the PM surface is covered by cortical ER (cER). Several proteins, including Ist2, Scs2/22, and Tcb1/2/3 are implicated in cER formation, but the specific roles of these molecules are poorly understood. Here, we use cryo-electron tomography to show that ER-PM tethers are key determinants of cER morphology. Notably, Tcb proteins (tricalbins) form peaks of extreme curvature on the cER membrane facing the PM. Combined modeling and functional assays suggest that Tcb-mediated cER peaks facilitate the transport of lipids between the cER and the PM, which is necessary to maintain PM integrity under heat stress. ER peaks were also present at other MCS, implying that membrane curvature enforcement may be a widespread mechanism to regulate MCS function.
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Affiliation(s)
- Javier Collado
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Institute of Neuropathology, University Medical Center Göttingen, Göttingen 37099, Germany; Graduate School of Quantitative Biosciences Munich, Munich 81337, Germany
| | - Maria Kalemanov
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Graduate School of Quantitative Biosciences Munich, Munich 81337, Germany
| | - Felix Campelo
- ICFO, Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels 08860, Spain
| | - Clélia Bourgoint
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Ffion Thomas
- MRC Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland; Swiss National Centre for Competence in Research, Program Chemical Biology, Geneva 1211, Switzerland
| | - Antonio Martínez-Sánchez
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Christopher J Stefan
- MRC Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
| | - Rubén Fernández-Busnadiego
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Institute of Neuropathology, University Medical Center Göttingen, Göttingen 37099, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
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13
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Nepal B, Leveritt J, Lazaridis T. Membrane Curvature Sensing by Amphipathic Helices: Insights from Implicit Membrane Modeling. Biophys J 2019; 114:2128-2141. [PMID: 29742406 DOI: 10.1016/j.bpj.2018.03.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/24/2018] [Accepted: 03/14/2018] [Indexed: 01/09/2023] Open
Abstract
Sensing and generation of lipid membrane curvature, mediated by the binding of specific proteins onto the membrane surface, play crucial roles in cell biology. A number of mechanisms have been proposed, but the molecular understanding of these processes is incomplete. All-atom molecular dynamics simulations have offered valuable insights but are extremely demanding computationally. Implicit membrane simulations could provide a viable alternative, but current models apply only to planar membranes. In this work, the implicit membrane model 1 is extended to spherical and tubular membranes. The geometric change from planar to curved shapes is straightforward but insufficient for capturing the full curvature effect, which includes changes in lipid packing. Here, these packing effects are taken into account via the lateral pressure profile. The extended implicit membrane model 1 is tested on the wild-types and mutants of the antimicrobial peptide magainin, the ALPS motif of arfgap1, α-synuclein, and an ENTH domain. In these systems, the model is in qualitative agreement with experiments. We confirm that favorable electrostatic interactions tend to weaken curvature sensitivity in the presence of strong hydrophobic interactions but may actually have a positive effect when those are weak. We also find that binding to vesicles is more favorable than binding to tubes of the same diameter and that the long helix of α-synuclein tends to orient along the axis of tubes, whereas shorter helices tend to orient perpendicular to it. Adoption of a specific orientation could provide a mechanism for coupling protein oligomerization to tubule formation.
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Affiliation(s)
- Binod Nepal
- Department of Chemistry, City College of New York, New York, New York
| | - John Leveritt
- Department of Chemistry, Newman University, Wichita, Kansas
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, New York, New York; Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York.
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14
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Directed Supramolecular Organization of N-BAR Proteins through Regulation of H0 Membrane Immersion Depth. Sci Rep 2018; 8:16383. [PMID: 30401832 PMCID: PMC6219572 DOI: 10.1038/s41598-018-34273-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/11/2018] [Indexed: 11/12/2022] Open
Abstract
Many membrane remodeling events rely on the ability of curvature-generating N-BAR membrane proteins to organize into distinctive supramolecular configurations. Experiments have revealed a conformational switch in N-BAR proteins resulting in vesicular or tubular membrane shapes, with shallow membrane immersion of the H0 amphipathic helices of N-BAR proteins on vesicles but deep H0 immersion on tubes. We develop here a minimal elastic model of the local thinning of the lipid bilayer resulting from H0 immersion. Our model predicts that the observed conformational switch in N-BAR proteins produces a corresponding switch in the bilayer-mediated N-BAR interactions due to the H0 helices. In agreement with experiments, we find that bilayer-mediated H0 interactions oppose N-BAR multimerization for the shallow H0 membrane immersion depths measured on vesicles, but promote self-assembly of supramolecular N-BAR chains for the increased H0 membrane immersion depths measured on tubes. Finally, we consider the possibility that bilayer-mediated H0 interactions might contribute to the concerted structural reorganization of N-BAR proteins suggested by experiments. Our results indicate that the membrane immersion depth of amphipathic protein helices may provide a general molecular control parameter for membrane organization.
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15
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Haucke V, Kozlov MM. Membrane remodeling in clathrin-mediated endocytosis. J Cell Sci 2018; 131:131/17/jcs216812. [PMID: 30177505 DOI: 10.1242/jcs.216812] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clathrin-mediated endocytosis is an essential cellular mechanism by which all eukaryotic cells regulate their plasma membrane composition to control processes ranging from cell signaling to adhesion, migration and morphogenesis. The formation of endocytic vesicles and tubules involves extensive protein-mediated remodeling of the plasma membrane that is organized in space and time by protein-protein and protein-phospholipid interactions. Recent studies combining high-resolution imaging with genetic manipulations of the endocytic machinery and with theoretical approaches have led to novel multifaceted phenomenological data of the temporal and spatial organization of the endocytic reaction. This gave rise to various - often conflicting - models as to how endocytic proteins and their association with lipids regulate the endocytic protein choreography to reshape the plasma membrane. In this Review, we discuss these findings in light of the hypothesis that endocytic membrane remodeling may be determined by an interplay between protein-protein interactions, the ability of proteins to generate and sense membrane curvature, and the ability of lipids to stabilize and reinforce the generated membrane shape through adopting their lateral distribution to the local membrane curvature.
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Affiliation(s)
- Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany .,Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Takustrasse 3, 14195 Berlin, Germany
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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16
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Wang G, Galli T. Reciprocal link between cell biomechanics and exocytosis. Traffic 2018; 19:741-749. [PMID: 29943478 DOI: 10.1111/tra.12584] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/03/2018] [Accepted: 06/03/2018] [Indexed: 12/16/2022]
Abstract
A cell is able to sense the biomechanical properties of the environment such as the rigidity of the extracellular matrix and adapt its tension via regulation of plasma membrane and underlying actomyosin meshwork properties. The cell's ability to adapt to the changing biomechanical environment is important for cellular homeostasis and also cell dynamics such as cell growth and motility. Membrane trafficking has emerged as an important mechanism to regulate cell biomechanics. In this review, we summarize the current understanding of the role of cell mechanics in exocytosis, and reciprocally, the role of exocytosis in regulating cell mechanics. We also discuss how cell mechanics and membrane trafficking, particularly exocytosis, can work together to regulate cell polarity and motility.
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Affiliation(s)
- Guan Wang
- Membrane Traffic in Healthy & Diseased Brain, Center of Psychiatry and Neurosciences, INSERM U894, Sorbonne Paris-Cité, Université Paris Descartes, Paris, France
| | - Thierry Galli
- Membrane Traffic in Healthy & Diseased Brain, Center of Psychiatry and Neurosciences, INSERM U894, Sorbonne Paris-Cité, Université Paris Descartes, Paris, France
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17
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Abstract
Despite the central role of Nuclear Pore Complexes (NPCs) as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm, their large size and dynamic nature have impeded a full structural and functional elucidation. Here, we have determined a subnanometer precision structure for the entire 552-protein yeast NPC by satisfying diverse data including stoichiometry, a cryo-electron tomography map, and chemical cross-links. The structure reveals the NPC’s functional elements in unprecedented detail. The NPC is built of sturdy diagonal columns to which are attached connector cables, imbuing both strength and flexibility, while tying together all other elements of the NPC, including membrane-interacting regions and RNA processing platforms. Inwardly-directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized in distinct functional units. Taken together, this integrative structure allows us to rationalize the architecture, transport mechanism, and evolutionary origins of the NPC.
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18
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Beaven AH, Sodt AJ, Pastor RW, Koeppe RE, Andersen OS, Im W. Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes. J Chem Theory Comput 2017; 13:5054-5064. [PMID: 28870079 DOI: 10.1021/acs.jctc.7b00400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Previous experiments have shown that the lifetime of a gramicidin A dimer channel (which forms from two nonconducting monomers) in a lipid bilayer is modulated by mutations of the tryptophan (Trp) residues at the bilayer-water interface. We explore this further using extensive molecular dynamics simulations of various gA dimer and monomer mutants at the Trp positions in phosphatidylcholine bilayers with different tail lengths. gA interactions with the surrounding bilayer are strongly modulated by mutating these Trp residues. There are three principal effects: eliminating residue hydrogen bonding ability (i.e., reducing the channel-monolayer coupling strength) reduces the extent of the bilayer deformation caused by the assembled dimeric channel; a residue's size and geometry affects its orientation, leading to different hydrogen bonding partners; and increasing a residue's hydrophobicity increases the depth of gA monomer insertion relative to the bilayer center, thereby increasing the lipid bending frustration.
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Affiliation(s)
- Andrew H Beaven
- Department of Chemistry, The University of Kansas , Lawrence, Kansas 66045, United States
| | | | | | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College , New York, New York 10065, United States
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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19
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Membrane Curvature and Lipid Composition Synergize To Regulate N-Ras Anchor Recruitment. Biophys J 2017; 113:1269-1279. [PMID: 28738989 DOI: 10.1016/j.bpj.2017.06.051] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 06/26/2017] [Accepted: 06/27/2017] [Indexed: 11/22/2022] Open
Abstract
Proteins anchored to membranes through covalently linked fatty acids and/or isoprenoid groups play crucial roles in all forms of life. Sorting and trafficking of lipidated proteins has traditionally been discussed in the context of partitioning to membrane domains of different lipid composition. We recently showed that membrane shape/curvature can in itself mediate the recruitment of lipidated proteins. However, exactly how membrane curvature and composition synergize remains largely unexplored. Here we investigated how three critical structural parameters of lipids, namely acyl chain saturation, headgroup size, and acyl chain length, modulate the capacity of membrane curvature to recruit lipidated proteins. As a model system we used the lipidated minimal membrane anchor of the GTPase, N-Ras (tN-Ras). Our data revealed complex synergistic effects, whereby tN-Ras binding was higher on planar DOPC than POPC membranes, but inversely higher on curved POPC than DOPC membranes. This variation in the binding to both planar and curved membranes leads to a net increase in the recruitment by membrane curvature of tN-Ras when reducing the acyl chain saturation state. Additionally, we found increased recruitment by membrane curvature of tN-Ras when substituting PC for PE, and when decreasing acyl chain length from 14 to 12 carbons (DMPC versus DLPC). However, these variations in recruitment ability had different origins, with the headgroup size primarily influencing tN-Ras binding to planar membranes whereas the change in acyl chain length primarily affected binding to curved membranes. Molecular field theory calculations recapitulated these findings and revealed lateral pressure as an underlying biophysical mechanism dictating how curvature and composition synergize to modulate recruitment of lipidated proteins. Our findings suggest that the different compositions of cellular compartments could modulate the potency of membrane curvature to recruit lipidated proteins and thereby synergistically regulate the trafficking and sorting of lipidated proteins.
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20
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Fedorov EG, Shemesh T. Physical Model for Stabilization and Repair of Trans-endothelial Apertures. Biophys J 2017; 112:388-397. [PMID: 28122224 DOI: 10.1016/j.bpj.2016.11.3207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 11/16/2016] [Accepted: 11/28/2016] [Indexed: 01/13/2023] Open
Abstract
Bacterial toxins that disrupt the stability of contractile structures in endothelial cells promote the opening of large-scale apertures, thereby breaching the endothelium barrier. These apertures are formed by fusion of the basal and apical membranes into a tunnel that spans the height of the cell. Subsequent to the aperture formation, an active repair process, driven by a stimulated polymerization of actin, results in asymmetrical membrane protrusions and, ultimately, the closure of the aperture. Here, we propose a physics-based model for the generation, stabilization and repair of trans-endothelial apertures. Our model is based on the mechanical interplay between tension in the plasma membrane and stresses that develop within different actin structures at the aperture's periphery. We suggest that accumulation of cytoskeletal fragments around the aperture's rim during the expansion phase results in parallel bundles of actin filaments and myosin motors, generating progressively greater contraction forces that resist further expansion of the aperture. Our results indicate that closure of the tunnel is driven by mechanical stresses that develop within a cross-linked actin gel that forms at localized regions of the aperture periphery. We show that stresses within the gel are due to continuous polymerization of actin filaments against the membrane surfaces of the aperture's edges. Based on our mechanical model, we construct a dynamic simulation of the aperture repair process. Our model fully accounts for the phenomenology of the trans-endothelial aperture formation and stabilization, and recaptures the experimentally observed asymmetry of the intermediate aperture shapes during closure. We make experimentally testable predictions for localization of myosin motors to the tunnel periphery and of adhesion complexes to the edges of apertures undergoing closure, and we estimate the minimal nucleation size of cross-linked actin gel that can lead to a successful repair of the aperture.
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Affiliation(s)
- Eduard G Fedorov
- Department of Biology, Israel Institute of Technology, Haifa, Israel
| | - Tom Shemesh
- Department of Biology, Israel Institute of Technology, Haifa, Israel.
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21
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Mahata P, Das SL. Generation of wavy structure on lipid membrane by peripheral proteins: a linear elastic analysis. FEBS Lett 2017; 591:1333-1348. [DOI: 10.1002/1873-3468.12661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Paritosh Mahata
- Department of Mechanical Engineering; Birla Institute of Technology Mesra; Ranchi India
| | - Sovan Lal Das
- Department of Mechanical Engineering; Indian Institute of Technology Kharagpur; India
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22
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Bacle A, Gautier R, Jackson CL, Fuchs PFJ, Vanni S. Interdigitation between Triglycerides and Lipids Modulates Surface Properties of Lipid Droplets. Biophys J 2017; 112:1417-1430. [PMID: 28402884 DOI: 10.1016/j.bpj.2017.02.032] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/07/2017] [Accepted: 02/23/2017] [Indexed: 12/12/2022] Open
Abstract
Intracellular lipid droplets (LDs) are the main cellular site of metabolic energy storage. Their structure is unique inside the cell, with a core of esterified fatty acids and sterols, mainly triglycerides and sterol esters, surrounded by a single monolayer of phospholipids. Numerous peripheral proteins, including several that were previously associated with intracellular compartments surrounded by a lipid bilayer, have been recently shown to target the surface of LDs, but how they are able to selectively target this organelle remains largely unknown. Here, we use atomistic and coarse-grained molecular dynamics simulations to investigate the molecular properties of the LD surface and to characterize how it differs from that of a lipid bilayer. Our data suggest that although several surface properties are remarkably similar between the two structures, key differences originate from the interdigitation between surface phospholipids and core neutral lipids that occurs in LDs. This property is extremely sensitive to membrane undulations, unlike in lipid bilayers, and it strongly affects both lipid-packing defects and the lateral pressure profile. We observed a marked change in overall surface properties for surface tensions >10 mN/m, indicative of a bimodal behavior. Our simulations provide a comprehensive molecular characterization of the unique surface properties of LDs and suggest how the molecular properties of the surface lipid monolayer can be modulated by the underlying neutral lipids.
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Affiliation(s)
- Amélie Bacle
- Institut Jacques Monod, UMR 7592, CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Romain Gautier
- Université Cote d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France
| | - Catherine L Jackson
- Institut Jacques Monod, UMR 7592, CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Patrick F J Fuchs
- Institut Jacques Monod, UMR 7592, CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.
| | - Stefano Vanni
- Université Cote d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France.
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23
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Dan N. Membrane-induced interactions between curvature-generating protein domains: the role of area perturbation. AIMS BIOPHYSICS 2017. [DOI: 10.3934/biophy.2017.1.107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Gómez-Llobregat J, Elías-Wolff F, Lindén M. Anisotropic Membrane Curvature Sensing by Amphipathic Peptides. Biophys J 2016; 110:197-204. [PMID: 26745422 DOI: 10.1016/j.bpj.2015.11.3512] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/29/2015] [Accepted: 11/11/2015] [Indexed: 12/29/2022] Open
Abstract
Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodeling cell membranes. However, the molecular driving forces behind these processes are not well understood. Here, we describe an approach to study curvature sensing by simulating the interactions of single molecules with a buckled lipid bilayer. We analyze three amphipathic antimicrobial peptides, a class of membrane-associated molecules that specifically target and destabilize bacterial membranes, and find qualitatively different sensing characteristics that would be difficult to resolve with other methods. Our findings provide evidence for direction-dependent curvature sensing mechanisms in amphipathic peptides and challenge existing theories of hydrophobic insertion. The buckling approach is generally applicable to a wide range of curvature-sensing molecules, and our results provide strong motivation to develop new experimental methods to track position and orientation of membrane proteins.
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Affiliation(s)
- Jordi Gómez-Llobregat
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Federico Elías-Wolff
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Martin Lindén
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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25
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Hohendahl A, Roux A, Galli V. Structural insights into the centronuclear myopathy-associated functions of BIN1 and dynamin 2. J Struct Biol 2016; 196:37-47. [PMID: 27343996 PMCID: PMC5039012 DOI: 10.1016/j.jsb.2016.06.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 01/10/2023]
Abstract
Centronuclear myopathies (CNMs) are genetic diseases whose symptoms are muscle weakness and atrophy (wasting) and centralised nuclei. Recent human genetic studies have isolated several groups of mutations. Among them, many are found in two interacting proteins essential to clathrin-mediated endocytosis, dynamin and the BIN-Amphiphysin-Rvs (BAR) protein BIN1/amphiphysin 2. In this review, by using structural and functional data from the study of endocytosis mainly, we discuss how the CNM mutations could affect the structure and the function of these ubiquitous proteins and cause the muscle-specific phenotype. The literature shows that both proteins are involved in the plasma membrane tubulation required for T-tubule biogenesis. However, this system also requires the regulation of the dynamin-mediated membrane fission, and the formation of a stable protein-scaffold to maintain the T-tubule structure. We discuss how the specific functions, isoforms and partners (myotubularin in particular) of these two proteins can lead to the establishment of muscle-specific features.
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Affiliation(s)
- Annika Hohendahl
- Biochemistry Department, University of Geneva, CH-1211 Geneva, Switzerland
| | - Aurélien Roux
- Biochemistry Department, University of Geneva, CH-1211 Geneva, Switzerland; Swiss National Centre for Competence in Research Programme Chemical Biology, CH-1211 Geneva, Switzerland.
| | - Valentina Galli
- Biochemistry Department, University of Geneva, CH-1211 Geneva, Switzerland
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26
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Schweitzer Y, Shemesh T, Kozlov MM. A Model for Shaping Membrane Sheets by Protein Scaffolds. Biophys J 2016; 109:564-73. [PMID: 26244738 DOI: 10.1016/j.bpj.2015.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/31/2015] [Accepted: 06/02/2015] [Indexed: 01/16/2023] Open
Abstract
Membranes of peripheral endoplasmic reticulum form intricate morphologies consisting of tubules and sheets as basic elements. The physical mechanism of endoplasmic-reticulum shaping has been suggested to originate from the elastic behavior of the sheet edges formed by linear arrays of oligomeric protein scaffolds. The heart of this mechanism, lying in the relationships between the structure of the protein scaffolds and the effective intrinsic shapes and elastic properties of the sheets' edges, has remained hypothetical. Here we provide a detailed computational analysis of these issues. By minimizing the elastic energy of membrane bending, we determine the effects of a rowlike array of semicircular arclike membrane scaffolds on generation of a membrane fold, which shapes the entire membrane surface into a flat double-membrane sheet. We show, quantitatively, that the sheet's edge line tends to adopt a positive or negative curvature depending on the scaffold's geometrical parameters. We compute the effective elastic properties of the sheet edge and analyze the dependence of the equilibrium distance between the scaffolds along the edge line on the scaffold geometry.
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Affiliation(s)
- Yonatan Schweitzer
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel; Nuclear Physics Division, Soreq Nuclear Research Center, Yavne, Israel
| | - Tom Shemesh
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel.
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27
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Destainville N, Schmidt TH, Lang T. Where Biology Meets Physics--A Converging View on Membrane Microdomain Dynamics. CURRENT TOPICS IN MEMBRANES 2015; 77:27-65. [PMID: 26781829 DOI: 10.1016/bs.ctm.2015.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
For several decades, the phenomenon of membrane component segregation into microdomains has been a well-known and highly debated subject, and varying concepts including the raft hypothesis, the fence-and-picket model, hydrophobic-mismatch, and specific protein-protein interactions have been offered as explanations. Here, we review the level of insight into the molecular architecture of membrane domains one is capable of obtaining through biological experimentation. Using SNARE proteins as a paradigm, comprehensive data suggest that several dozens of molecules crowd together into almost circular spots smaller than 100 nm. Such clusters are highly dynamical as they constantly capture and lose molecules. The organization has a strong influence on the functional availability of proteins and likely provides a molecular scaffold for more complex protein networks. Despite this high level of insight, fundamental open questions remain, applying not only to SNARE protein domains but more generally to all types of membrane domains. In this context, we explain the view of physical models and how they are beneficial in advancing our concept of micropatterning. While biological models generally remain qualitative and descriptive, physics aims towards making them quantitative and providing reproducible numbers, in order to discriminate between different mechanisms which have been proposed to account for experimental observations. Despite the fundamental differences in biological and physical approaches as far as cell membrane microdomains are concerned, we are able to show that convergence on common points of views is in reach.
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Affiliation(s)
- Nicolas Destainville
- Laboratoire de Physique Theorique (IRSAMC), Universite Toulouse 3-Paul Sabatier, UPS/CNRS, Toulouse, France
| | - Thomas H Schmidt
- Department of Membrane Biochemistry, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Thorsten Lang
- Department of Membrane Biochemistry, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
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28
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Grippa A, Buxó L, Mora G, Funaya C, Idrissi FZ, Mancuso F, Gomez R, Muntanyà J, Sabidó E, Carvalho P. The seipin complex Fld1/Ldb16 stabilizes ER-lipid droplet contact sites. J Cell Biol 2015; 211:829-44. [PMID: 26572621 PMCID: PMC4657162 DOI: 10.1083/jcb.201502070] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 10/16/2015] [Indexed: 01/11/2023] Open
Abstract
Mutations in the seipin complex components Fld1 and Ldb16 result in the loss of lipid droplet identity and phospholipid packing defects, revealing a role of this complex in the stabilization of ER–lipid droplet contact sites. Lipid droplets (LDs) are storage organelles consisting of a neutral lipid core surrounded by a phospholipid monolayer and a set of LD-specific proteins. Most LD components are synthesized in the endoplasmic reticulum (ER), an organelle that is often physically connected with LDs. How LD identity is established while maintaining biochemical and physical connections with the ER is not known. Here, we show that the yeast seipin Fld1, in complex with the ER membrane protein Ldb16, prevents equilibration of ER and LD surface components by stabilizing the contact sites between the two organelles. In the absence of the Fld1/Ldb16 complex, assembly of LDs results in phospholipid packing defects leading to aberrant distribution of lipid-binding proteins and abnormal LDs. We propose that the Fld1/Ldb16 complex facilitates the establishment of LD identity by acting as a diffusion barrier at the ER–LD contact sites.
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Affiliation(s)
- Alexandra Grippa
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Laura Buxó
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Gabriel Mora
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Charlotta Funaya
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Fatima-Zahra Idrissi
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Francesco Mancuso
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Raul Gomez
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Júlia Muntanyà
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Pedro Carvalho
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
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29
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Simunovic M, Voth GA, Callan-Jones A, Bassereau P. When Physics Takes Over: BAR Proteins and Membrane Curvature. Trends Cell Biol 2015; 25:780-792. [PMID: 26519988 DOI: 10.1016/j.tcb.2015.09.005] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/08/2015] [Accepted: 09/14/2015] [Indexed: 10/22/2022]
Abstract
Cell membranes become highly curved during membrane trafficking, cytokinesis, infection, immune response, or cell motion. Bin/amphiphysin/Rvs (BAR) domain proteins with their intrinsically curved and anisotropic shape are involved in many of these processes, but with a large spectrum of modes of action. In vitro experiments and multiscale computer simulations have contributed in identifying a minimal set of physical parameters, namely protein density on the membrane, membrane tension, and membrane shape, that control how bound BAR domain proteins behave on the membrane. In this review, we summarize the multifaceted coupling of BAR proteins to membrane mechanics and propose a simple phase diagram that recapitulates the effects of these parameters.
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Affiliation(s)
- Mijo Simunovic
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute and Computation Institute, The University of Chicago, 5735 S Ellis Avenue, Chicago, IL 60637, USA; Institut Curie, Centre de Recherche, F-75248 Paris, France
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute and Computation Institute, The University of Chicago, 5735 S Ellis Avenue, Chicago, IL 60637, USA
| | - Andrew Callan-Jones
- Université Paris Diderot, F-75205 Paris, France; CNRS, Matière et Systèmes Complexes, UMR 7057, F-75205 Paris, France
| | - Patricia Bassereau
- Institut Curie, Centre de Recherche, F-75248 Paris, France; CNRS, PhysicoChimie Curie, UMR 168, F-75248 Paris, France; Université Pierre et Marie Curie, F-75252 Paris, France.
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30
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Iversen L, Mathiasen S, Larsen JB, Stamou D. Membrane curvature bends the laws of physics and chemistry. Nat Chem Biol 2015; 11:822-5. [DOI: 10.1038/nchembio.1941] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Antonny B, Vanni S, Shindou H, Ferreira T. From zero to six double bonds: phospholipid unsaturation and organelle function. Trends Cell Biol 2015; 25:427-36. [DOI: 10.1016/j.tcb.2015.03.004] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 01/21/2023]
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Membrane tension controls the assembly of curvature-generating proteins. Nat Commun 2015; 6:7219. [PMID: 26008710 PMCID: PMC4455092 DOI: 10.1038/ncomms8219] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/18/2015] [Indexed: 12/16/2022] Open
Abstract
Proteins containing a Bin/Amphiphysin/Rvs (BAR) domain regulate membrane curvature in the cell. Recent simulations have revealed that BAR proteins assemble into linear aggregates, strongly affecting membrane curvature and its in-plane stress profile. Here, we explore the opposite question: do mechanical properties of the membrane impact protein association? By using coarse-grained molecular dynamics simulations, we show that increased surface tension significantly impacts the dynamics of protein assembly. While tensionless membranes promote a rapid formation of long-living linear aggregates of N-BAR proteins, increase in tension alters the geometry of protein association. At high tension, protein interactions are strongly inhibited. Increasing surface density of proteins leads to a wider range of protein association geometries, promoting the formation of meshes, which can be broken apart with membrane tension. Our work indicates that surface tension may play a key role in recruiting proteins to membrane-remodelling sites in the cell. BAR domain proteins are known to reshape cell membranes. Using coarse-grained molecular dynamics simulations, Simunovic and Voth demonstrate that membrane tension strongly affects the association of BAR proteins, in turn controlling their recruitment to membrane-remodelling sites.
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Ramakrishnan N, Ipsen JH, Rao M, Kumar PBS. Organelle morphogenesis by active membrane remodeling. SOFT MATTER 2015; 11:2387-2393. [PMID: 25672939 DOI: 10.1039/c4sm02311k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Intracellular organelles are subject to a steady flux of lipids and proteins through active, energy consuming transport processes. Active fission and fusion are promoted by GTPases, e.g., Arf-Coatamer and the Rab-Snare complexes, which both sense and generate local membrane curvature. Here we investigate, through Dynamical Triangulation Monte Carlo simulations, the role that these active processes play in determining the morphology and composition segregation in closed membranes. We find that the steady state shapes obtained as a result of such active processes, bear a striking resemblance to the ramified morphologies of organelles in vivo, pointing to the relevance of nonequilibrium fission-fusion in organelle morphogenesis.
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Affiliation(s)
- N Ramakrishnan
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India.
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Endocytic proteins drive vesicle growth via instability in high membrane tension environment. Proc Natl Acad Sci U S A 2015; 112:E1423-32. [PMID: 25775509 DOI: 10.1073/pnas.1418491112] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) is a key pathway for transporting cargo into cells via membrane vesicles; it plays an integral role in nutrient import, signal transduction, neurotransmission, and cellular entry of pathogens and drug-carrying nanoparticles. Because CME entails substantial local remodeling of the plasma membrane, the presence of membrane tension offers resistance to bending and hence, vesicle formation. Experiments show that in such high-tension conditions, actin dynamics is required to carry out CME successfully. In this study, we build on these pioneering experimental studies to provide fundamental mechanistic insights into the roles of two key endocytic proteins-namely, actin and BAR proteins-in driving vesicle formation in high membrane tension environment. Our study reveals an actin force-induced "snap-through instability" that triggers a rapid shape transition from a shallow invagination to a highly invaginated tubular structure. We show that the association of BAR proteins stabilizes vesicles and induces a milder instability. In addition, we present a rather counterintuitive role of BAR depolymerization in regulating the shape evolution of vesicles. We show that the dissociation of BAR proteins, supported by actin-BAR synergy, leads to considerable elongation and squeezing of vesicles. Going beyond the membrane geometry, we put forth a stress-based perspective for the onset of vesicle scission and predict the shapes and composition of detached vesicles. We present the snap-through transition and the high in-plane stress as possible explanations for the intriguing direct transformation of broad and shallow invaginations into detached vesicles in BAR mutant yeast cells.
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Beznoussenko GV, Pilyugin SS, Geerts WJC, Kozlov MM, Burger KNJ, Luini A, Derganc J, Mironov AA. Trans-membrane area asymmetry controls the shape of cellular organelles. Int J Mol Sci 2015; 16:5299-333. [PMID: 25761238 PMCID: PMC4394477 DOI: 10.3390/ijms16035299] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/04/2015] [Accepted: 02/13/2015] [Indexed: 01/08/2023] Open
Abstract
Membrane organelles often have complicated shapes and differ in their volume, surface area and membrane curvature. The ratio between the surface area of the cytosolic and luminal leaflets (trans-membrane area asymmetry (TAA)) determines the membrane curvature within different sites of the organelle. Thus, the shape of the organelle could be critically dependent on TAA. Here, using mathematical modeling and stereological measurements of TAA during fast transformation of organelle shapes, we present evidence that suggests that when organelle volume and surface area are constant, TAA can regulate transformation of the shape of the Golgi apparatus, endosomal multivesicular bodies, and microvilli of brush borders of kidney epithelial cells. Extraction of membrane curvature by small spheres, such as COPI-dependent vesicles within the Golgi (extraction of positive curvature), or by intraluminal vesicles within endosomes (extraction of negative curvature) controls the shape of these organelles. For instance, Golgi tubulation is critically dependent on the fusion of COPI vesicles with Golgi cisternae, and vice versa, for the extraction of membrane curvature into 50–60 nm vesicles, to induce transformation of Golgi tubules into cisternae. Also, formation of intraluminal ultra-small vesicles after fusion of endosomes allows equilibration of their TAA, volume and surface area. Finally, when microvilli of the brush border are broken into vesicles and microvilli fragments, TAA of these membranes remains the same as TAA of the microvilli. Thus, TAA has a significant role in transformation of organelle shape when other factors remain constant.
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Affiliation(s)
- Galina V Beznoussenko
- The FIRC Institute of Molecular Oncology, Milan 20139, Italy.
- Consorzio Mario Negri Sud, S. Maria Imbaro, Chieti 66030, Italy.
| | - Sergei S Pilyugin
- Department of Mathematics, University of Florida, Gainesville, FL 32611-8105, USA.
| | - Willie J C Geerts
- Department of Biochemical Physiology, Institute of Biomembranes, 3584 CH Utrecht, The Netherlands.
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Koert N J Burger
- Department of Biochemical Physiology, Institute of Biomembranes, 3584 CH Utrecht, The Netherlands.
| | - Alberto Luini
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Biochimica delle Proteine, Naples 80131, Italy.
| | - Jure Derganc
- Institute of Biophysics, University of Ljubljana, 1000 Ljubljana, Slovenia.
| | - Alexander A Mironov
- The FIRC Institute of Molecular Oncology, Milan 20139, Italy.
- Consorzio Mario Negri Sud, S. Maria Imbaro, Chieti 66030, Italy.
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Garten M, Prévost C, Cadart C, Gautier R, Bousset L, Melki R, Bassereau P, Vanni S. Methyl-branched lipids promote the membrane adsorption of α-synuclein by enhancing shallow lipid-packing defects. Phys Chem Chem Phys 2015; 17:15589-97. [DOI: 10.1039/c5cp00244c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reconstitution experiments on Giant Unilamellar Vesicles and Molecular Dynamics Simulations indicate that alpha-synuclein binds to neutral flat membranes in the presence of methyl-branched lipids.
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Affiliation(s)
| | | | | | - Romain Gautier
- Institut de Pharmacologie Moléculaire et Cellulaire
- Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique
- UMR 7275
- 06560 Valbonne
- France
| | - Luc Bousset
- CNRS
- Paris Saclay Institute of Neuroscience
- Gif-sur-Yvette
- France
| | - Ronald Melki
- CNRS
- Paris Saclay Institute of Neuroscience
- Gif-sur-Yvette
- France
| | | | - Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire
- Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique
- UMR 7275
- 06560 Valbonne
- France
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Vanni S, Hirose H, Barelli H, Antonny B, Gautier R. A sub-nanometre view of how membrane curvature and composition modulate lipid packing and protein recruitment. Nat Commun 2014; 5:4916. [PMID: 25222832 DOI: 10.1038/ncomms5916] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 08/05/2014] [Indexed: 02/07/2023] Open
Abstract
Two parameters of biological membranes, curvature and lipid composition, direct the recruitment of many peripheral proteins to cellular organelles. Although these traits are often studied independently, it is their combination that generates the unique interfacial properties of cellular membranes. Here, we use a combination of in vivo, in vitro and in silico approaches to provide a comprehensive map of how these parameters modulate membrane adhesive properties. The correlation between the membrane partitioning of model amphipathic helices and the distribution of lipid-packing defects in membranes of different shape and composition explains how macroscopic membrane properties modulate protein recruitment by changing the molecular topography of the membrane interfacial region. Furthermore, our results suggest that the range of conditions that can be obtained in a cellular context is remarkably large because lipid composition and curvature have, under most circumstances, cumulative effects.
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Affiliation(s)
- Stefano Vanni
- 1] Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 660 route des Lucioles, 06560 Valbonne, France [2]
| | - Hisaaki Hirose
- 1] Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 660 route des Lucioles, 06560 Valbonne, France [2]
| | - Hélène Barelli
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 660 route des Lucioles, 06560 Valbonne, France
| | - Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 660 route des Lucioles, 06560 Valbonne, France
| | - Romain Gautier
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 660 route des Lucioles, 06560 Valbonne, France
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