1
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Gentile L. Morphological Influence on a Nonionic Bilayer Bending Rigidity and Compression Modulus. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 39096503 DOI: 10.1021/acs.langmuir.4c02346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
The mechanical properties of multilamellar vesicles and their relevance to soft matter physics and material science are of significant interest. The bending rigidity, κ, and compression modulus, B, of three-dimensional (3D) finite nonspontaneous multilamellar vesicles, formed by a nonionic surfactant, are linked to nanoscale bilayer thickness, δ, estimated via small-angle X-ray scattering, and macroscopic elastic modulus measured through small-amplitude oscillatory shear experiments. κ and B significantly differ from the same system in the two-dimensional (2D) infinite nanostructured planar lamellar phase. Particularly, κ3D was found to be much smaller than κ2D, while an opposite behavior was seen for B. The 2D-to-3D morphology transition occurs under a transient mechanical field, resulting in rheopectic behavior. κ scales quadratically with δ, consistent with bilayer membrane theories, and linearly with vesicle radius in the densely packed state. These findings have implications for understanding and designing soft interfaces due to the influence of bending rigidity on transport properties.
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Affiliation(s)
- Luigi Gentile
- Department of Chemistry, University of Bari "Aldo Moro", Via Orabona 4, Bari 70126, Italy
- Center of Colloid and Surface Science (CSGI) Bari Unit, Via Orabona 4, Bari 70126, Italy
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2
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Pöhnl M, Trollmann MFW, Böckmann RA. Nonuniversal impact of cholesterol on membranes mobility, curvature sensing and elasticity. Nat Commun 2023; 14:8038. [PMID: 38081812 PMCID: PMC10713574 DOI: 10.1038/s41467-023-43892-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Biological membranes, composed mainly of phospholipids and cholesterol, play a vital role as cellular barriers. They undergo localized reshaping in response to environmental cues and protein interactions, with the energetics of deformations crucial for exerting biological functions. This study investigates the non-universal role of cholesterol on the structure and elasticity of saturated and unsaturated lipid membranes. Our study uncovers a highly cooperative relationship between thermal membrane bending and local cholesterol redistribution, with cholesterol showing a strong preference for the compressed membrane leaflet. Remarkably, in unsaturated membranes, increased cholesterol mobility enhances cooperativity, resulting in membrane softening despite membrane thickening and lipid compression caused by cholesterol. These findings elucidate the intricate interplay between thermodynamic forces and local molecular interactions that govern collective properties of membranes.
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Affiliation(s)
- Matthias Pöhnl
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Marius F W Trollmann
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Erlangen National High Perfomance Computing Center (NHR@FAU), Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
- Erlangen National High Perfomance Computing Center (NHR@FAU), Erlangen, Germany.
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3
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Konar S, Arif H, Allolio C. Mitochondrial membrane model: Lipids, elastic properties, and the changing curvature of cardiolipin. Biophys J 2023; 122:4274-4287. [PMID: 37798880 PMCID: PMC10645570 DOI: 10.1016/j.bpj.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/12/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023] Open
Abstract
Mammalian and Drosophila melanogaster model mitochondrial membrane compositions are constructed from experimental data. Simplified compositions for inner and outer mitochondrial membranes are provided, including an asymmetric inner mitochondrial membrane. We performed atomistic molecular dynamics simulations of these membranes and computed their material properties. When comparing these properties to those obtained by extrapolation from their constituting lipids, we find good overall agreement. Finally, we analyzed the curvature effect of cardiolipin, considering ion concentration effects, oxidation, and pH. We draw the conclusion that cardiolipin-negative curvature is most likely due to counterion effects, such as cation adsorption, in particular of H3O+. This oft-neglected effect might account for the puzzling behavior of this lipid.
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Affiliation(s)
- Sukanya Konar
- Faculty of Mathematics and Physics, Mathematical Institute, Charles University, Prague, Czech Republic
| | - Hina Arif
- Faculty of Mathematics and Physics, Mathematical Institute, Charles University, Prague, Czech Republic
| | - Christoph Allolio
- Faculty of Mathematics and Physics, Mathematical Institute, Charles University, Prague, Czech Republic.
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4
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Doktorova M, Khelashvili G, Ashkar R, Brown MF. Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics. Biophys J 2023; 122:984-1002. [PMID: 36474442 PMCID: PMC10111610 DOI: 10.1016/j.bpj.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/21/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022] Open
Abstract
Lipid bilayers form the main matrix of functional cell membranes, and their dynamics underlie a host of physical and biological processes. Here we show that elastic membrane properties and collective molecular dynamics (MD) are related by the mean-square amplitudes (order parameters) and relaxation rates (correlation times) of lipid acyl chain motions. We performed all-atom MD simulations of liquid-crystalline bilayers that allow direct comparison with carbon-hydrogen (CH) bond relaxations measured with NMR spectroscopy. Previous computational and theoretical approaches have assumed isotropic relaxation, which yields inaccurate description of lipid chain dynamics and incorrect data interpretation. Instead, the new framework includes a fixed bilayer normal (director axis) and restricted anisotropic motion of the CH bonds in accord with their segmental order parameters, enabling robust validation of lipid force fields. Simulated spectral densities of thermally excited CH bond fluctuations exhibited well-defined spin-lattice (Zeeman) relaxations analogous to those in NMR measurements. Their frequency signature could be fit to a simple power-law function, indicative of nematic-like collective dynamics. Moreover, calculated relaxation rates scaled as the squared order parameters yielding an apparent κC modulus for bilayer bending. Our results show a strong correlation with κC values obtained from solid-state NMR studies of bilayers without and with cholesterol as validated by neutron spin-echo measurements of membrane elasticity. The simulations uncover a critical role of interleaflet coupling in membrane mechanics and thus provide important insights into molecular sites of emerging elastic properties within lipid bilayers.
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Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York; Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, Virginia; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona; Department of Physics, University of Arizona, Tucson, Arizona; Program in Applied Mathematics, University of Arizona, Tucson, Arizona.
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5
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Svoboda M, Jiménez S MG, Kowalski A, Cooke M, Mendoza C, Lísal M. Structural properties of cationic surfactant-fatty alcohol bilayers: insights from dissipative particle dynamics. SOFT MATTER 2021; 17:9967-9984. [PMID: 34704992 DOI: 10.1039/d1sm00850a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bilayers, self-assembled by cationic surfactants and fatty alcohols in water, are the basic units of lamellar gel networks - creamy formulations extensively used in cosmetics and pharmaceutics. Mesoscopic modelling and study of the bilayers formed by single- or double-tail cationic surfactants (CTAC or DHDAC), and fatty alcohols (FAs) in the lamellar fluid and gel phases were employed. Fatty alcohols with alkyl tail equal to or greater than the surfactant alkyl tail, i.e., C16FA or C18FA and C22FA, were considered. A model formulation was explored with the FA concentration greater than that of the surfactant and the structure of the fluid and gel bilayers in tensionless state characterised via the density profiles across the bilayers, orientational order parameters of the surfactant and FA chains, intrinsic analysis of the bilayer interfaces, and bending rigidity. The intrinsic analysis allows identification and quantification of the coexistence of the interdigitated and non-interdigitated phases present within the gel bilayers. The FA chains were found to conform the primary scaffolding of the bilayers while the surfactant chains tessellate bilayer monolayers from their water-hydrophobic interface. Further, the overlap of the FA chains from the apposed monolayers of the fluid bilayers rises with increasing FA length. Finally, the prevalence of the non-interdigitated phase over the interdigitated phase within the gel bilayers becomes enhanced upon the FA length increase with a preference of the surfactant chains to reside in the non-interdigitated phase rather than the interdigitated phase.
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Affiliation(s)
- Martin Svoboda
- Department of Molecular and Mesoscopic Modelling, The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135/1, Prague, Czech Republic.
- Department of Physics, Faculty of Science, Jan Evangelista Purkyně University in Úst nad Labem, Pasteurova 1, Úst nad Labem, Czech Republic
| | | | - Adam Kowalski
- Unilever R&D, Port Sunlight Laboratory, Quarry Road East, Bebington, Wirral CH63 3JW, UK
| | - Michael Cooke
- Unilever R&D, Port Sunlight Laboratory, Quarry Road East, Bebington, Wirral CH63 3JW, UK
| | - César Mendoza
- Unilever R&D, Port Sunlight Laboratory, Quarry Road East, Bebington, Wirral CH63 3JW, UK
| | - Martin Lísal
- Department of Molecular and Mesoscopic Modelling, The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135/1, Prague, Czech Republic.
- Department of Physics, Faculty of Science, Jan Evangelista Purkyně University in Úst nad Labem, Pasteurova 1, Úst nad Labem, Czech Republic
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6
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Beaven AH, Arnarez C, Lyman E, Bennett WFD, Sodt AJ. Curvature Energetics Determined by Alchemical Simulation on Four Topologically Distinct Lipid Phases. J Phys Chem B 2021; 125:1815-1824. [PMID: 33570958 PMCID: PMC9069320 DOI: 10.1021/acs.jpcb.0c09458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The relative curvature energetics of two lipids are tested using thermodynamic integration (TI) on four topologically distinct lipid phases. Simulations use TI to switch between choline headgroup lipids (POPC; that prefers to be flat) and ethanolamine headgroup lipids (POPE; that prefer, for example, the inner monolayer of vesicles). The thermodynamical moving of the lipids between planar, inverse hexagonal (HII), cubic (QII; Pn3m space group), and vesicle topologies reveals differences in material parameters that were previously challenging to access. The methodology allows for predictions of two important lipid material properties: the difference in POPC/POPE monolayer intrinsic curvature (ΔJ0) and the difference in POPC/POPE monolayer Gaussian curvature modulus (Δκ̅m), both of which are connected to the energetics of topological variation. Analysis of the TI data indicates that, consistent with previous experiment and simulation, the J0 of POPE is more negative than POPC (ΔJ0 = -0.018 ± 0.001 Å-1). The theoretical framework extracts significant differences in κ̅m of which POPE is less negative than POPC by 2.0 to 4.0 kcal/mol. The range of these values is determined by considering subsets of the simulations, and disagreement between these subsets suggests separate mechanical parameters at very high curvature. Finally, the fit of the TI data to the model indicates that the position of the pivotal plane of curvature is not constant across topologies at high curvature. Overall, the results offer insights into lipid material properties, the limits of a single HC model, and how to test them using simulation.
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Affiliation(s)
- Andrew H Beaven
- Unit on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Clément Arnarez
- Department of Physics and Astronomy, Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Edward Lyman
- Department of Physics and Astronomy, Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - W F Drew Bennett
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Alexander J Sodt
- Unit on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
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7
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Schachter I, Allolio C, Khelashvili G, Harries D. Confinement in Nanodiscs Anisotropically Modifies Lipid Bilayer Elastic Properties. J Phys Chem B 2020; 124:7166-7175. [PMID: 32697588 PMCID: PMC7526989 DOI: 10.1021/acs.jpcb.0c03374] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
Lipid
nanodiscs are small synthetic lipid bilayer structures that
are stabilized in solution by special circumscribing (or scaffolding)
proteins or polymers. Because they create native-like environments
for transmembrane proteins, lipid nanodiscs have become a powerful
tool for structural determination of this class of systems when combined
with cryo-electron microscopy or nuclear magnetic resonance. The elastic
properties of lipid bilayers determine how the lipid environment responds
to membrane protein perturbations, and how the lipid in turn modifies
the conformational state of the embedded protein. However, despite
the abundant use of nanodiscs in determining membrane protein structure,
the elastic material properties of even pure lipid nanodiscs (i.e.,
without embedded proteins) have not yet been quantitatively investigated.
A major hurdle is due to the inherently nonlocal treatment of the
elastic properties of lipid systems implemented by most existing methods,
both experimental and computational. In addition, these methods are
best suited for very large “infinite” size lipidic assemblies,
or ones that contain periodicity, in the case of simulations. We have
previously described a computational analysis of molecular dynamics
simulations designed to overcome these limitations, so it allows quantification
of the bending rigidity (KC) and tilt
modulus (κt) on a local scale even for finite, nonperiodic
systems, such as lipid nanodiscs. Here we use this computational approach
to extract values of KC and κt for a set of lipid nanodisc systems that vary in size and
lipid composition. We find that the material properties of lipid nanodiscs
are different from those of infinite bilayers of corresponding lipid
composition, highlighting the effect of nanodisc confinement. Nanodiscs
tend to show higher stiffness than their corresponding macroscopic
bilayers, and moreover, their material properties vary spatially within
them. For small-size MSP1 nanodiscs, the stiffness decreases radially,
from a value that is larger in their center than the moduli of the
corresponding bilayers by a factor of ∼2–3. The larger
nanodiscs (MSP1E3D1 and MSP2N2) show milder spatial changes of moduli
that are composition dependent and can be maximal in the center or
at some distance from it. These trends in moduli correlate with spatially
varying structural properties, including the area per lipid and the
nanodisc thickness. Finally, as has previously been reported, nanodiscs
tend to show deformations from perfectly flat circular geometries
to varying degrees, depending on size and lipid composition. The modulations
of lipid elastic properties that we find should be carefully considered
when making structural and functional inferences concerning embedded
proteins.
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Affiliation(s)
- Itay Schachter
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Christoph Allolio
- Institute of Mathematics, Faculty of Mathematics and Physics, Charles University, Prague 18674, Czech Republic
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States.,Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
| | - Daniel Harries
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
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8
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Ohashi Y, Tremel S, Masson GR, McGinney L, Boulanger J, Rostislavleva K, Johnson CM, Niewczas I, Clark J, Williams RL. Membrane characteristics tune activities of endosomal and autophagic human VPS34 complexes. eLife 2020; 9:58281. [PMID: 32602837 PMCID: PMC7326497 DOI: 10.7554/elife.58281] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/04/2020] [Indexed: 12/14/2022] Open
Abstract
The lipid kinase VPS34 orchestrates diverse processes, including autophagy, endocytic sorting, phagocytosis, anabolic responses and cell division. VPS34 forms various complexes that help adapt it to specific pathways, with complexes I and II being the most prominent ones. We found that physicochemical properties of membranes strongly modulate VPS34 activity. Greater unsaturation of both substrate and non-substrate lipids, negative charge and curvature activate VPS34 complexes, adapting them to their cellular compartments. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) of complexes I and II on membranes elucidated structural determinants that enable them to bind membranes. Among these are the Barkor/ATG14L autophagosome targeting sequence (BATS), which makes autophagy-specific complex I more active than the endocytic complex II, and the Beclin1 BARA domain. Interestingly, even though Beclin1 BARA is common to both complexes, its membrane-interacting loops are critical for complex II, but have only a minor role for complex I.
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Affiliation(s)
- Yohei Ohashi
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Shirley Tremel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Glenn Robert Masson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Lauren McGinney
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Jerome Boulanger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Ksenia Rostislavleva
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Christopher M Johnson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | | | | | - Roger L Williams
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
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9
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Ramezanpour M, Schmidt ML, Bashe BYM, Pruim JR, Link ML, Cullis PR, Harper PE, Thewalt JL, Tieleman DP. Structural Properties of Inverted Hexagonal Phase: A Hybrid Computational and Experimental Approach. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:6668-6680. [PMID: 32437159 DOI: 10.1021/acs.langmuir.0c00600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Inverted/reverse hexagonal (HII) phases are of special interest in several fields of research, including nanomedicine. We used molecular dynamics (MD) simulation to study HII systems composed of dioleoylphosphatidylethanolamine (DOPE) and palmitoyloleoylphosphatidylethanolamine (POPE) at several hydration levels and temperatures. The effect of the hydration level on several HII structural parameters, including deuterium order parameters, was investigated. We further used MD simulations to estimate the maximum hydrations of DOPE and POPE HII lattices at several given temperatures. Finally, the effect of acyl chain unsaturation degree on the HII structure was studied via comparing the DOPE with POPE HII systems. In addition to MD simulations, we used deuterium nuclear magnetic resonance (2H NMR) and small-angle X-ray scattering (SAXS) experiments to measure the DOPE acyl chain order parameters, lattice plane distances, and the water core radius in HII phase DOPE samples at several temperatures in the presence of excess water. Structural parameters calculated from MD simulations are in excellent agreement with the experimental data. Dehydration decreases the radius of the water core. An increase in hydration level slightly increased the deuterium order parameter of lipids acyl chains, whereas an increase in temperature decreased it. Lipid cylinders undulated along the cylinder axis as a function of hydration level. The maximum hydration levels of PE HII phases at different temperatures were successfully predicted by MD simulations based on a single experimental measurement for the lattice plane distance in the presence of excess water. An increase in temperature decreases the maximum hydration and consequently the radius of the water core and lattice plane distances. Finally, DOPE formed HII structures with a higher curvature compared to POPE, as expected. We propose a general protocol for constructing computational HII systems that correspond to the experimental systems. This protocol could be used to study HII systems composed of molecules other than the PE systems used here and to improve and validate force field parameters by using the target data in the HII phase.
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Affiliation(s)
- M Ramezanpour
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - M L Schmidt
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - B Y M Bashe
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - J R Pruim
- Department of Physics and Astronomy, Calvin University, Grand Rapids, Michigan 49546, United States
| | - M L Link
- Department of Physics and Astronomy, Calvin University, Grand Rapids, Michigan 49546, United States
| | - P R Cullis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - P E Harper
- Department of Physics and Astronomy, Calvin University, Grand Rapids, Michigan 49546, United States
| | - J L Thewalt
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - D P Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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10
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Shi W. Role of Defects in Achieving Highly Asymmetric Lamellar Self-Assembly in Block Copolymer/Homopolymer Blends. J Phys Chem Lett 2020; 11:2724-2730. [PMID: 32203668 DOI: 10.1021/acs.jpclett.0c00459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lamellar structure is a prominent state in soft condensed matter. Swelling lamellar layers to highly asymmetric structures by a second component is a facile, cost-effective strategy to impart materials with adaptive size and tunable properties. One key question that remains unsolved is how defects form and affect the asymmetric lamellar order. This study unravels the role of defects by swelling a miktoarm block copolymer with a homopolymer. Ordered lamellae first lose translational order by a significant increase in the number of dislocations and then lose orientational order by the generation of disclinations. The homopolymers are not uniformly distributed in defective lamellae and primarily segregate in the vicinity of disclination cores. The free energy of defects is mainly contributed by molecular splay and significantly alleviated by an increased radius of local curvature. This study provides direct evidence to reveal the role of defects and lamellar order in block copolymer/homopolymer blends and also sheds light on understanding analogous structural transitions in other soft systems, including lyotropic liquid crystals, phospholipid membranes, and polymer nanocomposites.
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Affiliation(s)
- Weichao Shi
- Key Laboratory of Functional Polymer Materials (Ministry of Education) and Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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11
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Doktorova M, LeVine MV, Khelashvili G, Weinstein H. A New Computational Method for Membrane Compressibility: Bilayer Mechanical Thickness Revisited. Biophys J 2019; 116:487-502. [PMID: 30665693 DOI: 10.1016/j.bpj.2018.12.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/27/2018] [Accepted: 12/20/2018] [Indexed: 01/24/2023] Open
Abstract
Because lipid bilayers can bend and stretch in ways similar to thin elastic sheets, physical models of bilayer deformation have utilized mechanical constants such as the moduli for bending rigidity (κC) and area compressibility (KA). However, the use of these models to quantify the energetics of membrane deformation associated with protein-membrane interactions, and the membrane response to stress is often hampered by the shortage of experimental data suitable for the estimation of the mechanical constants of various lipid mixtures. Although computational tools such as molecular dynamics simulations can provide alternative means to estimate KA values, current approaches suffer significant technical limitations. Here, we present a novel, to our knowledge, computational framework that allows for a direct estimation of KA values for individual bilayer leaflets. The theory is based on the concept of elasticity and derives KA from real-space analysis of local thickness fluctuations sampled in molecular dynamics simulations. We explore and validate the model on a large set of single and multicomponent bilayers of different lipid compositions and sizes, simulated at different temperatures. The calculated bilayer compressibility moduli agree with values estimated previously from experiments and those obtained from a standard computational method based on a series of constrained tension simulations. We further validate our framework in a comparison with an existing polymer brush model and confirm the polymer brush model's predicted linear relationship with proportionality coefficient of 24, using elastic parameters calculated from the simulation trajectories. The robustness of the results that emerge from the method allows us to revisit the origins of the bilayer mechanical (compressible) thickness and in particular its dependence on acyl-chain unsaturation and the presence of cholesterol.
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Affiliation(s)
- Milka Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York.
| | - Michael V LeVine
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Greenberg Center, New York, New York
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Greenberg Center, New York, New York
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Greenberg Center, New York, New York
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12
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Boyd KJ, May ER. BUMPy: A Model-Independent Tool for Constructing Lipid Bilayers of Varying Curvature and Composition. J Chem Theory Comput 2018; 14:6642-6652. [PMID: 30431272 DOI: 10.1021/acs.jctc.8b00765] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics is a powerful tool to investigate atomistic and mesoscopic phenomena in lipid bilayer systems. These studies have progressed with the advent of increased computational power, and efforts are now increasingly being directed toward investigating the role of curvature and bilayer morphology, as these are critical features of biological processes. Computational studies of lipid bilayers benefit from tools that can create starting configurations for molecular dynamics simulations, but the majority of such tools are restricted to generating flat bilayers. Generating curved bilayer configurations comes with practical complications and potential ramifications on physical properties in the simulated system if the bilayer is initiated in a high-strain state. We present a new tool for creating curved lipid bilayers that combines flexibility of shape, force field, model resolution, and bilayer composition. A key aspect of our approach is the use of the monolayer pivotal plane location to accurately estimate interleaflet area differences in a curved bilayer. Our tool is named BUMPy (Building Unique Membranes in Python), is written in Python, is fast, and has a simple command line interface.
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Affiliation(s)
- Kevin J Boyd
- Department of Molecular and Cell Biology , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Eric R May
- Department of Molecular and Cell Biology , University of Connecticut , Storrs , Connecticut 06269 , United States
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13
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Allolio C, Haluts A, Harries D. A local instantaneous surface method for extracting membrane elastic moduli from simulation: Comparison with other strategies. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Doktorova M, Harries D, Khelashvili G. Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations. Phys Chem Chem Phys 2018. [PMID: 28627570 DOI: 10.1039/c7cp01921a] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have recently developed a novel computational methodology (termed RSF for Real-Space Fluctuations) to quantify the bending rigidity and tilt modulus of lipid membranes from real-space analysis of fluctuations in the tilt and splay degrees of freedom as sampled in molecular dynamics (MD) simulations. In this article, we present a comprehensive study that combines results from the application of the RSF method to a wide range of lipid bilayer systems that encompass membranes of different fluidities and sizes, including lipids with saturated and unsaturated lipid tails, single and multi-component lipid systems, as well as non-standard lipids such as the four-tailed cardiolipin. By comparing the material properties calculated with the RSF method to those obtained from experimental data and from other computational methodologies, we rigorously demonstrate the validity of our approach and show its robustness. This should allow for future applications of even more complex lipidic assemblies, whose material properties are not tractable by other computational techniques. In addition, we discuss the relationship between different definitions of the tilt modulus appearing in current literature to address some important unresolved discrepancies in the field.
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Affiliation(s)
- M Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
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Boyd KJ, Alder NN, May ER. Buckling Under Pressure: Curvature-Based Lipid Segregation and Stability Modulation in Cardiolipin-Containing Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6937-6946. [PMID: 28628337 PMCID: PMC5654595 DOI: 10.1021/acs.langmuir.7b01185] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Mitochondrial metabolic function is affected by the morphology and protein organization of the mitochondrial inner membrane. Cardiolipin (CL) is a unique tetra-acyl lipid that is involved in the maintenance of the highly curved shape of the mitochondrial inner membrane as well as spatial organization of the proteins necessary for respiration and oxidative phosphorylation. Cardiolipin has been suggested to self-organize into lipid domains due to its inverted conical molecular geometry, though the driving forces for this organization are not fully understood. In this work, we use coarse-grained molecular dynamics simulations to study the mechanical properties and lipid dynamics in heterogeneous bilayers both with and without CL, as a function of membrane curvature. We find that incorporation of CL increases bilayer deformability and that CL becomes highly enriched in regions of high negative curvature. We further show that another mitochondrial inverted conical lipid, phosphatidylethanolamine (PE), does not partition or increase the deformability of the membrane in a significant manner. Therefore, CL appears to possess some unique characteristics that cannot be inferred simply from molecular geometry considerations.
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Johner N, Harries D, Khelashvili G. Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations. BMC Bioinformatics 2016; 17:161. [PMID: 27071656 PMCID: PMC4830014 DOI: 10.1186/s12859-016-1003-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/27/2016] [Indexed: 12/13/2022] Open
Abstract
Background The importance of the material properties of membranes for diverse cellular processes is well established. Notably, the elastic properties of the membrane, which depend on its composition, can directly influence membrane reshaping and fusion processes as well as the organisation and function of membrane proteins. Determining these properties is therefore key for a mechanistic understanding of how the cell functions. Results We have developed a method to determine the bending rigidity and tilt modulus, for lipidic assemblies of arbitrary lipid composition and shape, from molecular dynamics simulations. The method extracts the elastic moduli from the distributions of microscopic tilts and splays of the lipid components. We present here an open source implementation of the method as a set of Python modules using the computational framework OpenStructure. These modules offer diverse algorithms typically used in the calculatation the elastic moduli, including routines to align MD trajectories of complex lipidic systems, to determine the water/lipid interface, to calculate lipid tilts and splays, as well as to fit the corresponding distributions to extract the elastic properties. We detail the implementation of the method and give several examples of how to use the modules in specific cases. Conclusions The method presented here is, to our knowledge, the only available computational approach allowing to quantify the elastic properties of lipidic assemblies of arbitrary shape and composition (including lipid mixtures). The implementation as python modules offers flexibility, which has already allowed the method to be applied to diverse lipid assembly types, ranging from bilayers in the liquid ordered and disordered phases to a study of the inverted-hexagonal phase, and with different force-fields (both all-atom and coarse grained representations). The modules are freely available through GitHub at https://github.com/njohner/ost_pymodules/ while OpenStructure can be obtained at http://www.openstructure.org.
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Affiliation(s)
- Niklaus Johner
- Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, Basel, Switzerland.
| | - Daniel Harries
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem, 91904, Israel
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, 10065, USA
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Diggins P, McDargh ZA, Deserno M. Curvature Softening and Negative Compressibility of Gel-Phase Lipid Membranes. J Am Chem Soc 2015; 137:12752-5. [PMID: 26413857 DOI: 10.1021/jacs.5b06800] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We show that gel-phase lipid membranes soften upon bending, leading to curvature localization and a negative compressibility. Using simulations of two very different lipid models to quantify shape and stress-strain relation of buckled membranes, we demonstrate that gel phase bilayers do not behave like Euler elastica and hence are not well described by a quadratic Helfrich Hamiltonian, much unlike their fluid-phase counterparts. We propose a theoretical framework which accounts for the observed softening through an energy density that smoothly crosses over from a quadratic to a linear curvature dependence beyond a critical new scale [Formula: see text](-1). This model captures both the shape and the stress-strain relation for our two sets of simulations and permits the extraction of bending moduli, which are found to be about an order of magnitude larger than the corresponding fluid phase values. We also find surprisingly large crossover lengths [Formula: see text], several times bigger than the bilayer thickness, rendering the exotic elasticity of gel-phase membranes more strongly pronounced than that of homogeneous compressible sheets and artificial metamaterials. We suggest that such membranes have unexpected potential as nanoscale systems with striking materials characteristics.
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Affiliation(s)
- Patrick Diggins
- Department of Physics, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Zachary A McDargh
- Department of Physics, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
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