1
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Ke PY. Molecular Mechanism of Autophagosome-Lysosome Fusion in Mammalian Cells. Cells 2024; 13:500. [PMID: 38534345 DOI: 10.3390/cells13060500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
In eukaryotes, targeting intracellular components for lysosomal degradation by autophagy represents a catabolic process that evolutionarily regulates cellular homeostasis. The successful completion of autophagy initiates the engulfment of cytoplasmic materials within double-membrane autophagosomes and subsequent delivery to autolysosomes for degradation by acidic proteases. The formation of autolysosomes relies on the precise fusion of autophagosomes with lysosomes. In recent decades, numerous studies have provided insights into the molecular regulation of autophagosome-lysosome fusion. In this review, an overview of the molecules that function in the fusion of autophagosomes with lysosomes is provided. Moreover, the molecular mechanism underlying how these functional molecules regulate autophagosome-lysosome fusion is summarized.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
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2
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Srivatsav AT, Kapoor S. Biophysical Interaction Landscape of Mycobacterial Mycolic Acids and Phenolic Glycolipids with Host Macrophage Membranes. ACS APPLIED BIO MATERIALS 2023; 6:5555-5562. [PMID: 38015441 DOI: 10.1021/acsabm.3c00748] [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: 11/29/2023]
Abstract
Lipidic adjuvant formulations consisting of immunomodulatory mycobacterial cell wall lipids interact with host cells following administration. The impact of this cross-talk on the host membrane's structure and function is rarely given enough consideration but is imperative to rule out nonspecific perturbation underlying the adjuvant. In this work, we investigated changes in the plasma membranes of live mammalian cells after exposure to mycobacterial mycolic acid (MA) and phenolic glycolipids, two strong candidates for lipidic adjuvant therapy. We found that phenolic glycolipid 1 softened the plasma membrane, lowering membrane tension and stiffness, but MA did not significantly change the membrane characteristics. Further, phenolic glycolipid 1 had a fluidizing impact on the host plasma membrane, increasing the fluidity and the abundance of fluid-ordered-disordered coexisting lipid domains. Notably, lipid diffusion was not impacted. Overall, MA and, to a lesser extent, phenolic glycolipid 1, due to minor disruption of host cell membranes, may serve as appropriate lipids in adjuvant formulations.
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Affiliation(s)
- Aswin T Srivatsav
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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3
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Larsen AH. Molecular Dynamics Simulations of Curved Lipid Membranes. Int J Mol Sci 2022; 23:ijms23158098. [PMID: 35897670 PMCID: PMC9331392 DOI: 10.3390/ijms23158098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma membrane to the highly curved membranes of organelles, vesicles, and membrane protrusions. These curvatures are generated and sustained by curvature-inducing proteins, peptides, and lipids, and describing these mechanisms is an important scientific challenge. In addition to that, some molecules can sense membrane curvature and thereby be trafficked to specific locations. The description of curvature sensing is another fundamental challenge. Curved lipid membranes and their interplay with membrane-associated proteins can be investigated with molecular dynamics (MD) simulations. Various methods for simulating curved membranes with MD are discussed here, including tools for setting up simulation of vesicles and methods for sustaining membrane curvature. The latter are divided into methods that exploit scaffolding virtual beads, methods that use curvature-inducing molecules, and methods applying virtual forces. The variety of simulation tools allow researcher to closely match the conditions of experimental studies of membrane curvatures.
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4
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Zhang X, Kang R, Liu Y, Yan Z, Xu Y, Yue T. From reversible to irreversible: When the membrane nanotube pearling is coupled with phase separation. Colloids Surf B Biointerfaces 2021; 209:112160. [PMID: 34736219 DOI: 10.1016/j.colsurfb.2021.112160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/17/2021] [Accepted: 10/07/2021] [Indexed: 12/11/2022]
Abstract
Membrane nanotubes, which are ubiquitous in biology and act as channels maintaining transport between different cells and organelles, readily undergo pearling in response to external stimuli. Membrane nanotube pearling involves generation of heterogeneous curvature coupled with redistribution of membrane components that may interfere with the shape recovery of pearled nanotubes. However, the mechanism underlying such delicate process remains unclear and difficult to study at the molecular scale in vivo. By means of molecular dynamics simulation, here we investigate pearling of multi-component membrane nanotubes and reversibility through manipulating system temperature and osmotic pressure. With the equilibrium shape of membrane nanotubes controlled by the osmotic pressure, our results demonstrate that the process of membrane nanotube pearling can be reversible or irreversible, depending on the phase segregation state. For the pearled nanotube releasing high surface energy, different lipid components redistribute along the tube axial direction. Lipids with unsaturated tails prefer gathering at the high-curvature shrinking region, whereas the swelling region is constituted by saturated lipids forming the liquid-ordered phase of a higher bending rigidity. Such curvature sensitive phase segregation minimizes the system free energy by reducing both the membrane bending energy and line tension at the phase boundary. As such, the pearled nanotube fails to recover its shape upon retracting stimuli, suggesting irreversibility of the membrane nanotube pearling coupled with phase separation. Given importance of membrane nanotube pearling in various cellular activities, these results provide a new mechanism of controlling equilibrium shapes of membrane nanotubes in complex cellular environment.
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Affiliation(s)
- Xiaoyang Zhang
- College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Runshan Kang
- College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Yingjie Liu
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology, Ministry of Education, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
| | - Zengshuai Yan
- National Laboratory of Solid State Microstructures, School of Physics, Nanjing University, Nanjing 210093, China
| | - Yan Xu
- College of Electronic Engineering and Automation, Shandong University of Science and Technology, Qingdao 266590, China
| | - Tongtao Yue
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology, Ministry of Education, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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5
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Siggel M, Bhaskara RM, Moesser MK, D̵ikić I, Hummer G. FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes. J Phys Chem Lett 2021; 12:1926-1931. [PMID: 33591770 PMCID: PMC8028312 DOI: 10.1021/acs.jpclett.1c00031] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/10/2021] [Indexed: 05/28/2023]
Abstract
Living cells constantly remodel the shape of their lipid membranes. In the endoplasmic reticulum (ER), the reticulon homology domain (RHD) of the reticulophagy regulator 1 (RETR1/FAM134B) forms dense autophagic puncta that are associated with membrane removal by ER-phagy. In molecular dynamics (MD) simulations, we find that FAM134B-RHD spontaneously forms clusters, driven in part by curvature-mediated attractions. At a critical size, as in a nucleation process, the FAM134B-RHD clusters induce the formation of membrane buds. The kinetics of budding depends sensitively on protein concentration and bilayer asymmetry. Our MD simulations shed light on the role of FAM134B-RHD in ER-phagy and show that membrane asymmetry can be used to modulate the kinetic barrier for membrane remodeling.
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Affiliation(s)
- Marc Siggel
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Ramachandra M. Bhaskara
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
- Institute
of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Buchmann
Institute of Molecular Life Sciences, Goethe
University Frankfurt, Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany
| | - Melanie K. Moesser
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Ivan D̵ikić
- Institute
of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Max
Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Buchmann
Institute of Molecular Life Sciences, Goethe
University Frankfurt, Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
- Institute
of Biophysics, Goethe University Frankfurt, 60438 Frankfurt
am Main, Germany
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6
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Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. Influence of membrane-cortex linkers on the extrusion of membrane tubes. Biophys J 2021; 120:598-606. [PMID: 33460596 PMCID: PMC7896025 DOI: 10.1016/j.bpj.2020.12.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/10/2020] [Accepted: 12/30/2020] [Indexed: 01/06/2023] Open
Abstract
The cell membrane is an inhomogeneous system composed of phospholipids, sterols, carbohydrates, and proteins that can be directly attached to underlying cytoskeleton. The protein linkers between the membrane and the cytoskeleton are believed to have a profound effect on the mechanical properties of the cell membrane and its ability to reshape. Here, we investigate the role of membrane-cortex linkers on the extrusion of membrane tubes using computer simulations and experiments. In simulations, we find that the force for tube extrusion has a nonlinear dependence on the density of membrane-cortex attachments: at a range of low and intermediate linker densities, the force is not significantly influenced by the presence of the membrane-cortex attachments and resembles that of the bare membrane. For large concentrations of linkers, however, the force substantially increases compared with the bare membrane. In both cases, the linkers provided membrane tubes with increased stability against coalescence. We then pulled tubes from HEK cells using optical tweezers for varying expression levels of the membrane-cortex attachment protein Ezrin. In line with simulations, we observed that overexpression of Ezrin led to an increased extrusion force, while Ezrin depletion had a negligible effect on the force. Our results shed light on the importance of local protein rearrangements for membrane reshaping at nanoscopic scales.
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Affiliation(s)
- Alexandru Paraschiv
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom; MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Thibaut J Lagny
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France; Sorbonne Université, Paris, France; Institut Curie, PSL Research University CNRS UMR 144, Paris, France
| | - Christian Vanhille Campos
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom; MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Evelyne Coudrier
- Institut Curie, PSL Research University CNRS UMR 144, Paris, France
| | - Patricia Bassereau
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France; Sorbonne Université, Paris, France
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom; MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom.
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7
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Venzmer J. Superspreading - Has the mystery been unraveled? Adv Colloid Interface Sci 2021; 288:102343. [PMID: 33359962 DOI: 10.1016/j.cis.2020.102343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
Superspreading is a fascinating phenomenon first observed about 30 years ago with dilute solutions of trisiloxane surfactants on hydrophobic substrates. Although many groups all over the world have contributed considerably to solve the scientific challenges involved, the reasons why only some trisiloxane surfactants promote superspreading, whereas others of similar chemical structure behave more like ordinary surfactants, has remained a mystery up to now. A number of original papers and reviews on superspreading have been published in recent years. The driving force still proposed today is most often Marangoni flow. This is, however, in contradiction with recent results showing that superspreading only starts after a surface tension gradient between apex and leading edge has been eliminated. From foam film experiments unrelated to wetting, there is evidence for "dangling" bilayers attached to the air/water interface only in case of the superspreading trisiloxane surfactants. By combining this and other published experimental findings, a new hypothesis of the mode of action is put forward: Advancing by "rolling action" at the leading edge, and the supply of surfactant by "unzippering" of the dangling bilayers all over the surface of the drop; this hypothesis even fulfills basic thermodynamic requirements.
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8
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Drabik D, Gavutis M, Valiokas RN, Ulčinas AR. Determination of the Mechanical Properties of Model Lipid Bilayers Using Atomic Force Microscopy Indentation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13251-13262. [PMID: 33125251 DOI: 10.1021/acs.langmuir.0c02181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
By conducting a systematic study of model lipid membranes using the atomic force microscopy (AFM) indentation, we demonstrate the importance of an experimental protocol on the determination of their mechanical parameters. We refine the experimental approach by analyzing the influence of the contact mechanics models used to process the data, substrate preparation, and indenter geometry. We show that both bending rigidity and area compressibility can be determined from a single AFM indentation measurement.
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Affiliation(s)
- Dominik Drabik
- Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Martynas Gavutis
- Department of Nanoengineering, Center for Physical Sciences and Technology, Savanoriu̧ 231, Vilnius LT-02300, Lithuania
| | - Ramu Nas Valiokas
- Department of Nanoengineering, Center for Physical Sciences and Technology, Savanoriu̧ 231, Vilnius LT-02300, Lithuania
| | - Artu Ras Ulčinas
- Department of Nanoengineering, Center for Physical Sciences and Technology, Savanoriu̧ 231, Vilnius LT-02300, Lithuania
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9
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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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10
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Li S, Yan Z, Huang F, Zhang X, Yue T. How a lipid bilayer membrane responds to an oscillating nanoparticle: Promoted membrane undulation and directional wave propagation. Colloids Surf B Biointerfaces 2019; 187:110651. [PMID: 31784121 DOI: 10.1016/j.colsurfb.2019.110651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/15/2019] [Accepted: 11/16/2019] [Indexed: 01/14/2023]
Abstract
Mechanical forces acting on a plasma membrane are of essential importance to cellular functioning via inducing delicate change of the membrane shape with the underlying mechanism yet to be elucidated. Here, we introduce an oscillating nanoparticle (NP) interaction with a lipid bilayer membrane, using the coarse-grained simulation to investigate the dynamic membrane response to constrained mechanical stimulation, which is ubiquitous in biology. Our results demonstrate that, the membrane responds to an oscillating NP by generating nanoscale undulation waves, which immediately propagate through the membrane. In dynamics, propagation of the generated membrane undulation waves always starts from flattening of the region where the NP locates, thus producing a lateral force to propel the waves away from the point of stimulation. The speed of membrane undulation wave propagation is proportional to that of NP oscillation and accelerated by increasing the integral membrane surface tension, suggesting that both the membrane bending and stretching contribute to the energy driving the unique response of membrane undulation wave propagation.
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Affiliation(s)
- Shixin Li
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Zengshuai Yan
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
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11
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Siggel M, Bhaskara RM, Hummer G. Phospholipid Scramblases Remodel the Shape of Asymmetric Membranes. J Phys Chem Lett 2019; 10:6351-6354. [PMID: 31566982 DOI: 10.1021/acs.jpclett.9b02531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The cell membrane and many organellar membranes are asymmetric and highly curved. In experiments, it is challenging to reconstitute and characterize membranes that differ in the lipid composition of their leaflets. Here we use molecular dynamics simulations to study the large-scale membrane shape changes associated with lipid shuttling between asymmetric leaflets. We exploit leaflet asymmetry to create a stable, near-spherical vesicle bud connected to a flat bilayer under periodic boundary conditions. Then we demonstrate how the lipid scramblase nhTMEM16 relaxes the lipid-number asymmetry. By mediating the flipping of lipids, this transmembrane protein dissipates the mechanochemical gradient between the leaflets and drives a large-scale membrane reorganization, converting the vesicle bud into a flat membrane. Our procedure to exploit bilayer asymmetry for simulations of highly curved membranes can be used to study the function of other lipid transporters and membrane-shaping proteins.
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Affiliation(s)
- Marc Siggel
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany
| | - Ramachandra M Bhaskara
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany
- Institute of Biophysics , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
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12
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Zgorski A, Pastor RW, Lyman E. Surface Shear Viscosity and Interleaflet Friction from Nonequilibrium Simulations of Lipid Bilayers. J Chem Theory Comput 2019; 15:6471-6481. [PMID: 31476126 DOI: 10.1021/acs.jctc.9b00683] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonequilibrium simulation protocols based on shear deformations are applied to determine the surface viscosity and interleaflet friction of lipid bilayers. At high shear rates, a non-Newtonian shear thinning regime is observed, but lower shear rates yield a Newtonian plateau and results that are consistent with equilibrium measurements based on fluctuation-dissipation theorems. Application to all-atom bilayers modeled with the CHARMM36 parameter set yields values for the surface viscosity that are consistent with microscopic measurements based on membrane protein diffusion but are approximately 10 times lower than more macroscopic experimental measurements. The interleaflet friction is about 10 times lower than experimental measurements. Trends across different lipids, temperatures, and ternary liquid-disordered phase mixtures produce results that are consistent with experimental diffusion constants. Application of the protocol to the liquid-ordered phase fails to yield a Newtonian plateau, suggesting more complex rheology.
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Affiliation(s)
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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13
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The late stage of COPI vesicle fission requires shorter forms of phosphatidic acid and diacylglycerol. Nat Commun 2019; 10:3409. [PMID: 31363100 PMCID: PMC6667475 DOI: 10.1038/s41467-019-11324-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/21/2019] [Indexed: 12/19/2022] Open
Abstract
Studies on vesicle formation by the Coat Protein I (COPI) complex have contributed to a basic understanding of how vesicular transport is initiated. Phosphatidic acid (PA) and diacylglycerol (DAG) have been found previously to be required for the fission stage of COPI vesicle formation. Here, we find that PA with varying lipid geometry can all promote early fission, but only PA with shortened acyl chains promotes late fission. Moreover, diacylglycerol (DAG) acts after PA in late fission, with this role of DAG also requiring shorter acyl chains. Further highlighting the importance of the short-chain lipid geometry for late fission, we find that shorter forms of PA and DAG promote the vesiculation ability of COPI fission factors. These findings advance a general understanding of how lipid geometry contributes to membrane deformation for vesicle fission, and also how proteins and lipids coordinate their actions in driving this process.
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14
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Papavasileiou KD, Peristeras LD, Bick A, Economou IG. Molecular Dynamics Simulation of Pure n-Alkanes and Their Mixtures at Elevated Temperatures Using Atomistic and Coarse-Grained Force Fields. J Phys Chem B 2019; 123:6229-6243. [PMID: 31251061 DOI: 10.1021/acs.jpcb.9b02840] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The properties of higher n-alkanes and their mixtures is a topic of significant interest for the oil and chemical industry. However, the experimental data at high temperatures are scarce. The present study focuses on simulating n-dodecane, n-octacosane, their binary mixture at a n-dodecane mole fraction of 0.3, and a model mixture of the commercially available hydrocarbon wax SX-70 to evaluate the performance of several force fields on the reproduction of properties such as liquid densities, surface tension, and viscosities. Molecular dynamics simulations over a broad temperature range from 323.15 to 573.15 K were employed in examining a broad set of atomistic molecular models assessed for the reproduction of experimental data. The well-established united atom TraPPE (TraPPE-UA) was compared against the all atom optimized potentials for liquid simulations (OPLS) reparametrization for long n-alkanes, L-OPLS, as well as Lipid14 and MARTINI force fields. All models qualitatively reproduce the temperature dependence of the aforementioned properties, but TraPPE-UA was found to reproduce liquid densities most accurately and consistently over the entire temperature range. TraPPE-UA and MARTINI were very successful in reproducing surface tensions, and L-OPLS was found to be the most accurate in reproducing the measured viscosities as compared to the other models. Our simulations show that these widely used force fields originating from the world of biomolecular simulations are suitable candidates in the study of n-alkane properties, both in the pure and mixture states.
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Affiliation(s)
- Konstantinos D Papavasileiou
- Institute of Nanoscience and Nanotechnology, Molecular Thermodynamics and Modelling of Materials Laboratory , National Center for Scientific Research "Demokritos" , Aghia Paraskevi, Attikis, GR-15310 Athens , Greece.,Scienomics SARL , 16 rue de l'Arcade , 75008 , Paris , France
| | - Loukas D Peristeras
- Institute of Nanoscience and Nanotechnology, Molecular Thermodynamics and Modelling of Materials Laboratory , National Center for Scientific Research "Demokritos" , Aghia Paraskevi, Attikis, GR-15310 Athens , Greece
| | - Andreas Bick
- Scienomics SARL , 16 rue de l'Arcade , 75008 , Paris , France
| | - Ioannis G Economou
- Institute of Nanoscience and Nanotechnology, Molecular Thermodynamics and Modelling of Materials Laboratory , National Center for Scientific Research "Demokritos" , Aghia Paraskevi, Attikis, GR-15310 Athens , Greece.,Chemical Engineering Program , Texas A&M University at Qatar , Education City , P.O. Box 23874, Doha , Qatar
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15
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Visualizing Biological Membrane Organization and Dynamics. J Mol Biol 2019; 431:1889-1919. [DOI: 10.1016/j.jmb.2019.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 11/22/2022]
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16
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Li S, Yan Z, Luo Z, Xu Y, Huang F, Zhang X, Yi X, Yue T. Mechanics of the Formation, Interaction, and Evolution of Membrane Tubular Structures. Biophys J 2019; 116:884-892. [PMID: 30795870 DOI: 10.1016/j.bpj.2019.01.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 01/07/2019] [Accepted: 01/29/2019] [Indexed: 01/27/2023] Open
Abstract
Membrane nanotubes, also known as membrane tethers, play important functional roles in many cellular processes, such as trafficking and signaling. Although considerable progresses have been made in understanding the physics regulating the mechanical behaviors of individual membrane nanotubes, relatively little is known about the formation of multiple membrane nanotubes due to the rapid occurring process involving strong cooperative effects and complex configurational transitions. By exerting a pair of external extraction upon two separate membrane regions, here, we combine molecular dynamics simulations and theoretical analysis to investigate how the membrane nanotube formation and pulling behaviors are regulated by the separation between the pulling forces and how the membrane protrusions interact with each other. As the force separation increases, different membrane configurations are observed, including an individual tubular protrusion, a relatively less deformed protrusion with two nanotubes on its top forming a V shape, a Y-shaped configuration through nanotube coalescence via a zipper-like mechanism, and two weakly interacting tubular protrusions. The energy profile as a function of the separation is determined. Moreover, the directional flow of lipid molecules accompanying the membrane shape transition is analyzed. Our results provide new, to our knowledge, insights at a molecular level into the interaction between membrane protrusions and help in understanding the formation and evolution of intra- and intercellular membrane tubular networks involved in numerous cell activities.
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Affiliation(s)
- Shixin Li
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao, China
| | - Zengshuai Yan
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Zhen Luo
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Yan Xu
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao, China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, China
| | - Xin Yi
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing, China; Beijing Innovation Center for Engineering Science and Advanced Technology, Peking University, Beijing, China.
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao, China; Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China.
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17
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Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chem Rev 2019; 119:6227-6269. [DOI: 10.1021/acs.chemrev.8b00384] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Boyd KJ, May ER. BUMPy: A Model-Independent Tool for Constructing Lipid Bilayers of Varying Curvature and Composition. J Chem Theory Comput 2018; 14:6642-6652. [PMID: 30431272 DOI: 10.1021/acs.jctc.8b00765] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics is a powerful tool to investigate atomistic and mesoscopic phenomena in lipid bilayer systems. These studies have progressed with the advent of increased computational power, and efforts are now increasingly being directed toward investigating the role of curvature and bilayer morphology, as these are critical features of biological processes. Computational studies of lipid bilayers benefit from tools that can create starting configurations for molecular dynamics simulations, but the majority of such tools are restricted to generating flat bilayers. Generating curved bilayer configurations comes with practical complications and potential ramifications on physical properties in the simulated system if the bilayer is initiated in a high-strain state. We present a new tool for creating curved lipid bilayers that combines flexibility of shape, force field, model resolution, and bilayer composition. A key aspect of our approach is the use of the monolayer pivotal plane location to accurately estimate interleaflet area differences in a curved bilayer. Our tool is named BUMPy (Building Unique Membranes in Python), is written in Python, is fast, and has a simple command line interface.
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Affiliation(s)
- Kevin J Boyd
- Department of Molecular and Cell Biology , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Eric R May
- Department of Molecular and Cell Biology , University of Connecticut , Storrs , Connecticut 06269 , United States
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19
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Baoukina S, Ingólfsson HI, Marrink SJ, Tieleman DP. Curvature-Induced Sorting of Lipids in Plasma Membrane Tethers. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800034] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Svetlana Baoukina
- Centre for Molecular Simulation and Department of Biological Sciences; University of Calgary, 2500 University Drive NW; Calgary, AB T2N 1N4 Canada
| | - Helgi I. Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials; University of Groningen, Nijenborgh 7; Groningen 9747 AG The Netherlands
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials; University of Groningen, Nijenborgh 7; Groningen 9747 AG The Netherlands
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences; University of Calgary, 2500 University Drive NW; Calgary, AB T2N 1N4 Canada
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20
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Wan M, Gao L, Fang W. Implicit-solvent dissipative particle dynamics force field based on a four-to-one coarse-grained mapping scheme. PLoS One 2018; 13:e0198049. [PMID: 29795682 PMCID: PMC5967728 DOI: 10.1371/journal.pone.0198049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/12/2018] [Indexed: 11/30/2022] Open
Abstract
A new set of efficient solvent-free dissipative particle dynamics (DPD) force fields was developed for phospholipids and peptides. To enhance transferability, this model maps around four heavy atoms and their connected hydrogen atoms into a coarse-grained elementary bead based on functional group. The effective hybrid potential between any pair of beads is composed of a short-range repulsive soft-core potential that directly adopts the form of an explicit-solvent DPD model and a long-range attractive hydrophobic potential. The parameters of the attractive potentials for lipid molecules were obtained by fitting the explicit-solvent DPD simulation of one bead of any type in a water box, then finely tuning it until the bilayer membrane properties obtained in the explicit-solvent model were matched. These parameters were further extended to amino acids according to bead type. The structural and elastic properties of bilayer membranes, free energy profiles for a lipid flip-flop and amino acid analogues translocating across the membrane, and membrane pore formation induced by antimicrobial peptides obtained from this solvent-free DPD force field considerably agreed with the explicit-solvent DPD results. Importantly, the efficiency of this method is guaranteed to accelerate the assembly of vesicles composed of several thousand lipids by up to 50-fold, rendering the experimental liposome dynamics as well as membrane-peptide interactions feasible at accessible computational expense.
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Affiliation(s)
- Mingwei Wan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Lianghui Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
- * E-mail:
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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21
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Li T, Liu J, Cai H, Wang B, Feng Y, Liu J. Incorporation of DDR2 clusters into collagen matrix via integrin-dependent posterior remnant tethering. Int J Biol Sci 2018; 14:654-666. [PMID: 29904280 PMCID: PMC6001655 DOI: 10.7150/ijbs.24765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/13/2018] [Indexed: 12/12/2022] Open
Abstract
Cell-matrix interactions play critical roles in cell adhesion, tissue remodeling and cancer metastasis. Discoidin domain receptor 2 (DDR2) is a collagen receptor belonging to receptor tyrosine kinase (RTK) family. It is a powerful regulator of collagen deposition in the extracellular matrix (ECM). Although the oligomerization of DDR extracellular domain (ECD) proteins can affect matrix remodeling by inhibiting fibrillogenesis, it is still unknown how cellular DDR2 is incorporated into collagen matrix. Using 3-dimentional (3D) imaging for migrating cells, we identified a novel mechanism that explains how DDR2 incorporating into collagen matrix, which we named as posterior remnant tethering. We followed the de novo formation of these remnants and identified that DDR2 clusters formed at the retracting phase of a pseudopodium, then these clusters were tethered to fibrillar collagen and peeled off from the cell body to generate DDR2 containing posterior remnants. Inhibition of β1-integrin or Rac1 activity abrogated the remnant formation. Thus, our findings unveil a special cellular mechanism for DDR2 clusters incorporating into collagen matrix in an integrin-dependent manner.
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Affiliation(s)
- Tingting Li
- Jiangsu key lab of Drug Screening, Jiangsu key lab of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing 210009, China
| | - Jin'e Liu
- Jiangsu key lab of Drug Screening, Jiangsu key lab of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing 210009, China
| | - Hao Cai
- Research Center for High Altitude Medicine, Qing Hai University, Xining 810001, China
| | - Baomei Wang
- Institute of Virology, Wenzhou University, Wenzhou, 325000, China
| | | | - Jun Liu
- Jiangsu key lab of Drug Screening, Jiangsu key lab of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing 210009, China
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22
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Manni MM, Tiberti ML, Pagnotta S, Barelli H, Gautier R, Antonny B. Acyl chain asymmetry and polyunsaturation of brain phospholipids facilitate membrane vesiculation without leakage. eLife 2018. [PMID: 29543154 PMCID: PMC5903860 DOI: 10.7554/elife.34394] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Phospholipid membranes form cellular barriers but need to be flexible enough to divide by fission. Phospholipids generally contain a saturated fatty acid (FA) at position sn1 whereas the sn2-FA is saturated, monounsaturated or polyunsaturated. Our understanding of the impact of phospholipid unsaturation on membrane flexibility and fission is fragmentary. Here, we provide a comprehensive view of the effects of the FA profile of phospholipids on membrane vesiculation by dynamin and endophilin. Coupled to simulations, this analysis indicates that: (i) phospholipids with two polyunsaturated FAs make membranes prone to vesiculation but highly permeable; (ii) asymmetric sn1-saturated-sn2-polyunsaturated phospholipids provide a tradeoff between efficient membrane vesiculation and low membrane permeability; (iii) When incorporated into phospholipids, docosahexaenoic acid (DHA; omega-3) makes membranes more deformable than arachidonic acid (omega-6). These results suggest an explanation for the abundance of sn1-saturated-sn2-DHA phospholipids in synaptic membranes and for the importance of the omega-6/omega-3 ratio on neuronal functions. Surrounding each living cell is a membrane that is mainly made of fat molecules called phospholipids. Similar membranes also surround many of the structures inside cells. It is important for life that these membranes are impermeable to many molecules; for example, they do not allow ions to cross them freely. The membranes also need to be flexible and allow cells to form different shapes. Flexible membranes also allow cells to move molecules around and to divide to produce new cells. Each phospholipid includes two long chains of atoms called fatty acids. There are many fatty acids but they are typically grouped into saturated and unsaturated based on their chemical structures. The omega-3 and omega-6 fats are both groups of unsaturated fatty acids that are found in brain cells. Many phospholipids in cell membranes contain one saturated and one unsaturated fatty acid but it is not clear why. By studying fat molecules in the laboratory and combining this with simulations, Manni et al. have now examined the effects of fatty acids on membranes. The investigation showed that phospholipids with both saturated and unsaturated fatty acids strike a balance between impermeable and flexible membranes. More unsaturated fatty acids make more flexible membranes but they are too permeable to be used in cells. The experiments also revealed that omega-3 unsaturated fats aid flexibility more than omega-6. This finding may help to explain why the relative amounts of omega-3 and -6 are so important in the membranes of brain cells. The connection between the fats we eat and the fatty acids in our cells is complex. Yet, findings like these serve to remind us that we need a balanced diet of different fats to keep all our cells healthy.
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Affiliation(s)
- Marco M Manni
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur et CNRS, Valbonne, France.,Instituto Biofisika (UPV/EHU, CSIC), Leioa, Spain
| | - Marion L Tiberti
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur et CNRS, Valbonne, France
| | - Sophie Pagnotta
- Centre Commun de Microscopie Appliquée, Université Côte d'Azur, Nice, France
| | - Hélène Barelli
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur et CNRS, Valbonne, France
| | - Romain Gautier
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur et CNRS, Valbonne, France
| | - Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur et CNRS, Valbonne, France
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23
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Tian F, Yue T, Dong W, Yi X, Zhang X. Size-dependent formation of membrane nanotubes: continuum modeling and molecular dynamics simulations. Phys Chem Chem Phys 2018; 20:3474-3483. [DOI: 10.1039/c7cp06212e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
With continuum theory and molecular dynamics simulations we demonstrated that the lipid membrane upon extraction exhibits size- and tension-dependent mechanical behaviors, and different structural lipid rearrangements in different leaflets.
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Affiliation(s)
- Falin Tian
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
- Laboratoire de Chimie
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao 266580
- China
| | - Wei Dong
- Laboratoire de Chimie
- Ecole Normale Superieure de Lyon
- 69364 Lyon Cedex 07
- France
| | - Xin Yi
- Department of Mechanics and Engineering Science
- College of Engineering
- Peking University
- Beijing 100871
- China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
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24
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Andolfi L, Murello A, Cassese D, Ban J, Dal Zilio S, Lazzarino M. High aspect ratio silicon nanowires control fibroblast adhesion and cytoskeleton organization. NANOTECHNOLOGY 2017; 28:155102. [PMID: 28177298 DOI: 10.1088/1361-6528/aa5f3a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cell-cell and cell-matrix interactions are essential to the survival and proliferation of most cells, and are responsible for triggering a wide range of biochemical pathways. More recently, the biomechanical role of those interactions was highlighted, showing, for instance, that adhesion forces are essential for cytoskeleton organization. Silicon nanowires (Si NWs) with their small size, high aspect ratio and anisotropic mechanical response represent a useful model to investigate the forces involved in the adhesion processes and their role in cellular development. In this work we explored and quantified, by single cell force spectroscopy (SCFS), the interaction of mouse embryonic fibroblasts with a flexible forest of Si NWs. We observed that the cell adhesion forces are comparable to those found on collagen and bare glass coverslip, analogously the membrane tether extraction forces are similar to that on collagen but stronger than that on bare flat glass. Cell survival did not depend significantly on the substrate, although a reduced proliferation after 36 h was observed. On the contrary both cell morphology and cytoskeleton organization revealed striking differences. The cell morphology on Si-NW was characterized by a large number of filopodia and a significant decrease of the cell mobility. The cytoskeleton organization was characterized by the absence of actin fibers, which were instead dominant on collagen and flat glass support. Such findings suggest that the mechanical properties of disordered Si NWs, and in particular their strong asymmetry, play a major role in the adhesion, morphology and cytoskeleton organization processes. Indeed, while adhesion measurements by SCFS provide out-of-plane forces values consistent with those measured on conventional substrates, weaker in-plane forces hinder proper cytoskeleton organization and migration processes.
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Affiliation(s)
- Laura Andolfi
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche (IOM-CNR) Basovizza, Area Science Park, I-34149 Trieste, Italy
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25
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Bubnis G, Risselada HJ, Grubmüller H. Exploiting Lipid Permutation Symmetry to Compute Membrane Remodeling Free Energies. PHYSICAL REVIEW LETTERS 2016; 117:188102. [PMID: 27834997 DOI: 10.1103/physrevlett.117.188102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Indexed: 05/26/2023]
Abstract
A complete physical description of membrane remodeling processes, such as fusion or fission, requires knowledge of the underlying free energy landscapes, particularly in barrier regions involving collective shape changes, topological transitions, and high curvature, where Canham-Helfrich (CH) continuum descriptions may fail. To calculate these free energies using atomistic simulations, one must address not only the sampling problem due to high free energy barriers, but also an orthogonal sampling problem of combinatorial complexity stemming from the permutation symmetry of identical lipids. Here, we solve the combinatorial problem with a permutation reduction scheme to map a structural ensemble into a compact, nondegenerate subregion of configuration space, thereby permitting straightforward free energy calculations via umbrella sampling. We applied this approach, using a coarse-grained lipid model, to test the CH description of bending and found sharp increases in the bending modulus for curvature radii below 10 nm. These deviations suggest that an anharmonic bending term may be required for CH models to give quantitative energetics of highly curved states.
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Affiliation(s)
- Greg Bubnis
- Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Herre Jelger Risselada
- Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen 37077, Germany
- Chemistry Department, Leibniz Institute of Surface Modification, Leipzig 04318, Germany
- Deptartment of Theoretical Physics, Georg-August University Göttingen, Göttingen 37077, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen 37077, Germany
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26
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Benítez R, Bolós VJ. Searching events in AFM force-extension curves: A wavelet approach. Microsc Res Tech 2016; 80:153-159. [DOI: 10.1002/jemt.22720] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 05/26/2016] [Accepted: 06/13/2016] [Indexed: 11/09/2022]
Affiliation(s)
- R. Benítez
- Dpto. Matemáticas; Centro Universitario de Plasencia, Universidad de Extremadura; Avda. Virgen del Puerto 2 Plasencia (Cáceres) 10600 Spain
| | - V. J. Bolós
- Dpto. Matemáticas para la Economía y la Empresa, Facultad de Economía; Universidad de Valencia; Avda. Tarongers s/n Valencia 46022 Spain
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27
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Wang X, Deserno M. Determining the Lipid Tilt Modulus by Simulating Membrane Buckles. J Phys Chem B 2016; 120:6061-73. [DOI: 10.1021/acs.jpcb.6b02016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Xin Wang
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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28
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Sarshar M, Lu T, Anvari B. Combined optical micromanipulation and interferometric topography (COMMIT). BIOMEDICAL OPTICS EXPRESS 2016; 7:1365-74. [PMID: 27446661 PMCID: PMC4929647 DOI: 10.1364/boe.7.001365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/09/2016] [Accepted: 03/14/2016] [Indexed: 05/13/2023]
Abstract
Optical tweezers have emerged as a prominent light-based tool for pico-Newton (pN) force microscopy in mechanobiological studies. However, the efficacy of optical tweezers are limited in applications where concurrent metrology of the nano-sized structures under interrogation is essential to the quantitative analysis of its mechanical properties and various mechanotransduction events. We have developed an all-optical platform delivering pN force resolution in parallel with nano-scale structural imaging of the biological sample by combining optical tweezers with interferometric quantitative phase microscopy. These capabilities allow real-time micromanipulation and label-free measurement of sample's nanostructures and nanomechanical responses, opening avenues to a wide range of new research possibilities and applications in biology.
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29
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Kataoka-Hamai C, Kaizuka Y, Taguchi T. Binding of Lipopolysaccharide and Cholesterol-Modified Gelatin on Supported Lipid Bilayers: Effect of Bilayer Area Confinement and Bilayer Edge Tension. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1250-1258. [PMID: 26735125 DOI: 10.1021/acs.langmuir.5b04302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Binding of amphiphilic molecules to supported lipid bilayers (SLBs) often results in lipid fibril extension from the SLBs. Previous studies proposed that amphiphiles with large and flexible hydrophilic regions trigger lipid fibril formation in SLBs by inducing membrane curvature via their hydrophilic regions. However, no experimental studies have verified this mechanism of fibril formation. In this work, we investigated the binding of lipopolysaccharide (LPS) and cholesterol-modified gelatin to SLBs using fluorescence microscopy. SLBs with restricted and unrestricted bilayer areas were employed to identify the mechanism of fibril generation. We show that the main cause of lipid fibril formation is an approximately 20% expansion in the bilayer area rather than increased membrane curvature. The data indicate that bilayer area confinement plays a critical role in morphological changes of SLBs even when bound amphiphilic molecules have a large hydrophilic domain. We also show that bilayer area change after LPS insertion is dependent on the patch shape of the SLB. When an SLB patch consists of a broad bilayer segment connected to a long thin streak, bilayer area expansion mainly occurs within the bilayer streak. The results indicate that LPS insertion causes net lipid flow from the broad bilayer region to the streak area. The differential increase in area is explained by the instability of planar bilayer streaks that originate from the large energetic contribution of line tension arising along the bilayer edge.
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Affiliation(s)
- Chiho Kataoka-Hamai
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science , 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Yoshihisa Kaizuka
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science , 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Tetsushi Taguchi
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science , 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
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30
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Yue T, Tian F, Sun M, Zhang X, Huang F. Inter-tube adhesion mediates a new pearling mechanism. Phys Chem Chem Phys 2016; 18:361-74. [PMID: 26616465 DOI: 10.1039/c5cp04579g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A common mechanism for intracellular transport is the controlled shape transformation, also known as pearling, of membrane tubes. Exploring how tube pearling takes place is thus of quite importance to not only understand the bio-functions of tubes, but also promote their potential biomedical applications. While the pearling mechanism of one single tube is well understood, both the pathway and the mechanism of pearling of multiple tubes still remain unclear. Herein, by means of computer simulations we show that the tube pearling can be mediated by the inter-tube adhesion. By increasing the inter-tube adhesion strength, each tube undergoes a discontinuous transition from no pearling to thorough pearling. The discontinuous pearling transition is ascribed to the competitive variation between tube surface tension and the extent of inter-tube adhesion. Besides, the final pearling instability is also affected by tube diameter and inter-tube orientation. Thinner tubes undergo inter-tube lipid diffusion before completion of pearling. The early lipid diffusion reduces the extent of inter-tube adhesion and thus restrains the subsequent pearling. Therefore, only partial or no pearling can take place for two thinner tubes. For two perpendicular tubes, the pearling is also observed, but with different pathways and higher efficiency. The finite size effect is discussed by comparing the pearling of tubes with different lengths. It is expected that this work will not only provide new insights into the mechanism of membrane tube pearling, but also shed light on the potential applications in biomaterials science and nanomedicine.
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Affiliation(s)
- Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China.
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31
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Yue T, Xu Y, Li S, Zhang X, Huang F. Lipid extraction mediates aggregation of carbon nanospheres in pulmonary surfactant monolayers. Phys Chem Chem Phys 2016; 18:18923-33. [DOI: 10.1039/c6cp01957a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our MD simulations demonstrate that the aggregation of carbon nanospheres in PSM is in fact size-dependent and mediated by lipid extractions.
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Affiliation(s)
- Tongtao Yue
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Yan Xu
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Shixin Li
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
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32
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Bochicchio D, Monticelli L. The Membrane Bending Modulus in Experiments and Simulations. ADVANCES IN BIOMEMBRANES AND LIPID SELF-ASSEMBLY 2016. [DOI: 10.1016/bs.abl.2016.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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33
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Quantifying Molecular-Level Cell Adhesion on Electroactive Conducting Polymers using Electrochemical-Single Cell Force Spectroscopy. Sci Rep 2015; 5:13334. [PMID: 26335299 PMCID: PMC4558606 DOI: 10.1038/srep13334] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 07/21/2015] [Indexed: 01/28/2023] Open
Abstract
Single Cell Force Spectroscopy was combined with Electrochemical-AFM to quantify the adhesion between live single cells and conducting polymers whilst simultaneously applying a voltage to electrically switch the polymer from oxidized to reduced states. The cell-conducting polymer adhesion represents the non-specific interaction between cell surface glycocalyx molecules and polymer groups such as sulfonate and dodecylbenzene groups, which rearrange their orientation during electrical switching. Single cell adhesion significantly increases as the polymer is switched from an oxidized to fully reduced state, indicating stronger cell binding to sulfonate groups as opposed to hydrophobic groups. This increase in single cell adhesion is concomitant with an increase in surface hydrophilicity and uptake of cell media, driven by cation movement, into the polymer film during electrochemical reduction. Binding forces between the glycocalyx and polymer surface are indicative of molecular-level interactions and during electrical stimulation there is a decrease in both the binding force and stiffness of the adhesive bonds. The study provides insight into the effects of electrochemical switching on cell adhesion at the cell-conducting polymer interface and is more broadly applicable to elucidating the binding of cell adhesion molecules in the presence of electrical fields and directly at electrode interfaces.
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34
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Jefferys E, Sands ZA, Shi J, Sansom MS, Fowler PW. Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries. J Chem Theory Comput 2015; 11:2743-2754. [PMID: 26089745 PMCID: PMC4467903 DOI: 10.1021/ct501111d] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 02/06/2023]
Abstract
A necessary step prior to starting any membrane protein computer simulation is the creation of a well-packed configuration of protein(s) and lipids. Here, we demonstrate a method, alchembed, that can simultaneously and rapidly embed multiple proteins into arrangements of lipids described using either atomistic or coarse-grained force fields. During a short simulation, the interactions between the protein(s) and lipids are gradually switched on using a soft-core van der Waals potential. We validate the method on a range of membrane proteins and determine the optimal soft-core parameters required to insert membrane proteins. Since all of the major biomolecular codes include soft-core van der Waals potentials, no additional code is required to apply this method. A tutorial is included in the Supporting Information.
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Affiliation(s)
- Elizabeth Jefferys
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Zara A. Sands
- UCB
NewMedicines, Chemin
du Foriest, 1420 Braine-l’Alleud, Belgium
| | - Jiye Shi
- UCB
NewMedicines, Chemin
du Foriest, 1420 Braine-l’Alleud, Belgium
| | - Mark S.
P. Sansom
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Philip W. Fowler
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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35
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Yue T, Wang X, Zhang X, Huang F. Molecular modeling of interaction between lipid monolayer and graphene nanosheets: implications for pulmonary nanotoxicity and pulmonary drug delivery. RSC Adv 2015. [DOI: 10.1039/c5ra04922a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Understanding how nanoparticles interact with the pulmonary surfactant monolayer (PSM) is of great importance for safe applications in biomedicine and for evaluation of both health and environment impacts.
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Affiliation(s)
- Tongtao Yue
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- People's Republic of China
| | - Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- People's Republic of China
| | - Xianren Zhang
- State Key Laboratory of Organic–Inorganic Composites
- Beijing University of Chemical Technology
- Beijing
- People's Republic of China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- People's Republic of China
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36
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Abstract
Molecular dynamics (MD) simulations at the atomic scale are a powerful tool to study the structure and dynamics of model biological systems. However, because of their high computational cost, the time and length scales of atomistic simulations are limited. Biologically important processes, such as protein folding, ion channel gating, signal transduction, and membrane remodeling, are difficult to investigate using atomistic simulations. Coarse-graining reduces the computational cost of calculations by reducing the number of degrees of freedom in the model, allowing simulations of larger systems for longer times. In the first part of this chapter we review briefly some of the coarse-grained models available for proteins, focusing on the specific scope of each model. Then we describe in more detail the MARTINI coarse-grained force field, and we illustrate how to set up and run a simulation of a membrane protein using the Gromacs software package. We explain step-by-step the preparation of the protein and the membrane, the insertion of the protein in the membrane, the equilibration of the system, the simulation itself, and the analysis of the trajectory.
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37
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Deserno M. Fluid lipid membranes: From differential geometry to curvature stresses. Chem Phys Lipids 2015; 185:11-45. [DOI: 10.1016/j.chemphyslip.2014.05.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/21/2014] [Accepted: 05/06/2014] [Indexed: 10/25/2022]
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38
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Li Y. Computer investigations of influences of molar fraction and acyl chain length of lipids on the nanoparticle–biomembrane interactions. RSC Adv 2015. [DOI: 10.1039/c4ra15249b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Structural variations of the heterogeneous membrane: (a) a water defect, (b) the membrane buckling.
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Affiliation(s)
- Yang Li
- School of Biomedical Engineering
- Tianjin Medical University
- Tianjin 300070
- P. R. China
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39
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Arnarez C, Uusitalo JJ, Masman MF, Ingólfsson HI, de Jong DH, Melo MN, Periole X, de Vries AH, Marrink SJ. Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent. J Chem Theory Comput 2014; 11:260-75. [DOI: 10.1021/ct500477k] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Clément Arnarez
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Jaakko J. Uusitalo
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Marcelo F. Masman
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Djurre H. de Jong
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Manuel N. Melo
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Alex H. de Vries
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
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40
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Falk K, Fillot N, Sfarghiu AM, Berthier Y, Loison C. Interleaflet sliding in lipidic bilayers under shear flow: comparison of the gel and fluid phases using reversed non-equilibrium molecular dynamics simulations. Phys Chem Chem Phys 2014; 16:2154-66. [PMID: 24346163 DOI: 10.1039/c3cp53238k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The friction between two rubbing surfaces lubricated by water can be diminished if they are coated with phospholipidic bilayers or brushes of polyelectrolytes. In the case of a coating by lipid membranes, the friction is lower when the lipids are in the gel phase rather than in the liquid phase. We investigated the response of fluid or gel bilayers to a mechanical load or under shear using non-equilibrium molecular dynamics simulations (NEMD) to understand whether this difference could come from intermonolayer sliding. The system is composed of a single fully hydrated bilayer of coarse grained phospholipids under a parallel shear with vorticity parallel to the bilayer. In both the liquid and the gel phases, an intermonolayer slip was measured in the velocity profile. In the liquid phase this slip is proportional to the shear stress. In the tilted gel phase of our model the stress is not systematically linear and relaxes differently when the shear is in the direction of the tilt or perpendicular to it. The impact of surface tension (or load) on the friction is different for the liquid and gel phases, but grossly the slip remains of the same order of magnitude.
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Affiliation(s)
- Kerstin Falk
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
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41
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Pinot M, Vanni S, Pagnotta S, Lacas-Gervais S, Payet LA, Ferreira T, Gautier R, Goud B, Antonny B, Barelli H. Lipid cell biology. Polyunsaturated phospholipids facilitate membrane deformation and fission by endocytic proteins. Science 2014; 345:693-7. [PMID: 25104391 DOI: 10.1126/science.1255288] [Citation(s) in RCA: 236] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Phospholipids (PLs) with polyunsaturated acyl chains are extremely abundant in a few specialized cellular organelles such as synaptic vesicles and photoreceptor discs, but their effect on membrane properties is poorly understood. Here, we found that polyunsaturated PLs increased the ability of dynamin and endophilin to deform and vesiculate synthetic membranes. When cells incorporated polyunsaturated fatty acids into PLs, the plasma membrane became more amenable to deformation by a pulling force and the rate of endocytosis was accelerated, in particular, under conditions in which cholesterol was limiting. Molecular dynamics simulations and biochemical measurements indicated that polyunsaturated PLs adapted their conformation to membrane curvature. Thus, by reducing the energetic cost of membrane bending and fission, polyunsaturated PLs may help to support rapid endocytosis.
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Affiliation(s)
- Mathieu Pinot
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Nice Sophia Antipolis and CNRS, 06560 Valbonne, France. Unité Mixte de Recherche 144, Institut Curie and CNRS, F-75248 Paris, France
| | - Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Nice Sophia Antipolis and CNRS, 06560 Valbonne, France
| | - Sophie Pagnotta
- Centre Commun de Microscopie Appliquée, Université Nice Sophia Antipolis, Parc Valrose, 06000 Nice, France
| | - Sandra Lacas-Gervais
- Centre Commun de Microscopie Appliquée, Université Nice Sophia Antipolis, Parc Valrose, 06000 Nice, France
| | - Laurie-Anne Payet
- Signalisation et Transports Ioniques Membranaires, Université de Poitiers and CNRS, Poitiers, France
| | - Thierry Ferreira
- Signalisation et Transports Ioniques Membranaires, Université de Poitiers and CNRS, Poitiers, France
| | - Romain Gautier
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Nice Sophia Antipolis and CNRS, 06560 Valbonne, France
| | - Bruno Goud
- Unité Mixte de Recherche 144, Institut Curie and CNRS, F-75248 Paris, France
| | - Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Nice Sophia Antipolis and CNRS, 06560 Valbonne, France.
| | - Hélène Barelli
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Nice Sophia Antipolis and CNRS, 06560 Valbonne, France
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42
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Chavent M, Reddy T, Goose J, Dahl ACE, Stone JE, Jobard B, Sansom MSP. Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems. Faraday Discuss 2014; 169:455-75. [PMID: 25341001 PMCID: PMC4208077 DOI: 10.1039/c3fd00145h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically comprise millions of particles. To tackle this issue, we have developed visual and quantitative analyses of molecular positions and their velocity field using path line, vector field and streamline techniques. This allows us to highlight large, transient flow-like movements of lipids and to better understand crowding within the lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics. However, the methods are flexible and can be readily applied to e.g. proteins and nanoparticles within large complex membranes. The protocols developed here are readily accessible both as a plugin for the molecular visualization program VMD and as a module for the MDAnalysis library.
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Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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43
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Sakuma Y, Taniguchi T, Kawakatsu T, Imai M. Tubular membrane formation of binary giant unilamellar vesicles composed of cylinder and inverse-cone-shaped lipids. Biophys J 2014; 105:2074-81. [PMID: 24209852 DOI: 10.1016/j.bpj.2013.09.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/20/2013] [Accepted: 09/09/2013] [Indexed: 11/28/2022] Open
Abstract
We have succeeded in controlling tubular membrane formations in binary giant unilamellar vesicles (GUVs) using a simple temperature changing between the homogeneous one-phase region and the two-phase coexistence region. The binary GUV is composed of inverse-cone (bulky hydrocarbon chains and a small headgroup) and cylinder-shaped lipids. When the temperature was set in the two-phase coexistence region, the binary GUV had a spherical shape with solidlike domains. By increasing the temperature to the homogeneous one-phase region, the excess area created by the chain melting of the lipid produced tubes inside the GUV. The tubes had a radius on the micrometer scale and were stable in the one-phase region. When we again decreased the temperature to the two-phase coexisting region, the tubes regressed and the GUVs recovered their phase-separated spherical shape. We infer that the tubular formation was based on the mechanical balance of the vesicle membrane (spontaneous tension) coupled with the asymmetric distribution of the inverse-cone-shaped lipids between the inner and outer leaflets of the vesicle (lipid sorting).
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Affiliation(s)
- Yuka Sakuma
- Department of Physics, Tohoku University, Aoba, Sendai, Japan.
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44
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Ingólfsson HI, Lopez CA, Uusitalo JJ, de Jong DH, Gopal SM, Periole X, Marrink SJ. The power of coarse graining in biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2014; 4:225-248. [PMID: 25309628 PMCID: PMC4171755 DOI: 10.1002/wcms.1169] [Citation(s) in RCA: 325] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large-scale biomolecular processes on time scales inaccessible to all-atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state-of-the-art examples of protein folding, membrane protein gating and self-assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling.
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Affiliation(s)
- Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Cesar A Lopez
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Djurre H de Jong
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Srinivasa M Gopal
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
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45
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Yue T, Zhang X, Huang F. Molecular modeling of membrane tube pearling and the effect of nanoparticle adsorption. Phys Chem Chem Phys 2014; 16:10799-809. [DOI: 10.1039/c4cp01201a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DPD simulations suggest that the membrane tube pearling can be regulated by the inner water pressure and NP adsorption.
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Affiliation(s)
- Tongtao Yue
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao, China
| | - Xianren Zhang
- Division of Molecular and Materials Simulation
- State Key Laboratory of Organic–Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao, China
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46
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Li Y. Computer simulation studies on passive recruitment dynamics of lipids induced by the adsorption of charged nanoparticles. Phys Chem Chem Phys 2014; 16:12818-25. [DOI: 10.1039/c4cp00553h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The recruitment dynamics of lipids in the biomembrane is believed to play an important role in a variety of cellular processes. (a) flip-flops, (b) lateral diffusion, (c) nanoscale domain, (d) protrusions.
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Affiliation(s)
- Yang Li
- School of Biomedical Engineering
- Tianjin Medical University
- Tianjin 300070, P. R. China
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47
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Takahashi K, Oda T, Naruse K. Coarse-grained molecular dynamics simulations of biomolecules. AIMS BIOPHYSICS 2014. [DOI: 10.3934/biophy.2014.1.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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48
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Hu M, de Jong DH, Marrink SJ, Deserno M. Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model. Faraday Discuss 2013; 161:365-82; discussion 419-59. [PMID: 23805750 DOI: 10.1039/c2fd20087b] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We calculate the Gaussian curvature modulus kappa of a systematically coarse-grained (CG) one-component lipid membrane by applying the method recently proposed by Hu et al. [Biophys. J., 2012, 102, 1403] to the MARTINI representation of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). We find the value kappa/kappa = -1.04 +/- 0.03 for the elastic ratio between the Gaussian and the mean curvature modulus and deduce kappa(m)/kappa(m) = -0.98 +/- 0.09 for the monolayer elastic ratio, where the latter is based on plausible assumptions for the distance z0 of the monolayer neutral surface from the bilayer midplane and the spontaneous lipid curvature K(0m). By also analyzing the lateral stress profile sigma0(z) of our system, two other lipid types and pertinent data from the literature, we show that determining K(0m) and kappa through the first and second moment of sigma0(z) gives rise to physically implausible values for these observables. This discrepancy, which we previously observed for a much simpler CG model, suggests that the moment conditions derived from simple continuum assumptions miss the effect of physically important correlations in the lipid bilayer.
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Affiliation(s)
- Mingyang Hu
- Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
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49
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Bennett WD, Chen AW, Donnini S, Groenhof G, Tieleman DP. Constant pH simulations with the coarse-grained MARTINI model — Application to oleic acid aggregates. CAN J CHEM 2013. [DOI: 10.1139/cjc-2013-0010] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Long chain fatty acids are biologically important molecules with complex and pH sensitive aggregation behavior. The carboxylic head group of oleic acid is ionizable, with the pKa shifting to larger values, even above a value of 7, in certain aggregate states. While experiments have determined the macroscopic phase behavior, we have yet to understand the molecular level details for this complex behavior. This level of detail is likely required to fully appreciate the role of fatty acids in biology and for nanoscale biotechnological and industrial applications. Here, we introduce the use of constant pH molecular dynamics (MD) simulations with the coarse-grained MARTINI model and apply the method to oleic acid aggregates and a model lipid bilayer. By running simulations at different constant pH values, we determined titration curves and the resulting pKa for oleic acid in different environments. The coarse-grained model predicts positive pKa shifts, with a shift from 4.8 in water to 6.5 in a small micelle, and 6.6 in a dioleoylphosphatidylcholine (DOPC) bilayer, similar to experimental estimates. The size of the micelles increased as the pH increased, and correlated with the fraction of deprotonated oleic acid. We show this combination of constant pH MD and the coarse-grained MARTINI model can be used to model pH-dependent surfactant phase behavior. This suggests a large number of potential new applications of large-scale MARTINI simulations in other biological systems with ionizable molecules.
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Affiliation(s)
- W.F. Drew Bennett
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Alexander W. Chen
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Serena Donnini
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Gerrit Groenhof
- Department of Chemistry and Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - D. Peter Tieleman
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
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50
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Xie X, Xu AM, Angle MR, Tayebi N, Verma P, Melosh NA. Mechanical model of vertical nanowire cell penetration. NANO LETTERS 2013; 13:6002-8. [PMID: 24237230 DOI: 10.1021/nl403201a] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Direct access into cells' interiors is essential for biomolecular delivery, gene transfection, and electrical recordings yet is challenging due to the cell membrane barrier. Recently, molecular delivery using vertical nanowires (NWs) has been demonstrated for introducing biomolecules into a large number of cells in parallel. However, the microscopic understanding of how and when the nanowires penetrate cell membranes is still lacking, and the degree to which actual membrane penetration occurs is controversial. Here we present results from a mechanical continuum model of elastic cell membrane penetration through two mechanisms, namely through "impaling" as cells land onto a bed of nanowires, and through "adhesion-mediated" penetration, which occurs as cells spread on the substrate and generate adhesion force. Our results reveal that penetration is much more effective through the adhesion mechanism, with NW geometry and cell stiffness being critically important. Stiffer cells have higher penetration efficiency, but are more sensitive to NW geometry. These results provide a guide to designing nanowires for applications in cell membrane penetration.
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Affiliation(s)
- Xi Xie
- Department of Materials Science and Engineering, Stanford University , Stanford, California 94305, United States
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