1
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Müller WA, Sarkis JR, Marczak LDF, Muniz AR. Molecular dynamics insights on temperature and pressure effects on electroporation. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184049. [PMID: 36113558 DOI: 10.1016/j.bbamem.2022.184049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/02/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
Electroporation is a cell-level phenomenon caused by an ionic imbalance in the membrane, being of great relevance in various fields of knowledge. A dependence of the pore formation kinetics on the environmental conditions (temperature and pressure) of the cell membrane has already been reported, but further clarification regarding how these variables affect the pore formation/resealing dynamics and the transport of molecules through the membrane is still lacking. The objective of the present study was to investigate the temperature (288-348 K) and pressure (1-5000 atm) effects on the electroporation kinetics using coarse-grained molecular dynamics simulations. Results shown that the time for pore formation and resealing increased with pressure and decreased with temperature, whereas the maximum pore radius increased with temperature and decreased with pressure. This behavior influenced the ion migration through the bilayer, and the higher ionic mobility was obtained in the 288 K/1000 atm simulations, i.e., a combination of low temperature and (not excessively) high pressure. These results were used to discuss some experimental observations regarding the extraction of intracellular compounds applying this technique. This study contributes to a better understanding of electroporation under different thermodynamic conditions and to an optimal selection of processing parameters in practical applications which exploit this phenomenon.
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Affiliation(s)
- Wagner Augusto Müller
- Universidade Federal do Rio Grande do Sul (UFRGS), Department of Chemical Engineering, Porto Alegre, RS, Brazil
| | - Júlia Ribeiro Sarkis
- Universidade Federal do Rio Grande do Sul (UFRGS), Department of Chemical Engineering, Porto Alegre, RS, Brazil
| | | | - André Rodrigues Muniz
- Universidade Federal do Rio Grande do Sul (UFRGS), Department of Chemical Engineering, Porto Alegre, RS, Brazil.
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2
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Maiti A, Daschakraborty S. Can Urea and Trimethylamine- N-oxide Prevent the Pressure-Induced Phase Transition of Lipid Membrane? J Phys Chem B 2022; 126:1426-1440. [PMID: 35139638 DOI: 10.1021/acs.jpcb.1c08891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Organisms dwelling in ocean trenches are exposed to the high hydrostatic pressure of ocean water. Increasing pressure can alter the membrane packing density and fluidity and trigger the fluid-to-gel phase transition. To combat environmental stress, the organisms synthesize small polar solutes, which are known as osmolytes. Urea and trimethylamine-N-oxide (TMAO) are two such solutes found in deep-sea creatures. While TMAO stabilizes protein, urea induces protein denaturation. These solutes strongly influence the packing density and membrane fluidity of the lipid bilayer at different conditions. But can these solutes affect the pressure-induced phase transition of the lipid membrane? In the present work, we have studied the effect of these two solutes on pressure-induced fluid-to-gel phase transition based on the all-atom molecular dynamics (MD) simulation approach. A high-pressure-stimulated fluid-to-gel phase transition of the membrane is seen at 800 bar, which is consistent with previous experiments. We have also observed that in the low-pressure region (1-400 bar), urea slightly increases the membrane fluidity where TMAO decreases the same. However, the phase transition pressure remains almost unchanged on the addition of urea while TMAO shifts the phase transition toward a lower pressure. We have found that the hydrogen (H)-bond interaction between lipid and urea plays an important role in preserving the fluidity of the membrane in the low-pressure zone. However, at a higher pressure, both water and urea are excluded from the membrane surface. TMAO is also excluded from the interfacial region of the membrane at all pressures. Exclusion from the membrane surface further triggers the phase transition of the lipid membrane from the fluid to gel phase at a high pressure.
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Affiliation(s)
- Archita Maiti
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India
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3
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Walter V, Ruscher C, Gola A, Marques CM, Benzerara O, Thalmann F. Ripple-like instability in the simulated gel phase of finite size phosphocholine bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183714. [PMID: 34331947 DOI: 10.1016/j.bbamem.2021.183714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/14/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022]
Abstract
Atomistic molecular dynamics simulations have reached a degree of maturity that makes it possible to investigate the lipid polymorphism of model bilayers over a wide range of temperatures. However if both the fluid Lα and tilted gel [Formula: see text] states are routinely obtained, the [Formula: see text] ripple phase of phosphatidylcholine lipid bilayers is still unsatifactorily described. Performing simulations of lipid bilayers made of different numbers of DPPC (1,2-dipalmitoylphosphatidylcholine) molecules ranging from 32 to 512, we demonstrate that the tilted gel phase [Formula: see text] expected below the pretransition cannot be obtained for large systems (equal or larger than 94 DPPC molecules) through common simulations settings or temperature treatments. Large systems are instead found in a disordered gel phase which display configurations, topography and energies reminiscent from the ripple phase [Formula: see text] observed between the pretransition and the main melting transition. We show how the state of the bilayers below the melting transition can be controlled and depends on thermal history and conditions of preparations. A mechanism for the observed topographic instability is suggested.
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Affiliation(s)
- Vivien Walter
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, SE1 1DB, London, United Kingdom.
| | - Céline Ruscher
- Institut Charles Sadron, CNRS and University of Strasbourg, 23 rue du Loess, F-67034 Strasbourg Cedex 2, France
| | - Adrien Gola
- Institut Charles Sadron, CNRS and University of Strasbourg, 23 rue du Loess, F-67034 Strasbourg Cedex 2, France
| | - Carlos M Marques
- Institut Charles Sadron, CNRS and University of Strasbourg, 23 rue du Loess, F-67034 Strasbourg Cedex 2, France
| | - Olivier Benzerara
- Institut Charles Sadron, CNRS and University of Strasbourg, 23 rue du Loess, F-67034 Strasbourg Cedex 2, 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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4
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Meinhardt S, Schmid F. Structure of lateral heterogeneities in a coarse-grained model for multicomponent membranes. SOFT MATTER 2019; 15:1942-1952. [PMID: 30662989 DOI: 10.1039/c8sm02261e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We study the lateral domain structure in a coarse-grained molecular model for multicomponent lipid bilayers by semi-grandcanonical Monte Carlo simulations. The membranes are filled with liquid ordered (lo) domains surrounded by a liquid disordered (ld) matrix. Depending on the membrane composition and temperature, we identify different morphological regimes: one regime (I) where the lo domains are small and relatively compact, and two regimes (II, II') where they are larger and often interconnected. In the latter two regimes, the ld matrix forms a network of disordered trenches separating the lo domains, with a relatively high content of interdigitated line defects. Since such defects are also a structural element of the modulated ripple phase in one component membranes, we argue that the regimes II, II' may be amorphous equivalents of the ripple phase in multicomponent membranes. We also analyze the local structure and provide evidence that the domains in regime I are stabilized by a monolayer curvature mechanism postulated in earlier work [S. Meinhardt et al., PNAS, 2013, 110, 4476].
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Affiliation(s)
- Sebastian Meinhardt
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, USA
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5
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Oroskar PA, Jameson CJ, Murad S. Molecular-Level "Observations" of the Behavior of Gold Nanoparticles in Aqueous Solution and Interacting with a Lipid Bilayer Membrane. Methods Mol Biol 2019; 2000:303-359. [PMID: 31148024 DOI: 10.1007/978-1-4939-9516-5_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We use coarse-grained molecular dynamics simulations to "observe" details of interactions between ligand-covered gold nanoparticles and a lipid bilayer model membrane. In molecular dynamics simulations, one puts the individual atoms and groups of atoms of the physical system to be "observed" into a simulation box, specifies the forms of the potential energies of interactions between them (ultimately quantum based), and lets them individually move classically according to Newton's equations of motion, based on the forces arising from the assumed potential energy forms. The atoms that are chemically bonded to each other stay chemically bonded, following known potentials (force fields) that permit internal degrees of freedom (internal rotation, torsion, vibrations), and the interactions between nonbonded atoms are simplified to Lennard-Jones forms (in our case) and coulombic (where electrical charges are present) in which the parameters are previously optimized to reproduce thermodynamic properties or are based on quantum electronic calculations. The system is started out at a reasonable set of coordinates for all atoms or groups of atoms, and then permitted to develop according to the equations of motion, one small step (usually 10 fs time step) at a time, for millions of steps until the system is at a quasi-equilibrium (usually reached after hundreds of nanoseconds). We then let the system play out its motions further for many nanoseconds to observe the behavior, periodically taking snapshots (saving all positions and energies), and post-processing the snapshots to obtain various average descriptions of the system. Alkanethiols of various lengths serve as examples of hydrophobic ligands and methyl-terminated PEG with various numbers of monomer units serve as examples of hydrophilic ligands. Spherical gold particles of various diameters as well as gold nanorods form the core to which ligands are attached. The nanoparticles are characterized at the molecular level, especially the distributions of ligand configurations and their dependence on ligand length, and surface coverage. Self-assembly of the bilayer from an isotropic solution and observation of membrane properties that correspond well to experimental values validate the simulations. The mechanism of permeation of a gold NP coated with either a hydrophobic or a hydrophilic ligand, and its dependence on surface coverage, ligand length, core diameter, and core shape, is investigated. Lipid response such as lipid flip-flops, lipid extraction, and changes in order parameter of the lipid tails are examined in detail. The mechanism of permeation of a PEGylated nanorod is shown to occur by tilting, lying down, rotating, and straightening up. The nature of the information provided by molecular dynamics simulations permits understanding of the detailed behavior of gold nanoparticles interacting with lipid membranes which in turn helps to understand why some known systems work better than others and aids the design of new particles and improvement of methods for preparing existing ones.
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Affiliation(s)
- Priyanka A Oroskar
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Cynthia J Jameson
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Sohail Murad
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Chemical Engineering, Illinois Institute of Technology, Chicago, IL, USA.
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6
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Schumann-Gillett A, O'Mara ML. The effects of oxidised phospholipids and cholesterol on the biophysical properties of POPC bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:210-219. [DOI: 10.1016/j.bbamem.2018.07.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/04/2018] [Accepted: 07/23/2018] [Indexed: 10/28/2022]
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7
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The effect of H 3O + on the membrane morphology and hydrogen bonding of a phospholipid bilayer. Biophys Rev 2018; 10:1371-1376. [PMID: 30219992 DOI: 10.1007/s12551-018-0454-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/06/2018] [Indexed: 12/30/2022] Open
Abstract
At the 2017 meeting of the Australian Society for Biophysics, we presented the combined results from two recent studies showing how hydronium ions (H3O+) modulate the structure and ion permeability of phospholipid bilayers. In the first study, the impact of H3O+ on lipid packing had been identified using tethered bilayer lipid membranes in conjunction with electrical impedance spectroscopy and neutron reflectometry. The increased presence of H3O+ (i.e. lower pH) led to a significant reduction in membrane conductivity and increased membrane thickness. A first-order explanation for the effect was assigned to alterations in the steric packing of the membrane lipids. Changes in packing were described by a critical packing parameter (CPP) related to the interfacial area and volume and shape of the membrane lipids. We proposed that increasing the concentraton of H3O+ resulted in stronger hydrogen bonding between the phosphate oxygens at the water-lipid interface leading to a reduced area per lipid and slightly increased membrane thickness. At the meeting, a molecular model for these pH effects based on the result of our second study was presented. Multiple μs-long, unrestrained molecular dynamic (MD) simulations of a phosphatidylcholine lipid bilayer were carried out and showed a concentration dependent reduction in the area per lipid and an increase in bilayer thickness, in agreement with experimental data. Further, H3O+ preferentially accumulated at the water-lipid interface, suggesting the localised pH at the membrane surface is much lower than the bulk bathing solution. Another significant finding was that the hydrogen bonds formed by H3O+ ions with lipid headgroup oxygens are, on average, shorter in length and longer-lived than the ones formed in bulk water. In addition, the H3O+ ions resided for longer periods in association with the carbonyl oxygens than with either phosphate oxygen in lipids. In summary, the MD simulations support a model where the hydrogen bonding capacity of H3O+ for carbonyl and phosphate oxygens is the origin of the pH-induced changes in lipid packing in phospholipid membranes. These molecular-level studies are an important step towards a better understanding of the effect of pH on biological membranes.
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8
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Otero-Mato JM, Montes-Campos H, Calvelo M, García-Fandiño R, Gallego LJ, Piñeiro Á, Varela LM. GADDLE Maps: General Algorithm for Discrete Object Deformations Based on Local Exchange Maps. J Chem Theory Comput 2018; 14:466-478. [DOI: 10.1021/acs.jctc.7b00861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- J. Manuel Otero-Mato
- Nanomaterials,
Photonics and Soft Matter Group, Departamento de Física de
Partículas y Departamento de Física Aplicada, Facultade
de Física, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Hadrián Montes-Campos
- Nanomaterials,
Photonics and Soft Matter Group, Departamento de Física de
Partículas y Departamento de Física Aplicada, Facultade
de Física, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Martín Calvelo
- Department
of Organic Chemistry, Center for Research in Biological Chemistry
and Molecular Materials, University of Santiago de Compostela, Campus
Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Rebeca García-Fandiño
- CIQUP,
Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, R. Campo alegre, 687, P-4169-007 Porto, Portugal
| | - Luis J. Gallego
- Nanomaterials,
Photonics and Soft Matter Group, Departamento de Física de
Partículas y Departamento de Física Aplicada, Facultade
de Física, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Ángel Piñeiro
- Soft
Matter and Molecular Biophysics Group, Departamento de Física
Aplicada, Facultade de Física, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Luis M. Varela
- Nanomaterials,
Photonics and Soft Matter Group, Departamento de Física de
Partículas y Departamento de Física Aplicada, Facultade
de Física, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
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9
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Deplazes E, Poger D, Cornell B, Cranfield CG. The effect of hydronium ions on the structure of phospholipid membranes. Phys Chem Chem Phys 2018; 20:357-366. [DOI: 10.1039/c7cp06776c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This work studies the mechanisms by which hydronium ions modulate the structure of phospholipid bilayers.
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Affiliation(s)
- Evelyne Deplazes
- School of Biomedical Sciences
- Curtin Health Innovation Research Institute and Curtin Institute for Computation
- Curtin University
- Perth
- Australia
| | - David Poger
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
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10
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Ding W, Palaiokostas M, Shahane G, Wang W, Orsi M. Effects of High Pressure on Phospholipid Bilayers. J Phys Chem B 2017; 121:9597-9606. [PMID: 28926699 DOI: 10.1021/acs.jpcb.7b07119] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The response of lipid membranes to changes in external pressure is important for many biological processes, and it can also be exploited for technological applications. In this work, we employ all-atom molecular dynamics simulations to characterize the changes in the physical properties of phospholipid bilayers brought about by high pressure (1000 bar). In particular, we study how the response differs, in relation to different chain unsaturation levels, by comparing monounsaturated 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and biunsaturated dioleoyl-phosphatidylcholine (DOPC) bilayers. Various structural, mechanical, and dynamical features are found to be altered by the pressure increase in both bilayers. Notably, for most properties, including bilayer area and thickness, lipid order parameters, lateral pressure profile, and curvature frustration energy, we observe significantly more pronounced effects for monounsaturated POPC than biunsaturated DOPC. Possible biological implications of the results obtained are discussed, especially in relation to how different lipids can control the structure and function of membrane proteins.
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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
| | - Ganesh Shahane
- 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
- Department of Applied Sciences, University of the West of England , Coldharbour Lane, Bristol BS16 1QY, U.K
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11
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Mangiapia G, Gvaramia M, Kuhrts L, Teixeira J, Koutsioubas A, Soltwedel O, Frielinghaus H. Effect of benzocaine and propranolol on phospholipid-based bilayers. Phys Chem Chem Phys 2017; 19:32057-32071. [DOI: 10.1039/c7cp06077g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Drug/bilayer interactions are fundamental in determining the action mechanism of active ingredients. Neutron techniques represent unique tools for having a clear comprehension of such interactions.
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Affiliation(s)
- G. Mangiapia
- Forschungszentrum Jülich GmbH
- Jülich Centre for Neutron Science Außenstelle am Heinz Maier-Leibnitz Zentrum
- D-85747 Garching
- Germany
| | - M. Gvaramia
- Forschungszentrum Jülich GmbH
- Jülich Centre for Neutron Science Außenstelle am Heinz Maier-Leibnitz Zentrum
- D-85747 Garching
- Germany
- Ivane Javakhishvili Tbilisi State University
| | - L. Kuhrts
- Forschungszentrum Jülich GmbH
- Jülich Centre for Neutron Science Außenstelle am Heinz Maier-Leibnitz Zentrum
- D-85747 Garching
- Germany
| | - J. Teixeira
- Laboratoire Léon Brillouin (CEA-CNRS)
- CEA-Saclay
- F-91191 Gif-sur-Yvette CEDEX
- France
| | - A. Koutsioubas
- Forschungszentrum Jülich GmbH
- Jülich Centre for Neutron Science Außenstelle am Heinz Maier-Leibnitz Zentrum
- D-85747 Garching
- Germany
| | - O. Soltwedel
- Heinz Maier-Leibnitz Zentrum
- Technische Universität München
- D-85747 Garching
- Germany
| | - H. Frielinghaus
- Forschungszentrum Jülich GmbH
- Jülich Centre for Neutron Science Außenstelle am Heinz Maier-Leibnitz Zentrum
- D-85747 Garching
- Germany
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12
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Laner M, Hünenberger PH. Phase-transition properties of glycerol–dipalmitate lipid bilayers investigated using molecular dynamics simulation. J Mol Graph Model 2015; 59:136-47. [DOI: 10.1016/j.jmgm.2015.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 11/29/2022]
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13
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Goto M, Endo T, Yano T, Tamai N, Kohlbrecher J, Matsuki H. Comprehensive characterization of temperature- and pressure-induced bilayer phase transitions for saturated phosphatidylcholines containing longer chain homologs. Colloids Surf B Biointerfaces 2015; 128:389-397. [DOI: 10.1016/j.colsurfb.2015.02.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 01/06/2015] [Accepted: 02/17/2015] [Indexed: 11/25/2022]
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14
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Caron B, Mark AE, Poger D. Some Like It Hot: The Effect of Sterols and Hopanoids on Lipid Ordering at High Temperature. J Phys Chem Lett 2014; 5:3953-3957. [PMID: 26276476 DOI: 10.1021/jz5020778] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Sterols and hopanoids have been suggested to reinforce membranes and protect against unfavorable environmental conditions. In particular, hopanoids are found in high concentrations in membranes of thermotolerant and thermophilic bacteria. However, the mechanism whereby sterols and hopanoids stabilize membranes at elevated temperatures is poorly understood. Here, the effect of temperature on the ordering of lipids in bilayers containing cholesterol or the hopanoids bacteriohopanetetrol and diplopterol was explored using molecular dynamics simulations. It is shown that cholesterol induces a high level of ordering over a wide range of temperatures. Bacteriohopanetetrol promotes order within the lipid tails but enhances fluid-like properties of the head groups at high temperatures. In contrast, diplopterol partitions in the midplane of the bilayer. This suggests that individual hopanoids fulfill distinct functions in membranes, with the ordering properties of bacteriohopanetetrol being particularly well suited to maintain the integrity of membranes at temperatures preferred by thermotolerant and thermophilic bacteria.
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Affiliation(s)
- Bertrand Caron
- †School of Chemistry and Molecular Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alan E Mark
- †School of Chemistry and Molecular Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David Poger
- †School of Chemistry and Molecular Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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15
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Laner M, Horta BAC, Hünenberger PH. Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation. J Mol Graph Model 2014; 55:48-64. [PMID: 25437095 DOI: 10.1016/j.jmgm.2014.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
Abstract
The occurrence of long-timescale motions in glycerol-1-monopalmitate (GMP) lipid bilayers is investigated based on previously reported 600 ns molecular dynamics simulations of a 2×8×8 GMP bilayer patch in the temperature range 302-338 K, performed at three different hydration levels, or in the presence of the cosolutes methanol or trehalose at three different concentrations. The types of long-timescale motions considered are: (i) the possible phase transitions; (ii) the precession of the relative collective tilt-angle of the two leaflets in the gel phase; (iii) the trans-gauche isomerization of the dihedral angles within the lipid aliphatic tails; and (iv) the flipping of single lipids across the two leaflets. The results provide a picture of GMP bilayers involving a rich spectrum of events occurring on a wide range of timescales, from the 100-ps range isomerization of single dihedral angles, via the 100-ns range of tilt precession motions, to the multi-μs range of phase transitions and lipid-flipping events.
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Affiliation(s)
- Monika Laner
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Bruno A C Horta
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland; Dpto. de Engenharia Elétrica, PUC-Rio, Rio de Janeiro, Brazil; Dpto. de Ciências Biológicas, UEZO, Rio de Janeiro, Brazil.
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16
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Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:517-44. [DOI: 10.1007/s00249-014-0982-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/16/2014] [Accepted: 07/24/2014] [Indexed: 10/24/2022]
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17
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Schmid F, Dolezel S, Lenz O, Meinhardt S. On ripples and rafts: Curvature induced nanoscale structures in lipid membranes. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/1742-6596/487/1/012004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Weiß K, Neef A, Van Q, Kramer S, Gregor I, Enderlein J. Quantifying the diffusion of membrane proteins and peptides in black lipid membranes with 2-focus fluorescence correlation spectroscopy. Biophys J 2014; 105:455-62. [PMID: 23870266 DOI: 10.1016/j.bpj.2013.06.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 06/04/2013] [Accepted: 06/05/2013] [Indexed: 10/26/2022] Open
Abstract
Protein diffusion in lipid membranes is a key aspect of many cellular signaling processes. To quantitatively describe protein diffusion in membranes, several competing theoretical models have been proposed. Among these, the Saffman-Delbrück model is the most famous. This model predicts a logarithmic dependence of a protein's diffusion coefficient on its inverse hydrodynamic radius (D ∝ ln 1/R) for small radius values. For large radius values, it converges toward a D ∝ 1/R scaling. Recently, however, experimental data indicate a Stokes-Einstein-like behavior (D ∝ 1/R) of membrane protein diffusion at small protein radii. In this study, we investigate protein diffusion in black lipid membranes using dual-focus fluorescence correlation spectroscopy. This technique yields highly accurate diffusion coefficients for lipid and protein diffusion in membranes. We find that despite its simplicity, the Saffman-Delbrück model is able to describe protein diffusion extremely well and a Stokes-Einstein-like behavior can be ruled out.
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Affiliation(s)
- Kerstin Weiß
- III. Institute of Physics, Georg-August-University Göttingen, Göttingen, Germany
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Rahmani A, Knight C, Morrow MR. Response to hydrostatic pressure of bicellar dispersions containing an anionic lipid: pressure-induced interdigitation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:13481-13490. [PMID: 24116385 DOI: 10.1021/la4035694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bicellar dispersions of chain perdeuterated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC-d54), 1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DMPG), and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), with molar ratios of 3:1:1, were studied using variable-pressure (2)H NMR spectroscopy at hydrostatic pressures up to 125 MPa. Upon warming of the dispersions, spectra at ambient pressure indicated a progressive coalescence from small bilayered disks undergoing isotropic reorientation to more extended micellar structures in which spectra indicated anisotropic reorientation and, under some conditions, magnetic orientation and finally to randomly oriented lamellae or multilamellar vesicles. Temperatures for the onsets of anisotropic reorientation and random lamellar orientation increased with pressure at rates of 0.22 and 0.15 °C/MPa, respectively. In the 3.5-T magnetic field used for this work, magnetic orientation within the intermediate phase was not observed at 83 MPa or higher pressures. Comparison of spectra obtained at fixed pressure showed significant asymmetry between behaviors upon warming and cooling. For samples of DMPC-d54/DMPG/DHPC (3:1:1), but not DMPC-d54/DHPC (4:1), a persistent interdigitated phase was formed after repeated cooling from high temperature at 83 MPa. This is likely a metastable phase and might reflect kinetic trapping of the short-chain lipid component, DHPC, in a nonequilibrium spatial distribution as temperature is lowered at high pressure. Bicellar dispersions typically behave differently upon warming and cooling, and these observations could provide some insight into the observed behaviors in such systems. This work also suggests the possibility of trapping bicellar dispersions in persistent nonequilibrium morphologies.
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Affiliation(s)
- Ashkan Rahmani
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland , St. John's, Newfoundland and Labrador, Canada A1B 3X7
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FTIR spectroscopy study of the pressure-dependent behaviour of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1-palmitoyl-2-oleolyl-sn-glycero-3-phosphocholine (POPC) at low degrees of hydration. Chem Phys Lipids 2013; 170-171:33-40. [DOI: 10.1016/j.chemphyslip.2013.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/18/2013] [Accepted: 02/19/2013] [Indexed: 11/22/2022]
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Computational Studies of Biomembrane Systems: Theoretical Considerations, Simulation Models, and Applications. FROM SINGLE MOLECULES TO NANOSCOPICALLY STRUCTURED MATERIALS 2013. [DOI: 10.1007/12_2013_258] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Corradi V, Singh G, Tieleman DP. The human transporter associated with antigen processing: molecular models to describe peptide binding competent states. J Biol Chem 2012; 287:28099-111. [PMID: 22700967 PMCID: PMC3431710 DOI: 10.1074/jbc.m112.381251] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human transporter associated with antigen processing (TAP) is a member of the ATP binding cassette (ABC) transporter superfamily. TAP plays an essential role in the antigen presentation pathway by translocating cytosolic peptides derived from proteasomal degradation into the endoplasmic reticulum lumen. Here, the peptides are loaded into major histocompatibility class I molecules to be in turn exposed at the cell surface for recognition by T-cells. TAP is a heterodimer formed by the association of two half-transporters, TAP1 and TAP2, with a typical ABC transporter core that consists of two nucleotide binding domains and two transmembrane domains. Despite the availability of biological data, a full understanding of the mechanism of action of TAP is limited by the absence of experimental structures of the full-length transporter. Here, we present homology models of TAP built on the crystal structures of P-glycoprotein, ABCB10, and Sav1866. The models represent the transporter in inward- and outward-facing conformations that could represent initial and final states of the transport cycle, respectively. We described conserved regions in the endoplasmic reticulum-facing loops with a role in the opening and closing of the cavity. We also identified conserved π-stacking interactions in the cytosolic part of the transmembrane domains that could explain the experimental data available for TAP1-Phe-265. Electrostatic potential calculations gave structural insights into the role of residues involved in peptide binding, such as TAP1-Val-288, TAP2-Cys-213, TAP2-Met-218. Moreover, these calculations identified additional residues potentially involved in peptide binding, in turn verified with replica exchange simulations performed on a peptide bound to the inward-facing models.
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Affiliation(s)
- Valentina Corradi
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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Lai K, Wang B, Zhang Y, Zhang Y. High pressure effect on phase transition behavior of lipid bilayers. Phys Chem Chem Phys 2012; 14:5744-52. [DOI: 10.1039/c2cp24140d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Correlation between the ripple phase and stripe domains in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2849-58. [DOI: 10.1016/j.bbamem.2011.08.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 08/12/2011] [Accepted: 08/16/2011] [Indexed: 12/19/2022]
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