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Zhang H, Pan F, Li S. Self-Assembly of Lipid Molecules under Shear Flows: A Dissipative Particle Dynamics Simulation Study. Biomolecules 2023; 13:1359. [PMID: 37759759 PMCID: PMC10526246 DOI: 10.3390/biom13091359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
The self-assembly of lipid molecules in aqueous solution under shear flows was investigated using the dissipative particle dynamics simulation method. Three cases were considered: zero shear flow, weak shear flow and strong shear flow. Various self-assembled structures, such as double layers, perforated double layers, hierarchical discs, micelles, and vesicles, were observed. The self-assembly behavior was investigated in equilibrium by constructing phase diagrams based on chain lengths. Results showed the remarkable influence of chain length, shear flow and solution concentration on the self-assembly process. Furthermore, the self-assembly behavior of lipid molecules was analyzed using the system energy, particle number and shape factor during the dynamic processes, where the self-assembly pathways were observed and analyzed for the typical structures. The results enhance our understanding of biomacromolecule self-assembly in a solution and hold the potential for applications in biomedicine.
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Affiliation(s)
- Huan Zhang
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Fan Pan
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou 325035, China
| | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou 325035, China
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2
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Benazieb O, Loison C, Thalmann F. Rheology of sliding leaflets in coarse-grained DSPC lipid bilayers. Phys Rev E 2021; 104:054802. [PMID: 34942802 DOI: 10.1103/physreve.104.054802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/06/2021] [Indexed: 11/07/2022]
Abstract
Amphiphilic lipid bilayers modify the friction properties of the surfaces on top of which they are deposited. In particular, the measured sliding friction coefficient can be significantly reduced compared with the native surface. We investigate in this work the friction properties of a numerical coarse-grained model of DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine) lipid bilayer subject to longitudinal shear. The interleaflet friction coefficient is obtained from out-of-equilibrium pulling or from relaxation simulations. In particular, we gain access to the transient viscoelastic response of a sheared bilayer. The bilayer mechanical response is found to depend significantly on the membrane physical state, with evidence in favor of a linear response regime in the fluid but not in the gel region. The linear response validity domain is established, and the timescales appearing in the membrane response discussed.
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Affiliation(s)
- Othmene Benazieb
- Institut Charles Sadron, CNRS and University of Strasbourg, 23 rue du Loess, F-67034 Strasbourg cedex 2, France
| | - Claire Loison
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
| | - Fabrice Thalmann
- Institut Charles Sadron, CNRS and University of Strasbourg, 23 rue du Loess, F-67034 Strasbourg cedex 2, France
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3
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Mao D, Wang X, Wu Y, Gu Z, Wang C, Tu Y. Unexpected hydrophobicity on self-assembled monolayers terminated with two hydrophilic hydroxyl groups. NANOSCALE 2021; 13:19604-19609. [PMID: 34812817 DOI: 10.1039/d1nr05048f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules onto the surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations show an unexpected hydrophobicity with a contact angle of 82° on a flexible self-assembled monolayer terminated only with two hydrophilic OH groups ((OH)2-SAM). This hydrophobicity, verified by a water slip phenomenon characterizing the friction on the (OH)2-SAM surface, is attributed to the formation of a hexagonal-ice-like H-bonding structure in the OH matrix of (OH)2-SAM, which sharply reduces the hydrogen bonds between the surface and the water molecules above. The unique simple interface presented here offers a significant molecular-level platform for examining the bio-interfacial interactions ranging from biomolecule binding to cell adhesion.
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Affiliation(s)
- Dangxin Mao
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
| | - Xian Wang
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
| | - Yuanyan Wu
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
| | - Zonglin Gu
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
| | - Chunlei Wang
- Zhangjiang Lab, Interdisplinary Research Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yusong Tu
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
- Key Laboratory of Polar Materials and Devices Ministry of Education, School of Physics and Electrical Science, East China Normal University, Shanghai 200241, China
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4
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Chen Y, Wang Z, Ji Y, He L, Wang X, Li S. Asymmetric Lipid Membranes under Shear Flows: A Dissipative Particle Dynamics Study. MEMBRANES 2021; 11:655. [PMID: 34564472 PMCID: PMC8465239 DOI: 10.3390/membranes11090655] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/12/2021] [Accepted: 08/20/2021] [Indexed: 12/03/2022]
Abstract
We investigate the phase behavior of the asymmetric lipid membranes under shear flows, using the dissipative particle dynamics simulation. Two cases, the weak and strong shear flows, are considered for the asymmetric lipid microstructures. Three typical asymmetric structures, the membranes, tubes, and vesicle, are included in the phase diagrams, where the effect of two different types of lipid chain length on the formation of asymmetric membranes is evaluated. The dynamic processes are demonstrated for the asymmetric membranes by calculating the average radius of gyration and shape factor. The result indicates that different shear flows will affect the shape of the second type of lipid molecules; the shape of the first type of lipid molecules is more stable than that of the second type of lipid molecules. The mechanical properties are investigated for the asymmetric membranes by analyzing the interface tension. The results reveal an absolute pressure at the junctions of different types of particles under the weak shear flow; the other positions are almost in a state of no pressure; there is almost no pressure inside the asymmetric lipid membrane structure under the strong shear flow. The findings will help us to understand the potential applications of asymmetric lipid microstructures in the biological and medical fields.
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Affiliation(s)
| | | | | | | | | | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou 325035, China; (Y.C.); (Z.W.); (Y.J.); (L.H.); (X.W.)
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5
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Girard M, Bereau T. Regulating Lipid Composition Rationalizes Acyl Tail Saturation Homeostasis in Ectotherms. Biophys J 2020; 119:892-899. [PMID: 32814063 DOI: 10.1016/j.bpj.2020.07.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/16/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Cell membranes mainly consist of lipid bilayers with an actively regulated composition. The underlying processes are still poorly understood, in particular, how the hundreds of components are controlled. Cholesterol has been found to correlate with phospholipid saturation for reasons that remain unclear. To better understand the link between cell membrane regulation and chemical composition, we establish a computational framework based on chemical reaction networks, resulting in multiple semigrand canonical ensembles. By running computer simulations, we show that regulating the chemical potential of lipid species is sufficient to reproduce the experimentally observed increase in acyl tail saturation with added cholesterol. Our model proposes a different picture of lipid regulation in which components can be regulated passively instead of actively. In this picture, phospholipid acyl tail composition naturally adapts to added molecules such as cholesterol or proteins. A comparison between regulated membranes with commonly studied ternary model membranes shows stark differences: for instance, correlation lengths and viscosities observed are independent of lipid chemical affinity.
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Affiliation(s)
- Martin Girard
- Max Planck Institute for Polymer Research, Mainz, Germany.
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany; Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam, the Netherlands
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6
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Shear-induced microstructures and dynamics processes of phospholipid cylinders in solutions. Sci Rep 2019; 9:15393. [PMID: 31659204 PMCID: PMC6817888 DOI: 10.1038/s41598-019-51933-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/09/2019] [Indexed: 11/08/2022] Open
Abstract
Shear-induced microstructures and their corresponding dynamic processes are investigated for phospholipid cylinders in aqueous solution by dissipative particle dynamic simulation. Various phospholipid cylinders with cross-sections, which are formed under shear-free flow, are selected to examine the effects of shear flow on their structures and dynamic processes. Shear flow induces the transition from cylinders into vesicles at weak rate and the transition into vesicle–lamella mixtures with increased shear rate and lamella structures at the strong shear rate. Then, the average radius of gyration and shape factors of the polymer chains in the dynamic processes are discussed in detail. Results show that shear flow causes the structure of the polymer chains to be elongated along the shear direction, and the configuration of the polymer chain can be rapidly transformed into an ellipsoid structure under strong shear.
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7
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Shan Y, Wang X, Ji Y, He L, Li S. Self-assembly of phospholipid molecules in solutions under shear flows: Microstructures and phase diagrams. J Chem Phys 2019; 149:244901. [PMID: 30599738 DOI: 10.1063/1.5056229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Shear-induced microstructures and their phase diagrams were investigated for phospholipid molecules in aqueous solution by dissipative particle dynamic simulation. Self-assembled microstructures, including spherical and cylindrical micelles, spherical vesicles, lamellae, undulated lamellae, perforated lamellae, and continuous networks, were observed under various shear flows and phospholipid concentrations, where the spatial inhomogeneity and symmetry were analysed. A series of phase diagrams were constructed based on the chain lengths under various phospholipid concentrations. The phase distributions showed that the structures with spherical symmetry could be shear-induced to structures with cylindrical symmetry in the dilute solutions. In the semi-concentrated solutions, the lamellae were located in most spaces under zero shear flows, which could be shear-induced into undulated lamellae and then into cylindrical micelles. For the concentrated solutions, the strong shear flows oriented the directions of multilayer lamellae and phase transitions appeared between several cylindrical network structures. These observations on shear-induced microstructures and their distributions revealed a promising approach that could be used to design bio-microstructures based on phospholipid molecules under shear flows.
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Affiliation(s)
- Yue Shan
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Xianghong Wang
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Yongyun Ji
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Linli He
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
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8
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To TBT, Le Goff T, Pierre-Louis O. Adhesion dynamics of confined membranes. SOFT MATTER 2018; 14:8552-8569. [PMID: 30328887 DOI: 10.1039/c8sm01567h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We report on the modeling of the dynamics of confined lipid membranes. We derive a thin film model in the lubrication limit which describes an inextensible liquid membrane with bending rigidity confined between two adhesive walls. The resulting equations share similarities with the Swift-Hohenberg model. However, inextensibility is enforced by a time-dependent nonlocal tension. Depending on the excess membrane area available in the system, three different dynamical regimes, denoted as A, B and C, are found from the numerical solution of the model. In regime A, membranes with small excess area form flat adhesion domains and freeze. Such freezing is interpreted by means of an effective model for curvature-driven domain wall motion. The nonlocal membrane tension tends to a negative value corresponding to the linear stability threshold of flat domain walls in the Swift-Hohenberg equation. In regime B, membranes with intermediate excess areas exhibit endless coarsening with coexistence of flat adhesion domains and wrinkle domains. The tension tends to the nonlinear stability threshold of flat domain walls in the Swift-Hohenberg equation. The fraction of the system covered by the wrinkle phase increases linearly with the excess area in regime B. In regime C, membranes with large excess area are completely covered by a frozen labyrinthine pattern of wrinkles. As the excess area is increased, the tension increases and the wavelength of the wrinkles decreases. For large membrane area, there is a crossover to a regime where the extrema of the wrinkles are in contact with the walls. In all regimes after an initial transient, robust localised structures form, leading to an exact conservation of the number of adhesion domains.
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Affiliation(s)
- Tung B T To
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France.
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9
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Le Goff T, To TBT, Pierre-Louis O. Thixotropy and shear thinning of lubricated contacts with confined membranes. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017; 40:44. [PMID: 28389826 DOI: 10.1140/epje/i2017-11532-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/13/2017] [Indexed: 06/07/2023]
Abstract
We have modeled the nonlinear dynamics and the rheological behavior of a system under shear containing a membrane confined between two attractive walls. The presence of the membrane induces additional tangential forces on the walls that always increase the global friction. At low shear rates, the membrane exhibits chaotic dynamics with slow coarsening leading to thixotropy, i.e. to a slow decrease of the membrane-induced tangential forces on the walls. At intermediate shear rates, the membrane profile presents stationary periodic patterns. At higher shear rates, membrane dynamics are governed by a nonlinear evolution equation which is similar to the Kuramoto-Sivashinski equation, but with a sixth-order stabilizing term. The membrane experiences chaotic dynamics without coarsening. As a consequence of the nonlinear dynamics of the membrane at intermediate and large shear rates, the system exhibits shear thinning.
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Affiliation(s)
- Thomas Le Goff
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne, France
| | - Tung B T To
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne, France
| | - Olivier Pierre-Louis
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne, France.
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10
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Venable RM, Ingólfsson HI, Lerner MG, Perrin BS, Camley BA, Marrink SJ, Brown FLH, Pastor RW. Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions. J Phys Chem B 2017; 121:3443-3457. [PMID: 27966982 DOI: 10.1021/acs.jpcb.6b09111] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The periodic Saffman-Delbrück (PSD) model, an extension of the Saffman-Delbrück model developed to describe the effects of periodic boundary conditions on the diffusion constants of lipids and proteins obtained from simulation, is tested using the coarse-grained Martini and all-atom CHARMM36 (C36) force fields. Simulations of pure Martini dipalmitoylphosphatidylcholine (DPPC) bilayers and those with one embedded gramicidin A (gA) dimer or one gA monomer with sizes ranging from 512 to 2048 lipids support the PSD model. Underestimates of D∞ (the value of the diffusion constant for an infinite system) from the 512-lipid system are 35% for DPPC, 45% for the gA monomer, and 70% for the gA dimer. Simulations of all-atom DPPC and dioleoylphosphatidylcholine (DOPC) bilayers yield diffusion constants not far from experiment. However, the PSD model predicts that diffusion constants at the sizes of the simulation should underestimate experiment by approximately a factor of 3 for DPPC and 2 for DOPC. This likely implies a deficiency in the C36 force field. A Bayesian method for extrapolating diffusion constants of lipids and proteins in membranes obtained from simulation to infinite system size is provided.
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Affiliation(s)
- Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Michael G Lerner
- Department of Chemistry & Biochemistry and Department of Physics and Astronomy, Earlham College , Richmond, Indiana 47374, United States
| | - B Scott Perrin
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Brian A Camley
- Department of Physics, University of California , San Diego, California 92093, United States
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Frank L H Brown
- Department of Chemistry & Biochemistry and Department of Physics, University of California , Santa Barbara, California 93106, United States
| | - 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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11
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Camley BA, Lerner MG, Pastor RW, Brown FLH. Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes. J Chem Phys 2016; 143:243113. [PMID: 26723598 DOI: 10.1063/1.4932980] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Saffman-Delbrück hydrodynamic model for lipid-bilayer membranes is modified to account for the periodic boundary conditions commonly imposed in molecular simulations. Predicted lateral diffusion coefficients for membrane-embedded solid bodies are sensitive to box shape and converge slowly to the limit of infinite box size, raising serious doubts for the prospects of using detailed simulations to accurately predict membrane-protein diffusivities and related transport properties. Estimates for the relative error associated with periodic boundary artifacts are 50% and higher for fully atomistic models in currently feasible simulation boxes. MARTINI simulations of LacY membrane protein diffusion and LacY dimer diffusion in DPPC membranes and lipid diffusion in pure DPPC bilayers support the underlying hydrodynamic model.
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Affiliation(s)
- Brian A Camley
- Center for Theoretical Biological Physics and Department of Physics, University of California, San Diego, California 92093, USA
| | - Michael G Lerner
- Department of Physics and Astronomy, Earlham College, Richmond, Indiana 47374, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Frank L H Brown
- Department of Physics, University of California, Santa Barbara, California 93106, USA
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12
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Boţan A, Joly L, Fillot N, Loison C. Mixed Mechanism of Lubrication by Lipid Bilayer Stacks. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:12197-12202. [PMID: 26381720 DOI: 10.1021/acs.langmuir.5b02786] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Although the key role of lipid bilayer stacks in biological lubrication is generally accepted, the mechanisms underlying their extreme efficiency remain elusive. In this article, we report molecular dynamics simulations of lipid bilayer stacks undergoing load and shear. When the hydration level is reduced, the velocity accommodation mechanism changes from viscous shear in hydration water to interlayer sliding in the bilayers. This enables stacks of hydrated lipid bilayers to act as efficient boundary lubricants for various hydration conditions, structures, and mechanical loads. We also propose an estimation for the friction coefficient; thanks to the strong hydration forces between lipid bilayers, the high local viscosity is not in contradiction with low friction coefficients.
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Affiliation(s)
- Alexandru Boţan
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon , 69622 Villeurbanne, France
| | - Laurent Joly
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon , 69622 Villeurbanne, France
| | - Nicolas Fillot
- LaMCoS, UMR5259 INSA-Lyon-CNRS, Université de Lyon , 69622 Villeurbanne, France
| | - Claire Loison
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon , 69622 Villeurbanne, France
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13
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Soussi J, Chalopin Y. Electric polarizability of lipid bilayers: The influence of the structure. J Chem Phys 2015; 143:144904. [DOI: 10.1063/1.4932340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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14
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Le Goff T, Politi P, Pierre-Louis O. Frozen states and order-disorder transition in the dynamics of confined membranes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:032114. [PMID: 25314402 DOI: 10.1103/physreve.90.032114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Indexed: 06/04/2023]
Abstract
The adhesion dynamics of a membrane confined between two permeable walls is studied using a two-dimensional hydrodynamic model. The membrane morphology decomposes into adhesion patches on the upper and the lower walls and obeys a nonlinear evolution equation that resembles that of phase-separation dynamics, which is known to lead to coarsening, i.e., to the endless growth of the adhesion patches. However, due to the membrane bending rigidity, the system evolves toward a frozen state without coarsening. This frozen state exhibits an order-disorder transition when increasing the permeability of the walls.
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Affiliation(s)
- Thomas Le Goff
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France
| | - Paolo Politi
- Istituto dei Sistemi Complessi, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy and INFN Sezione di Firenze, via G. Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Olivier Pierre-Louis
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France
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15
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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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16
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Brandt EG. Fluctuating hydrodynamics simulations of coarse-grained lipid membranes under steady-state conditions and in shear flow. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:012714. [PMID: 23944498 DOI: 10.1103/physreve.88.012714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Indexed: 06/02/2023]
Abstract
The stochastic Eulerian-Lagrangian method (SELM) is used to simulate coarse-grained lipid membrane models under steady-state conditions and in shear flow. SELM is an immersed boundary method which combines the efficiency of particle-based simulations with the realistic solvent dynamics provided by fluctuating hydrodynamics. Membrane simulations in SELM are shown to give structural properties in accordance with equilibrium statistical mechanics and dynamic properties in agreement with previous simulations of highly detailed membrane models in explicit solvent. Simulations of sheared membranes are used to calculate surface shear viscosities and inter-monolayer friction coefficients. The membrane models are shown to be shear thinning under a wide range of applied shear rates.
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Affiliation(s)
- Erik G Brandt
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
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17
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Kyrychenko A, Ladokhin AS. Molecular dynamics simulations of depth distribution of spin-labeled phospholipids within lipid bilayer. J Phys Chem B 2013; 117:5875-85. [PMID: 23614631 DOI: 10.1021/jp4026706] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spin-labeled lipids are commonly used as fluorescence quenchers in studies of membrane penetration of dye-labeled proteins and peptides using depth-dependent quenching. Accurate calculations of depth of the fluorophore rely on the use of several spin labels placed in the membrane at various positions. The depth of the quenchers (spin probes) has to be determined independently; however, experimental determination of transverse distributions of spin probe depths is difficult. In this Article, we use molecular dynamics (MD) simulations to study the membrane behavior and depth distributions of spin-labeled phospholipids in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. To probe different depths within the bilayer, a series containing five Doxyl-labeled lipids (n-Doxyl PC) has been studied, in which a spin moiety was covalently attached to nth carbon atoms (where n = 5, 7, 10, 12, and 14) of the sn-2 stearoyl chain of the host phospholipid. Our results demonstrate that the chain-attached spin labels are broadly distributed across the model membrane and their environment is characterized by a high degree of mobility and structural heterogeneity. Despite the high thermal disorder, the depth distributions of the Doxyl labels were found to correlate well with their attachment positions, indicating that the distribution of the spin label within the model membrane is dictated by the depth of the nth lipid carbon atom and not by intrinsic properties of the label. In contrast, a much broader and heterogeneous distribution was observed for a headgroup-attached Tempo spin label of Tempo-PC lipids. MD simulations reveal that, due to the hydrophobic nature, a Tempo moiety favors partitioning from the headgroup region deeper into the membrane. Depending on the concentration of Tempo-PC lipids, the probable depth of the Tempo moiety could span a range from 14.4 to 18.2 Å from the membrane center. Comparison of the MD-estimated immersion depths of Tempo and n-Doxyl labels with their suggested experimental depth positions allows us to review critically the possible sources of error in depth-dependent fluorescence quenching studies.
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Affiliation(s)
- Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160-7421, USA.
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Pyrpassopoulos S, Feeser EA, Mazerik JN, Tyska MJ, Ostap EM. Membrane-bound myo1c powers asymmetric motility of actin filaments. Curr Biol 2012; 22:1688-92. [PMID: 22863317 PMCID: PMC3461085 DOI: 10.1016/j.cub.2012.06.069] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/08/2012] [Accepted: 06/27/2012] [Indexed: 12/31/2022]
Abstract
Class I myosins are molecular motors that link cellular membranes to the actin cytoskeleton and play roles in membrane tension generation, membrane dynamics, and mechanosignal transduction. The widely expressed myosin-Ic (myo1c) isoform binds tightly to phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P(2)] via a pleckstrin homology domain located in the myo1c tail, which is important for its proper cellular localization. In this study, we found that myo1c can power actin motility on fluid membranes composed of physiological concentrations of PtdIns(4,5)P(2) and that this motility is inhibited by high concentrations of anionic phospholipids. Strikingly, this motility occurs along curved paths in a counterclockwise direction (i.e., the actin filaments turn in leftward circles). A biotinylated myo1c construct containing only the motor domain and the lever arm anchored via streptavidin on a membrane containing biotinylated lipid can also generate asymmetric motility, suggesting that the tail domain is not required for the counterclockwise turning. We found that the ability to produce counterclockwise motility is not a universal characteristic of myosin-I motors, as membrane-bound myosin-Ia (myo1a) and myosin-Ib (myo1b) are able to power actin gliding, but the actin gliding has no substantial turning bias. This work reveals a possible mechanism for establishing asymmetry in relationship to the plasma membrane.
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Affiliation(s)
- Serapion Pyrpassopoulos
- The Pennsylvania Muscle Institute and Department of Physiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia PA 19104-6085
| | - Elizabeth A. Feeser
- The Pennsylvania Muscle Institute and Department of Physiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia PA 19104-6085
| | - Jessica N. Mazerik
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Matthew J. Tyska
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - E. Michael Ostap
- The Pennsylvania Muscle Institute and Department of Physiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia PA 19104-6085
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Karimi-Varzaneh HA, Qian HJ, Chen X, Carbone P, Müller-Plathe F. IBIsCO: A molecular dynamics simulation package for coarse-grained simulation. J Comput Chem 2011; 32:1475-87. [DOI: 10.1002/jcc.21717] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 10/19/2010] [Indexed: 11/07/2022]
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