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Sarkar S, Tran N, Rashid MH, Le TC, Yarovsky I, Conn CE, Drummond CJ. Toward Cell Membrane Biomimetic Lipidic Cubic Phases: A High-Throughput Exploration of Lipid Compositional Space. ACS APPLIED BIO MATERIALS 2018; 2:182-195. [DOI: 10.1021/acsabm.8b00539] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Sampa Sarkar
- School of Science, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Nhiem Tran
- School of Science, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Md Harunur Rashid
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Tu C. Le
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Charlotte E. Conn
- School of Science, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Calum J. Drummond
- School of Science, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
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52
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NOMOTO T, TAKAHASHI M, FUJII T, CHIARI L, TOYOTA T, FUJINAMI M. Effects of Cholesterol Concentration and Osmolarity on the Fluidity and Membrane Tension of Free-standing Black Lipid Membranes. ANAL SCI 2018; 34:1237-1242. [DOI: 10.2116/analsci.18p200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Tomonori NOMOTO
- Department of Applied Chemistry and Biotechnology, Chiba University
| | | | - Takuya FUJII
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Luca CHIARI
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Taro TOYOTA
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
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53
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Wenzel M, Vischer NOE, Strahl H, Hamoen LW. Assessing Membrane Fluidity and Visualizing Fluid Membrane Domains in Bacteria Using Fluorescent Membrane Dyes. Bio Protoc 2018; 8:e3063. [PMID: 34532528 DOI: 10.21769/bioprotoc.3063] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/06/2018] [Accepted: 10/29/2018] [Indexed: 11/02/2022] Open
Abstract
Membrane fluidity is a key parameter of bacterial membranes that undergoes quick adaptation in response to environmental challenges and has recently emerged as an important factor in the antibacterial mechanism of membrane-targeting antibiotics. The specific level of membrane fluidity is not uniform across the bacterial cell membrane. Rather, specialized microdomains associated with different cellular functions can exhibit fluidity values that significantly deviate from the average. Assessing changes in the overall membrane fluidity and formation of membrane microdomains is therefore pivotal to understand both the functional organization of the bacterial cell membrane as well as antibiotic mechanisms. Here we describe how two fluorescent membrane dyes, laurdan and DiIC12, can be employed to assess membrane fluidity in living bacteria. We focus on Bacillus subtilis, since this organism has been relatively well-studied with respect to membrane domains. However, we also describe how these assays can be adapted for other bacteria such as Staphylococcus aureus and Streptococcus pneumoniae.
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Affiliation(s)
- Michaela Wenzel
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.,Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Location VUMC, Amsterdam, The Netherlands
| | - Norbert O E Vischer
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Leendert W Hamoen
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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54
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Distribution of mechanical stress in the Escherichia coli cell envelope. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2566-2575. [PMID: 30278180 DOI: 10.1016/j.bbamem.2018.09.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 09/14/2018] [Accepted: 09/26/2018] [Indexed: 01/05/2023]
Abstract
The cell envelope in Gram-negative bacteria comprises two distinct membranes with a cell wall between them. There has been a growing interest in understanding the mechanical adaptation of this cell envelope to the osmotic pressure (or turgor pressure), which is generated by the difference in the concentration of solutes between the cytoplasm and the external environment. However, it remains unexplored how the cell wall, the inner membrane (IM), and the outer membrane (OM) effectively protect the cell from this pressure by bearing the resulting surface tension, thus preventing the formation of inner membrane bulges, abnormal cell morphology, spheroplasts and cell lysis. In this study, we have used molecular dynamics (MD) simulations combined with experiments to resolve how and to what extent models of the IM, OM, and cell wall respond to changes in surface tension. We calculated the area compressibility modulus of all three components in simulations from tension-area isotherms. Experiments on monolayers mimicking individual leaflets of the IM and OM were also used to characterize their compressibility. While the membranes become softer as they expand, the cell wall exhibits significant strain stiffening at moderate to high tensions. We integrate these results into a model of the cell envelope in which the OM and cell wall share the tension at low turgor pressure (0.3 atm) but the tension in the cell wall dominates at high values (>1 atm).
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55
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Accurate In Silico Modeling of Asymmetric Bilayers Based on Biophysical Principles. Biophys J 2018; 115:1638-1643. [PMID: 30297133 DOI: 10.1016/j.bpj.2018.09.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/20/2018] [Accepted: 09/07/2018] [Indexed: 12/24/2022] Open
Abstract
Technological advances in the last decade have enabled the study of ever more complex and physiologically relevant model membranes to help dispel the mystery surrounding the role of plasma membrane asymmetry in various cellular processes. The slowly accumulating body of experimental data is fueling renewed interest in and the need for computational methods to support interpretations and address a wide range of problems that are still not amenable to direct experimental study. The specific appeal of molecular dynamics simulations for this purpose lies in their ability to access information at atomic resolution, which is useful for the formulation of testable mechanistic hypotheses. But, the range of questions that can be addressed reliably with such simulations is determined by the appropriate construction and simulation of asymmetric bilayer models. One essential way to achieve this goal is to follow rigorous biophysical criteria and principles. In this context, we show that the requirement for a robust comparison between the properties of simulated asymmetric and symmetric model membranes is for the tension in each bilayer leaflet to be zero. Commonly used methods for constructing asymmetric bilayers, including matching the average areas of the leaflets from the corresponding symmetric systems, do not ensure zero leaflet tension, thus precluding physically realistic changes in the areas of the two leaflets. We present, to our knowledge, a new method for identifying the ideal lipid packing in bilayers with different leaflet compositions that achieves the zero-tension goal, and discuss the basic principles underlying the biophysically correct computational study of asymmetric membranes.
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56
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Holme M, Rashid MH, Thomas MR, Barriga HMG, Herpoldt K, Heenan RK, Dreiss CA, Bañuelos JL, Xie HN, Yarovsky I, Stevens MM. Fate of Liposomes in the Presence of Phospholipase C and D: From Atomic to Supramolecular Lipid Arrangement. ACS CENTRAL SCIENCE 2018; 4:1023-1030. [PMID: 30159399 PMCID: PMC6107861 DOI: 10.1021/acscentsci.8b00286] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Indexed: 05/04/2023]
Abstract
Understanding the origins of lipid membrane bilayer rearrangement in response to external stimuli is an essential component of cell biology and the bottom-up design of liposomes for biomedical applications. The enzymes phospholipase C and D (PLC and PLD) both cleave the phosphorus-oxygen bonds of phosphate esters in phosphatidylcholine (PC) lipids. The atomic position of this hydrolysis reaction has huge implications for the stability of PC-containing self-assembled structures, such as the cell wall and lipid-based vesicle drug delivery vectors. While PLC converts PC to diacylglycerol (DAG), the interaction of PC with PLD produces phosphatidic acid (PA). Here we present a combination of small-angle scattering data and all-atom molecular dynamics simulations, providing insights into the effects of atomic-scale reorganization on the supramolecular assembly of PC membrane bilayers upon enzyme-mediated incorporation of DAG or PA. We observed that PC liposomes completely disintegrate in the presence of PLC, as conversion of PC to DAG progresses. At lower concentrations, DAG molecules within fluid PC bilayers form hydrogen bonds with backbone carbonyl oxygens in neighboring PC molecules and burrow into the hydrophobic region. This leads initially to membrane thinning followed by a swelling of the lamellar phase with increased DAG. At higher DAG concentrations, localized membrane tension causes a change in lipid phase from lamellar to the hexagonal and micellar cubic phases. Molecular dynamics simulations show that this destabilization is also caused in part by the decreased ability of DAG-containing PC membranes to coordinate sodium ions. Conversely, PLD-treated PC liposomes remain stable up to extremely high conversions to PA. Here, the negatively charged PA headgroup attracts significant amounts of sodium ions from the bulk solution to the membrane surface, leading to a swelling of the coordinated water layer. These findings are a vital step toward a fundamental understanding of the degradation behavior of PC lipid membranes in the presence of these clinically relevant enzymes, and toward the rational design of diagnostic and drug delivery technologies for phospholipase-dysregulation-based diseases.
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Affiliation(s)
- Margaret
N. Holme
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - M. Harunur Rashid
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Michael R. Thomas
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Hanna M. G. Barriga
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Karla−Luise Herpoldt
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Richard K. Heenan
- STFC ISIS
Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Cécile A. Dreiss
- School
of Cancer and Pharmaceutical Sciences, King’s
College London, London SE1 9NH, United Kingdom
| | - José Leobardo Bañuelos
- STFC ISIS
Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
- Department
of Physics, The University of Texas at El
Paso, El Paso, Texas 79968, United States
| | - Hai-nan Xie
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Irene Yarovsky
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
- E-mail:
| | - Molly M. Stevens
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- E-mail:
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57
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Trantidou T, Friddin MS, Salehi-Reyhani A, Ces O, Elani Y. Droplet microfluidics for the construction of compartmentalised model membranes. LAB ON A CHIP 2018; 18:2488-2509. [PMID: 30066008 DOI: 10.1039/c8lc00028j] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The design of membrane-based constructs with multiple compartments is of increasing importance given their potential applications as microreactors, as artificial cells in synthetic-biology, as simplified cell models, and as drug delivery vehicles. The emergence of droplet microfluidics as a tool for their construction has allowed rapid scale-up in generation throughput, scale-down of size, and control over gross membrane architecture. This is true on several levels: size, level of compartmentalisation and connectivity of compartments can all be programmed to various degrees. This tutorial review explains and explores the reasons behind this. We discuss microfluidic strategies for the generation of a family of compartmentalised systems that have lipid membranes as the basic structural motifs, where droplets are either the fundamental building blocks, or are precursors to the membrane-bound compartments. We examine the key properties associated with these systems (including stability, yield, encapsulation efficiency), discuss relevant device fabrication technologies, and outline the technical challenges. In doing so, we critically review the state-of-play in this rapidly advancing field.
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Affiliation(s)
- T Trantidou
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK.
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58
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Spindler S, Sibold J, Gholami Mahmoodabadi R, Steinem C, Sandoghdar V. High-Speed Microscopy of Diffusion in Pore-Spanning Lipid Membranes. NANO LETTERS 2018; 18:5262-5271. [PMID: 30047737 DOI: 10.1021/acs.nanolett.8b02240] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Pore-spanning membranes (PSMs) provide a highly attractive model system for investigating fundamental processes in lipid bilayers. We measure and compare lipid diffusion in the supported and suspended regions of PSMs prepared on a microfabricated porous substrate. Although some properties of the suspended regions in PSMs have been characterized using fluorescence studies, it has not been possible to examine the mobility of membrane components on the supported membrane parts. Here, we resolve this issue by employing interferometric scattering microscopy (iSCAT). We study the location-dependent diffusion of DOPE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) lipids (DOPE) labeled with gold nanoparticles in (1,2-dioleoyl-sn-glycero-3-phosphocholine) (DOPC) bilayers prepared on holey silicon nitride substrates that were either (i) oxygen-plasma-treated or (ii) functionalized with gold and 6-mercapto-1-hexanol. For both substrate treatments, diffusion in regions suspended on pores with diameters of 5 μm is found to be free. In the case of functionalization with gold and 6-mercapto-1-hexanol, similar diffusion coefficients are obtained for both the suspended and the supported regions, whereas for oxygen-plasma-treated surfaces, diffusion is almost 4 times slower in the supported parts of the membranes. We attribute this reduced diffusion on the supported parts in the case of oxygen-plasma-treated surfaces to larger membrane-substrate interactions, which lead to a higher membrane tension in the freestanding membrane parts. Furthermore, we find clear indications for a decrease of the diffusion constant in the freestanding regions away from the pore center. We provide a detailed characterization of the diffusion behavior in these membrane systems and discuss future directions.
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Affiliation(s)
- Susann Spindler
- Max Planck Institute for the Science of Light , Staudtstraße 2 , 91058 Erlangen , Germany
- Department of Physics , Friedrich Alexander University Erlangen-Nuremberg , Staudtstraße 5 , 91058 Erlangen , Germany
| | - Jeremias Sibold
- Institute for Organic and Biomolecular Chemistry , Tammannstraße 2 . 37077 Göttingen , Germany
| | - Reza Gholami Mahmoodabadi
- Max Planck Institute for the Science of Light , Staudtstraße 2 , 91058 Erlangen , Germany
- Department of Physics , Friedrich Alexander University Erlangen-Nuremberg , Staudtstraße 5 , 91058 Erlangen , Germany
| | - Claudia Steinem
- Institute for Organic and Biomolecular Chemistry , Tammannstraße 2 . 37077 Göttingen , Germany
- Max Planck Institute for Dynamics and Self-Organization , Am Faßberg 17 , 37077 Göttingen , Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light , Staudtstraße 2 , 91058 Erlangen , Germany
- Department of Physics , Friedrich Alexander University Erlangen-Nuremberg , Staudtstraße 5 , 91058 Erlangen , Germany
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59
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Hasan M, Saha SK, Yamazaki M. Effect of membrane tension on transbilayer movement of lipids. J Chem Phys 2018; 148:245101. [DOI: 10.1063/1.5035148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Moynul Hasan
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
| | - Samiron Kumar Saha
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
| | - Masahito Yamazaki
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
- Nanomaterials Research Division, Research Institute of Electronics, Shizuoka University, 836 Oya, Suruga-ku, Shizuoka 422-8529, Japan
- Department of Physics, Faculty of Science, Shizuoka University, Shizuoka 422-8529, Japan
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60
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Woodward X, Stimpson EE, Kelly CV. Single-lipid tracking on nanoscale membrane buds: The effects of curvature on lipid diffusion and sorting. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2064-2075. [PMID: 29856992 DOI: 10.1016/j.bbamem.2018.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/30/2018] [Accepted: 05/19/2018] [Indexed: 01/25/2023]
Abstract
Nanoscale membrane curvature in cells is critical for endocytosis/exocytosis and membrane trafficking. However, the biophysical ramifications of nanoscale membrane curvature on the behavior of lipids remain poorly understood. Here, we created an experimental model system of membrane curvature at a physiologically-relevant scale and obtained nanoscopic information on single-lipid distributions and dynamics. Supported lipid bilayers were created over 50 and 70 nm radius nanoparticles to create membrane buds. Single-molecule localization microscopy was performed with diverse mixtures of fluorescent and non-fluorescent lipids. Variations in lipid acyl tales length, saturation, head-group, and fluorescent labeling strategy were tested while maintaining a single fluid lipid phase throughout the membrane. Monte Carlo simulations were used to fit our experimental results and quantify the effects of curvature on the lipid diffusion and sorting. Whereas varying the composition of the non-fluorescent lipids yielded minimal changes to the curvature effects, the labeling strategy of the fluorescent lipids yielded highly varying effects of curvature. Most conditions yield single-population Brownian diffusion throughout the membrane; however, curvature-induced lipid sorting, slowing, and aggregation were observed in some conditions. Head-group labeled lipids such as DPPE-Texas Red and POPE-Rhodamine diffused >2.4× slower on the curved vs. the planar membranes; tail-labeled lipids such as NBD-PPC, TopFluor-PPC, and TopFluor-PIP2, as well as DiIC12 and DiIC18 displayed no significant changes in diffusion due to the membrane curvature. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
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Affiliation(s)
- Xinxin Woodward
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States
| | - Eric E Stimpson
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States
| | - Christopher V Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States.
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61
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Gilmore SF, Carpenter TS, Ingólfsson HI, Peters SKG, Henderson PT, Blanchette CD, Fischer NO. Lipid composition dictates serum stability of reconstituted high-density lipoproteins: implications for in vivo applications. NANOSCALE 2018; 10:7420-7430. [PMID: 29564446 PMCID: PMC7485573 DOI: 10.1039/c7nr09690a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanolipoprotein particles (NLPs) are reconstituted high-density lipoproteins, consisting of a phospholipid bilayer stabilized by an apolipoprotein scaffold protein. This class of nanoparticle has been a vital tool in the study of membrane proteins, and in recent years has been increasingly used for in vivo applications. Previous work demonstrated that the composition of the lipid bilayer component affects the stability of these particles in serum solutions. In the current study, NLPs assembled with phosphatidylcholine lipids featuring different acyl chain structures were systematically tested to understand the effect that lipid composition has on NLP stability in both neat serum and cell culture media supplemented with 10% serum by volume. The time at which 50% of the particles dissociate, as well as the fraction of the initial population that remains resistant to dissociation, were correlated to key parameters obtained from all-atom simulations of the corresponding lipid bilayers. A significant correlation was observed between the compressibility modulus of the lipid bilayer and particle stability in these complex biological milieu. These results can be used as a reference to tune the stability of these versatile biological nanoparticles for in vitro and in vivo applications.
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Affiliation(s)
- Sean F Gilmore
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | | | | | | | - Paul T Henderson
- University of California-Davis (UC Davis) and UC Davis Comprehensive Cancer Center, Sacramento, California 95817, USA
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62
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Effect of 5-trans Isomer of Arachidonic Acid on Model Liposomal Membranes Studied by a Combined Simulation and Experimental Approach. J Membr Biol 2018; 251:475-489. [PMID: 29610947 DOI: 10.1007/s00232-018-0029-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 03/08/2018] [Indexed: 02/07/2023]
Abstract
Unsaturated fatty acids are found in humans predominantly in the cis configuration. Fatty acids in the trans configuration are primarily the result of human processing (trans fats), but can also be formed endogenously by radical stress. The cis-trans isomerization of fatty acids by free radicals could be connected to several pathologies. Trans fats have been linked to an increased risk of coronary artery disease; however, the reasons for the resulting pathogenesis remain unclear. Here, we investigate the effect of a mono-trans isomer of arachidonic acid (C20:4-5trans, 8cis, 11cis, 14cis) produced by free radicals in physiological concentration on a model erythrocyte membrane using a combined experimental and theoretical approach. Molecular Dynamics (MD) simulations of two model lipid bilayers containing arachidonic acid and its 5-trans isomer in 3 mol% were carried out for this purpose. The 5-trans isomer formation in the phospholipids was catalyzed by HOCH2CH2S· radicals, generated from the corresponding thiol by γ-irradiation, in multilamellar vesicles of SAPC. Large unilamellar vesicles were made by the extrusion method (LUVET) as a biomimetic model for cis-trans isomerization. Atomic Force Microscopy and Dynamic Light Scattering were used to measure the average size, morphology, and the z-potential of the liposomes. Both results from MD simulations and experiments are in agreement and indicate that the two model membranes display different physicochemical properties in that the bilayers containing the trans fatty acids were more ordered and more rigid than those containing solely the cis arachidonic acid. Correspondingly, the average size of the liposomes containing trans isomers was smaller than the ones without.
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63
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Meckes B, Banga RJ, Nguyen ST, Mirkin CA. Enhancing the Stability and Immunomodulatory Activity of Liposomal Spherical Nucleic Acids through Lipid-Tail DNA Modifications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:10.1002/smll.201702909. [PMID: 29226611 PMCID: PMC5815854 DOI: 10.1002/smll.201702909] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/06/2017] [Indexed: 05/22/2023]
Abstract
Liposomal spherical nucleic acids (LSNAs) are an attractive therapeutic platform for gene regulation and immunomodulation due to their biocompatibility, chemically tunable structures, and ability to enter cells rapidly without the need for ancillary transfection agents. Such structures consist of small (<100 nm) liposomal cores functionalized with a dense, highly oriented nucleic acid shell, both of which are key components in facilitating their biological activity. Here, the properties of LSNAs synthesized using conventional methods, anchoring cholesterol terminated oligonucleotides into a liposomal core, are compared to LSNAs made by directly modifying the surface of a liposomal core containing azide-functionalized lipids with dibenzocyclooctyl-terminated oligonucleotides. The surface densities of the oligonucleotides are measured for both types of LSNAs, with the lipid-modified structures having approximately twice the oligonucleotide surface coverage. The stabilities and cellular uptake properties of these structures are also evaluated. The higher density, lipid-functionalized structures are markedly more stable than conventional cholesterol-based structures in the presence of other unmodified liposomes and serum proteins as evidenced by fluorescence assays. Significantly, this new form of LSNA exhibits more rapid cellular uptake and increased sequence-specific toll-like receptor activation in immune reporter cell lines, making it a promising candidate for immunotherapy.
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Affiliation(s)
- Brian Meckes
- Department of Chemistry, International Institute for Nanotechnology, Evanston, IL, 60208, USA
| | - Resham J Banga
- Department of Chemical and Biological Engineering, Northwestern University, International Institute for Nanotechnology, Evanston, IL, 60208, USA
| | - SonBinh T Nguyen
- Department of Chemistry, International Institute for Nanotechnology, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Chemistry, International Institute for Nanotechnology, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, International Institute for Nanotechnology, Evanston, IL, 60208, USA
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64
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Thoms VL, Hormel TT, Reyer MA, Parthasarathy R. Tension Independence of Lipid Diffusion and Membrane Viscosity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:12510-12515. [PMID: 28984459 DOI: 10.1021/acs.langmuir.7b02917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The diffusion of biomolecules at lipid membranes is governed by the viscosity of the underlying two-dimensionally fluid lipid bilayer. For common three-dimensional fluids, viscosity can be modulated by hydrostatic pressure, and pressure-viscosity data have been measured for decades. Remarkably, the two-dimensional analogue of this relationship, the dependence of molecular mobility on tension, has to the best of our knowledge never been measured for lipid bilayers, limiting our understanding of cellular mechanotransduction as well as the fundamental fluid mechanics of membranes. Here we report both molecular-scale and mesoscopic measures of fluidity in giant lipid vesicles as a function of mechanical tension applied using micropipette aspiration. Both molecular-scale data, from fluorescence recovery after photobleaching, and micron-scale data, from tracking the diffusion of phase-separated domains, show a surprisingly weak dependence of viscosity on tension, in contrast to predictions of recent molecular dynamics simulations, highlighting fundamental gaps in our understanding of membrane fluidity.
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Affiliation(s)
- Vincent L Thoms
- Department of Physics and Materials Science Institute, The University of Oregon , Eugene, Oregon 97403-1274, United States
| | - Tristan T Hormel
- Department of Physics and Materials Science Institute, The University of Oregon , Eugene, Oregon 97403-1274, United States
| | - Matthew A Reyer
- Department of Physics and Materials Science Institute, The University of Oregon , Eugene, Oregon 97403-1274, United States
| | - Raghuveer Parthasarathy
- Department of Physics and Materials Science Institute, The University of Oregon , Eugene, Oregon 97403-1274, United States
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65
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Alam Shibly SU, Ghatak C, Sayem Karal MA, Moniruzzaman M, Yamazaki M. Experimental Estimation of Membrane Tension Induced by Osmotic Pressure. Biophys J 2017; 111:2190-2201. [PMID: 27851942 DOI: 10.1016/j.bpj.2016.09.043] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 01/08/2023] Open
Abstract
Osmotic pressure (Π) induces the stretching of plasma membranes of cells or lipid membranes of vesicles, which plays various roles in physiological functions. However, there have been no experimental estimations of the membrane tension of vesicles upon exposure to Π. In this report, we estimated experimentally the lateral tension of the membranes of giant unilamellar vesicles (GUVs) when they were transferred into a hypotonic solution. First, we investigated the effect of Π on the rate constant, kp, of constant-tension (σex)-induced rupture of dioleoylphosphatidylcholine (DOPC)-GUVs using the method developed by us recently. We obtained the σex dependence of kp in GUVs under Π and by comparing this result with that in the absence of Π, we estimated the tension of the membrane due to Π at the swelling equilibrium, σosmeq. Next, we measured the volume change of DOPC-GUVs under small Π. The experimentally obtained values of σosmeq and the volume change agreed with their theoretical values within the limits of the experimental errors. Finally, we investigated the characteristics of the Π-induced pore formation in GUVs. The σosmeq corresponding to the threshold Π at which pore formation is induced is similar to the threshold tension of the σex-induced rupture. The time course of the radius change of GUVs in the Π-induced pore formation depends on the total membrane tension, σt; for small σt, the radius increased with time to an equilibrium one, which remained constant for a long time until pore formation, but for large σt, the radius increased with time and pore formation occurred before the swelling equilibrium was reached. Based on these results, we discussed the σosmeq and the Π-induced pore formation in lipid membranes.
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Affiliation(s)
- Sayed Ul Alam Shibly
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Chiranjib Ghatak
- Nanomaterials Research Division, Research Institute of Electronics, Shizuoka University, Shizuoka, Japan
| | - Mohammad Abu Sayem Karal
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Md Moniruzzaman
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Masahito Yamazaki
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan; Nanomaterials Research Division, Research Institute of Electronics, Shizuoka University, Shizuoka, Japan; Department of Physics, Faculty of Science, Shizuoka University, Shizuoka, Japan.
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66
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Alipour E, Halverson D, McWhirter S, Walker GC. Phospholipid Bilayers: Stability and Encapsulation of Nanoparticles. Annu Rev Phys Chem 2017; 68:261-283. [DOI: 10.1146/annurev-physchem-040215-112634] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Elnaz Alipour
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada;, , ,
| | - Duncan Halverson
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada;, , ,
| | - Samantha McWhirter
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada;, , ,
| | - Gilbert C. Walker
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada;, , ,
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67
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Osella S, Knippenberg S. Triggering On/Off States of Photoswitchable Probes in Biological Environments. J Am Chem Soc 2017; 139:4418-4428. [DOI: 10.1021/jacs.6b13024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Silvio Osella
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Stefan Knippenberg
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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68
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Willems N, Urtizberea A, Verre AF, Iliut M, Lelimousin M, Hirtz M, Vijayaraghavan A, Sansom MSP. Biomimetic Phospholipid Membrane Organization on Graphene and Graphene Oxide Surfaces: A Molecular Dynamics Simulation Study. ACS NANO 2017; 11:1613-1625. [PMID: 28165704 DOI: 10.1021/acsnano.6b07352] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Supported phospholipid membrane patches stabilized on graphene surfaces have shown potential in sensor device functionalization, including biosensors and biocatalysis. Lipid dip-pen nanolithography (L-DPN) is a method useful in generating supported membrane structures that maintain lipid functionality, such as exhibiting specific interactions with protein molecules. Here, we have integrated L-DPN, atomic force microscopy, and coarse-grained molecular dynamics simulation methods to characterize the molecular properties of supported lipid membranes (SLMs) on graphene and graphene oxide supports. We observed substantial differences in the topologies of the stabilized lipid structures depending on the nature of the surface (polar graphene oxide vs nonpolar graphene). Furthermore, the addition of water to SLM systems resulted in large-scale reorganization of the lipid structures, with measurable effects on lipid lateral mobility within the supported membranes. We also observed reduced lipid ordering within the supported structures relative to free-standing lipid bilayers, attributed to the strong hydrophobic interactions between the lipids and support. Together, our results provide insight into the molecular effects of graphene and graphene oxide surfaces on lipid bilayer membranes. This will be important in the design of these surfaces for applications such as biosensor devices.
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Affiliation(s)
- Nathalie Willems
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Ainhoa Urtizberea
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT) , 76344 Eggenstein-Leopoldshafen, Germany
| | - Andrea F Verre
- School of Materials and National Graphene Institute, University of Manchester , Manchester M13 9PL, United Kingdom
| | - Maria Iliut
- School of Materials and National Graphene Institute, University of Manchester , Manchester M13 9PL, United Kingdom
| | - Mickael Lelimousin
- CERMAV, CNRS and Université Grenoble Alpes , BP 53, Grenoble 38041 Cedex 9, France
| | - Michael Hirtz
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT) , 76344 Eggenstein-Leopoldshafen, Germany
| | - Aravind Vijayaraghavan
- School of Materials and National Graphene Institute, University of Manchester , Manchester M13 9PL, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
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69
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Abstract
Studying how the membrane modulates ion channel and transporter activity is challenging because cells actively regulate membrane properties, whereas existing in vitro systems have limitations, such as residual solvent and unphysiologically high membrane tension. Cell-sized giant unilamellar vesicles (GUVs) would be ideal for in vitro electrophysiology, but efforts to measure the membrane current of intact GUVs have been unsuccessful. In this work, two challenges for obtaining the "whole-GUV" patch-clamp configuration were identified and resolved. First, unless the patch pipette and GUV pressures are precisely matched in the GUV-attached configuration, breaking the patch membrane also ruptures the GUV. Second, GUVs shrink irreversibly because the membrane/glass adhesion creating the high-resistance seal (>1 GΩ) continuously pulls membrane into the pipette. In contrast, for cell-derived giant plasma membrane vesicles (GPMVs), breaking the patch membrane allows the GPMV contents to passivate the pipette surface, thereby dynamically blocking membrane spreading in the whole-GMPV mode. To mimic this dynamic passivation mechanism, beta-casein was encapsulated into GUVs, yielding a stable, high-resistance, whole-GUV configuration for a range of membrane compositions. Specific membrane capacitance measurements confirmed that the membranes were truly solvent-free and that membrane tension could be controlled over a physiological range. Finally, the potential for ion transport studies was tested using the model ion channel, gramicidin, and voltage-clamp fluorometry measurements were performed with a voltage-dependent fluorophore/quencher pair. Whole-GUV patch-clamping allows ion transport and other voltage-dependent processes to be studied while controlling membrane composition, tension, and shape.
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70
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Osella S, Murugan NA, Jena NK, Knippenberg S. Investigation into Biological Environments through (Non)linear Optics: A Multiscale Study of Laurdan Derivatives. J Chem Theory Comput 2016; 12:6169-6181. [DOI: 10.1021/acs.jctc.6b00906] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Silvio Osella
- Division of Theoretical
Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - N. Arul Murugan
- Division of Theoretical
Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Naresh K. Jena
- Division of Theoretical
Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Stefan Knippenberg
- Division of Theoretical
Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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71
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Gallardo-Rodríguez JJ, López-Rosales L, Sánchez-Mirón A, García-Camacho F, Molina-Grima E, Chalmers JJ. New insights into shear-sensitivity in dinoflagellate microalgae. BIORESOURCE TECHNOLOGY 2016; 200:699-705. [PMID: 26556404 DOI: 10.1016/j.biortech.2015.10.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/30/2015] [Accepted: 10/31/2015] [Indexed: 06/05/2023]
Abstract
A modification of a flow contraction device was used to subject shear-sensitive microalgae to well-defined hydrodynamic forces. The aim of the study was to elucidate if the inhibition of shear-induced growth commonly observed in dinoflagellate microalgae is in effect due to cell fragility that results in cell breakage even at low levels of turbulence. The microalgae assayed did not show any cell breakage even at energy dissipation rates (EDR) around 10(12)Wm(-3), implausible in culture devices. Conversely, animal cells, tested for comparison purposes, showed high physical cell damage at average EDR levels of 10(7)Wm(-3). Besides, very short exposures to high levels of EDR promoted variations in the membrane fluidity of the microalgae assayed, which might trigger mechanosensory cellular mechanisms. Average EDR values of only about 4·10(5)Wm(-3) increased cell membrane fluidity in microalgae whereas, in animal cells, they did not.
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Affiliation(s)
| | - L López-Rosales
- Chemical Engineering Area, University of Almería, 04120 Almería, Spain
| | - A Sánchez-Mirón
- Chemical Engineering Area, University of Almería, 04120 Almería, Spain
| | - F García-Camacho
- Chemical Engineering Area, University of Almería, 04120 Almería, Spain
| | - E Molina-Grima
- Chemical Engineering Area, University of Almería, 04120 Almería, Spain
| | - J J Chalmers
- Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH 43210, USA
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72
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Ding W, Palaiokostas M, Wang W, Orsi M. Effects of Lipid Composition on Bilayer Membranes Quantified by All-Atom Molecular Dynamics. J Phys Chem B 2015; 119:15263-74. [PMID: 26560961 DOI: 10.1021/acs.jpcb.5b06604] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological bilayer membranes typically contain varying amounts of lamellar and nonlamellar lipids. Lamellar lipids, such as dioleoylphosphatidylcholine (DOPC), are defined by their tendency to form the lamellar phase, ubiquitous in biology. Nonlamellar lipids, such as dioleoylphosphatidylethanolamine (DOPE), prefer instead to form nonlamellar phases, which are mostly nonbiological. However, nonlamellar lipids mix with lamellar lipids in biomembrane structures that remain overall lamellar. Importantly, changes in the lamellar vs nonlamellar lipid composition are believed to affect membrane function and modulate membrane proteins. In this work, we employ atomistic molecular dynamics simulations to quantify how a range of bilayer properties are altered by variations in the lamellar vs nonlamellar lipid composition. Specifically, we simulate five DOPC/DOPE bilayers at mixing ratios of 1/0, 3/1, 1/1, 1/3, and 0/1. We examine properties including lipid area and bilayer thickness, as well as the transmembrane profiles of electron density, lateral pressure, electric field, and dipole potential. While the bilayer structure is only marginally altered by lipid composition changes, dramatic effects are observed for the lateral pressure, electric field, and dipole potential profiles. Possible implications for membrane function are discussed.
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Affiliation(s)
- Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
| | - Wen Wang
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
| | - Mario Orsi
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
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73
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Bovigny C, Tamò G, Lemmin T, Maïno N, Dal Peraro M. LipidBuilder: A Framework To Build Realistic Models for Biological Membranes. J Chem Inf Model 2015; 55:2491-9. [PMID: 26606666 DOI: 10.1021/acs.jcim.5b00501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The physical and chemical characterization of biological membranes is of fundamental importance for understanding the functional role of lipid bilayers in shaping cells and organelles, steering vesicle trafficking and promoting membrane-protein signaling. Molecular dynamics simulations stand as a powerful tool to probe the properties of membranes at atomistic level. However, the biological membrane is highly complex, and closely mimicking its physiological constitution in silico is not a straightforward task. Here, we present LipidBuilder, a framework for creating and storing models of biologically relevant phospholipid species with acyl tails of heterogeneous composition. LipidBuilder also enables the assembly of these database-stored lipids into realistic bilayers featuring asymmetric distribution on layer leaflets and concentration of given membrane constituents as defined, for example, by lipidomics experiments. The ability of LipidBuilder to assemble robust membrane models was validated by simulating membranes of homogeneous lipid composition for which experimental data are available. Furthermore, taking advantage of the extensive lipid headgroup repertoire, we assembled models of membranes of heterogeneous nature as naturally found in viral (phage PRD1), bacterial (Salmonella enterica, Laurinavicius , S. ; Kakela , R. ; Somerharju , P. ; Bamford , D. H. ; Virology 2004 , 322 , 328 - 336 ) and plant (Chlorella kessleri, Rezanka , T. ; Podojil , M. ; J. Chromatogr. 1989 , 463 , 397 - 408 ) organisms. These realistic membrane models were built using a near-exact lipid composition revealed from analytical chemistry experiments. We suggest LipidBuilder as a useful tool to model biological membranes of near-biological complexity, and as a robust complement to the current efforts to characterize the biophysical properties of biological membrane using molecular simulation.
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Affiliation(s)
- Christophe Bovigny
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB) , CH-1015 Lausanne, Switzerland
| | - Giorgio Tamò
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB) , CH-1015 Lausanne, Switzerland
| | - Thomas Lemmin
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Nicolas Maïno
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB) , CH-1015 Lausanne, Switzerland
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74
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Gupta R, Rai B. Molecular Dynamics Simulation Study of Skin Lipids: Effects of the Molar Ratio of Individual Components over a Wide Temperature Range. J Phys Chem B 2015; 119:11643-55. [DOI: 10.1021/acs.jpcb.5b02093] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rakesh Gupta
- Tata Research Development
and Design Centre, Tata Consultancy Services, 54B, Hadapsar Industrial Estate, Pune - 411013, India
| | - Beena Rai
- Tata Research Development
and Design Centre, Tata Consultancy Services, 54B, Hadapsar Industrial Estate, Pune - 411013, India
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75
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Wang J, Liu KW, Biswal SL. Characterizing α-Helical Peptide Aggregation on Supported Lipid Membranes Using Microcantilevers. Anal Chem 2014; 86:10084-90. [DOI: 10.1021/ac501343b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jinghui Wang
- Department of Chemical and
Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Kai-Wei Liu
- Department of Chemical and
Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Sibani Lisa Biswal
- Department of Chemical and
Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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76
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Wang LYJ, Tong R, Kohane DS. Synthesis and proton NMR spectroscopy of intra-vesicular gamma-aminobutyric acid (GABA). ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2014; 2013:1093-5. [PMID: 24109882 DOI: 10.1109/embc.2013.6609695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report the synthesis of vesicles containing gamma-aminobutyric acid (GABA), and their proton nuclear magnetic resonance ((1)H NMR) spectra. These vesicles were constructed to more closely mimic the intracellular environment wherein GABA exists. For this study, these GABA-containing vesicles were examined under (1)H NMR as a potential platform for future studies on the differences between aqueous phantoms, ex vivo brain extracts, and in vivo magnetic resonance spectroscopy results. We found that intra-vesicular GABA faithfully yielded the chemical shifts and J-coupling constants of free aqueous GABA, alongside the chemical shift signals of the vesicle wall.
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77
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Kinnun JJ, Mallikarjunaiah KJ, Petrache HI, Brown MF. Elastic deformation and area per lipid of membranes: atomistic view from solid-state deuterium NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:246-59. [PMID: 24946141 DOI: 10.1016/j.bbamem.2014.06.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 06/06/2014] [Indexed: 12/17/2022]
Abstract
This article reviews the application of solid-state ²H nuclear magnetic resonance (NMR) spectroscopy for investigating the deformation of lipid bilayers at the atomistic level. For liquid-crystalline membranes, the average structure is manifested by the segmental order parameters (SCD) of the lipids. Solid-state ²H NMR yields observables directly related to the stress field of the lipid bilayer. The extent to which lipid bilayers are deformed by osmotic pressure is integral to how lipid-protein interactions affect membrane functions. Calculations of the average area per lipid and related structural properties are pertinent to bilayer remodeling and molecular dynamics (MD) simulations of membranes. To establish structural quantities, such as area per lipid and volumetric bilayer thickness, a mean-torque analysis of ²H NMR order parameters is applied. Osmotic stress is introduced by adding polymer solutions or by gravimetric dehydration, which are thermodynamically equivalent. Solid-state NMR studies of lipids under osmotic stress probe membrane interactions involving collective bilayer undulations, order-director fluctuations, and lipid molecular protrusions. Removal of water yields a reduction of the mean area per lipid, with a corresponding increase in volumetric bilayer thickness, by up to 20% in the liquid-crystalline state. Hydrophobic mismatch can shift protein states involving mechanosensation, transport, and molecular recognition by G-protein-coupled receptors. Measurements of the order parameters versus osmotic pressure yield the elastic area compressibility modulus and the corresponding bilayer thickness at an atomistic level. Solid-state ²H NMR thus reveals how membrane deformation can affect protein conformational changes within the stress field of the lipid bilayer.
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Affiliation(s)
- Jacob J Kinnun
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA; Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | | | - Horia I Petrache
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael F Brown
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA; Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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78
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Li H, Gorfe AA. Membrane Remodeling by Surface-Bound Protein Aggregates: Insights from Coarse-Grained Molecular Dynamics Simulation. J Phys Chem Lett 2014; 5:1457-1462. [PMID: 24803997 PMCID: PMC3999789 DOI: 10.1021/jz500451a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 04/03/2014] [Indexed: 06/03/2023]
Abstract
The mechanism of curvature generation in membranes has been studied for decades due to its important role in many cellular functions. However, it is not clear if, or how, aggregates of lipid-anchored proteins might affect the geometry and elastic property of membranes. As an initial step toward addressing this issue, we performed structural, geometrical, and stress field analyses of coarse-grained molecular dynamics trajectories of a domain-forming bilayer in which an aggregate of lipidated proteins was asymmetrically bound. The results suggest a general mechanism whereby asymmetric incorporation of lipid-modified protein aggregates curve multidomain membranes primarily by expanding the surface area of the monolayer in which the lipid anchor is inserted.
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79
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Molecular dynamics simulations of lipid membranes with lateral force: Rupture and dynamic properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:994-1002. [DOI: 10.1016/j.bbamem.2013.12.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 12/15/2013] [Accepted: 12/18/2013] [Indexed: 01/06/2023]
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80
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The interaction of dipole modifiers with amphotericin-ergosterol complexes. Effects of phospholipid and sphingolipid membrane composition. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:207-15. [DOI: 10.1007/s00249-014-0946-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/30/2014] [Accepted: 02/05/2014] [Indexed: 10/25/2022]
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81
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Mori T, Jung J, Sugita Y. Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems. J Chem Theory Comput 2013; 9:5629-40. [PMID: 26592297 DOI: 10.1021/ct400445k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Conformational sampling is fundamentally important for simulating complex biomolecular systems. The generalized-ensemble algorithm, especially the temperature replica-exchange molecular dynamics method (T-REMD), is one of the most powerful methods to explore structures of biomolecules such as proteins, nucleic acids, carbohydrates, and also of lipid membranes. T-REMD simulations have focused on soluble proteins rather than membrane proteins or lipid bilayers, because explicit membranes do not keep their structural integrity at high temperature. Here, we propose a new generalized-ensemble algorithm for membrane systems, which we call the surface-tension REMD method. Each replica is simulated in the NPγT ensemble, and surface tensions in a pair of replicas are exchanged at certain intervals to enhance conformational sampling of the target membrane system. We test the method on two biological membrane systems: a fully hydrated DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine) lipid bilayer and a WALP23-POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane system. During these simulations, a random walk in surface tension space is realized. Large-scale lateral deformation (shrinking and stretching) of the membranes takes place in all of the replicas without collapse of the lipid bilayer structure. There is accelerated lateral diffusion of DPPC lipid molecules compared with conventional MD simulation, and a much wider range of tilt angle of the WALP23 peptide is sampled due to large deformation of the POPC lipid bilayer and through peptide-lipid interactions. Our method could be applicable to a wide variety of biological membrane systems.
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Affiliation(s)
- Takaharu Mori
- RIKEN Quantitative Biology Center, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Jaewoon Jung
- RIKEN Advanced Institute for Computational Science, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- RIKEN Quantitative Biology Center, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.,RIKEN Advanced Institute for Computational Science, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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82
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The stretching elasticity of biomembranes determines their line tension and bending rigidity. Biomech Model Mechanobiol 2013; 12:1233-42. [PMID: 23460499 DOI: 10.1007/s10237-013-0478-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 02/13/2013] [Indexed: 10/27/2022]
Abstract
In this work, some implications of a recent model for the mechanical behavior of biological membranes (Deseri et al. in Continuum Mech Thermodyn 20(5):255-273, 2008) are exploited by means of a prototypical one-dimensional problem. We show that the knowledge of the membrane stretching elasticity permits to establish a precise connection among surface tension, bending rigidities and line tension during phase transition phenomena. For a specific choice of the stretching energy density, we evaluate these quantities in a membrane with coexistent fluid phases, showing a satisfactory comparison with the available experimental measurements. Finally, we determine the thickness profile inside the boundary layer where the order-disorder transition is observed.
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