1
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Xu J, Karra V, Large DE, Auguste DT, Hung FR. Understanding the Mechanical Properties of Ultradeformable Liposomes Using Molecular Dynamics Simulations. J Phys Chem B 2023; 127:9496-9512. [PMID: 37879075 PMCID: PMC10641833 DOI: 10.1021/acs.jpcb.3c04386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/19/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Improving drug delivery efficiency to solid tumor sites is a central challenge in anticancer therapeutic research. Our previous experimental study (Guo et al., Nat. Commun. 2018, 9, 130) showed that soft, elastic liposomes had increased uptake and accumulation in cancer cells and tumors in vitro and in vivo respectively, relative to rigid particles. As a first step toward understanding how liposomes' molecular structure and composition modulates their elasticity, we performed all-atom and coarse-grained classical molecular dynamics (MD) simulations of lipid bilayers formed by mixing a long-tailed unsaturated phospholipid with a short-tailed saturated lipid with the same headgroup. The former types of phospholipids considered were 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dipalmitoleoyl-sn-glycero-3-phosphocholine (termed here DPMPC). The shorter saturated lipids examined were 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), 1,2-didecanoyl-sn-glycero-3-phosphocholine (DDPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Several lipid concentrations and surface tensions were considered. Our results show that DOPC or DPMPC systems having 25-35 mol % of the shortest lipids DHPC or DDPC are the least rigid, having area compressibility moduli KA that are ∼10% smaller than the values observed in pure DOPC or DPMPC bilayers. These results agree with experimental measurements of the stretching modulus and lysis tension in liposomes with the same compositions. These mixed systems also have lower areas per lipid and form more uneven x-y interfaces with water, the tails of both primary and secondary lipids are more disordered, and the terminal methyl groups in the tails of the long lipid DOPC or DPMPC wriggle more in the vertical direction, compared to pure DOPC or DPMPC bilayers or their mixtures with the longer saturated lipid DLPC or DMPC. These observations confirm our hypothesis that adding increasing concentrations of the short unsaturated lipid DHPC or DDPC to DOPC or DPMPC bilayers alters lipid packing and thus makes the resulting liposomes more elastic and less rigid. No formation of lipid nanodomains was noted in our simulations, and no clear trends were observed in the lateral diffusivities of the lipids as the concentration, type of secondary lipid, and surface tension were varied.
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Affiliation(s)
- Jiaming Xu
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Vyshnavi Karra
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Danielle E. Large
- Department
of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Debra T. Auguste
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Francisco R. Hung
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
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2
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Shafieenezhad A, Mitra S, Wassall SR, Tristram-Nagle S, Nagle JF, Petrache HI. Location of dopamine in lipid bilayers and its relevance to neuromodulator function. Biophys J 2023; 122:1118-1129. [PMID: 36804668 PMCID: PMC10111280 DOI: 10.1016/j.bpj.2023.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/18/2022] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Dopamine (DA) is a neurotransmitter that also acts as a neuromodulator, with both functions being essential to brain function. Here, we present the first experimental measurement of DA location in lipid bilayers using x-ray diffuse scattering, solid-state deuterium NMR, and electron paramagnetic resonance. We find that the association of DA with lipid headgroups as seen in electron density profiles leads to an increase of intermembrane repulsion most likely due to electrostatic charging. DA location in the lipid headgroup region also leads to an increase of the cross-sectional area per lipid without affecting the bending rigidity significantly. The order parameters measured by solid-state deuterium NMR decrease in the presence of DA for the acyl chains of PC and PS lipids, consistent with an increase in the area per lipid due to DA. Most importantly, these results support the hypothesis that three-dimensional diffusion of DA to target membranes could be followed by relatively more efficient two-dimensional diffusion to receptors within those membranes.
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Affiliation(s)
- Azam Shafieenezhad
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | - Saheli Mitra
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Stephen R Wassall
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | | | - John F Nagle
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Horia I Petrache
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana.
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3
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Santos G, Díaz M. Dimensional Changes in Lipid Rafts from Human Brain Cortex Associated to Development of Alzheimer's Disease. Predictions from an Agent-Based Mathematical Model. Int J Mol Sci 2021; 22:ijms222212181. [PMID: 34830060 PMCID: PMC8620379 DOI: 10.3390/ijms222212181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/02/2021] [Accepted: 11/07/2021] [Indexed: 11/30/2022] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease caused by abnormal functioning of critical physiological processes in nerve cells and aberrant accumulation of protein aggregates in the brain. The initial cause remains elusive—the only unquestionable risk factor for the most frequent variant of the disease is age. Lipid rafts are microdomains present in nerve cell membranes and they are known to play a significant role in the generation of hallmark proteinopathies associated to AD, namely senile plaques, formed by aggregates of amyloid β peptides. Recent studies have demonstrated that human brain cortex lipid rafts are altered during early neuropathological phases of AD as defined by Braak and Braak staging. The lipid composition and physical properties of these domains appear altered even before clinical symptoms are detected. Here, we use a coarse grain molecular dynamics mathematical model to predict the dimensional evolution of these domains using the experimental data reported by our group in human frontal cortex. The model predicts significant size and frequency changes which are detectable at the earliest neuropathological stage (ADI/II) of Alzheimer’s disease. Simulations reveal a lower number and a larger size in lipid rafts from ADV/VI, the most advanced stage of AD. Paralleling these changes, the predictions also indicate that non-rafts domains undergo simultaneous alterations in membrane peroxidability, which support a link between oxidative stress and AD progression. These synergistic changes in lipid rafts dimensions and non-rafts peroxidability are likely to become part of a positive feedback loop linked to an irreversible amyloid burden and neuronal death during the evolution of AD neuropathology.
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Affiliation(s)
- Guido Santos
- Systems Biology and Mathematical Modelling Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Biology Section, Science School, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain
- Correspondence:
| | - Mario Díaz
- Laboratory of Membrane Physiology and Biophysics, Department of Animal Biology, Edaphology and Geology, Biology Section, Science School, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain;
- IUETSP (Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias), Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain
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4
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Dynamic "Molecular Portraits" of Biomembranes Drawn by Their Lateral Nanoscale Inhomogeneities. Int J Mol Sci 2021; 22:ijms22126250. [PMID: 34200697 PMCID: PMC8230387 DOI: 10.3390/ijms22126250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 01/22/2023] Open
Abstract
To date, it has been reliably shown that the lipid bilayer/water interface can be thoroughly characterized by a sophisticated so-called "dynamic molecular portrait". The latter reflects a combination of time-dependent surface distributions of various physicochemical properties, inherent in both model lipid bilayers and natural multi-component cell membranes. One of the most important features of biomembranes is their mosaicity, which is expressed in the constant presence of lateral inhomogeneities, the sizes and lifetimes of which vary in a wide range-from 1 to 103 nm and from 0.1 ns to milliseconds. In addition to the relatively well-studied macroscopic domains (so-called "rafts"), the analysis of micro- and nanoclusters (or domains) that form an instantaneous picture of the distribution of structural, dynamic, hydrophobic, electrical, etc., properties at the membrane-water interface is attracting increasing interest. This is because such nanodomains (NDs) have been proven to be crucial for the proper membrane functioning in cells. Therefore, an understanding with atomistic details the phenomena associated with NDs is required. The present mini-review describes the recent results of experimental and in silico studies of spontaneously formed NDs in lipid membranes. The main attention is paid to the methods of ND detection, characterization of their spatiotemporal parameters, the elucidation of the molecular mechanisms of their formation. Biological role of NDs in cell membranes is briefly discussed. Understanding such effects creates the basis for rational design of new prospective drugs, therapeutic approaches, and artificial membrane materials with specified properties.
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5
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Sarmento MJ, Hof M, Šachl R. Interleaflet Coupling of Lipid Nanodomains - Insights From in vitro Systems. Front Cell Dev Biol 2020; 8:284. [PMID: 32411705 PMCID: PMC7198703 DOI: 10.3389/fcell.2020.00284] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/02/2020] [Indexed: 01/09/2023] Open
Abstract
The plasma membrane is a complex system, consisting of two layers of lipids and proteins compartmentalized into small structures called nanodomains. Despite the asymmetric composition of both leaflets, coupling between the layers is surprisingly strong. This can be evidenced, for example, by recent experimental studies performed on phospholipid giant unilamellar vesicles showing that nanodomains formed in the outer layer are perfectly registered with those in the inner leaflet. Similarly, microscopic phase separation in one leaflet can induce phase separation in the opposing leaflet that would otherwise be homogeneous. In this review, we summarize the current theoretical and experimental knowledge that led to the current view that domains are – irrespective of their size – commonly registered across the bilayer. Mechanisms inducing registration of nanodomains suggested by theory and calculations are discussed. Furthermore, domain coupling is evidenced by experimental studies based on the sparse number of methods that can resolve registered from independent nanodomains. Finally, implications that those findings using model membrane studies might have for cellular membranes are discussed.
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Affiliation(s)
- Maria J Sarmento
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova, Prague, Czechia
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova, Prague, Czechia
| | - Radek Šachl
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova, Prague, Czechia
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6
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Jin Y, Liang Q, Tieleman DP. Interactions between Band 3 Anion Exchanger and Lipid Nanodomains in Ternary Lipid Bilayers: Atomistic Simulations. J Phys Chem B 2020; 124:3054-3064. [DOI: 10.1021/acs.jpcb.0c01055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yapan Jin
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
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7
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Role of Transmembrane Proteins for Phase Separation and Domain Registration in Asymmetric Lipid Bilayers. Biomolecules 2019; 9:biom9080303. [PMID: 31349669 PMCID: PMC6723173 DOI: 10.3390/biom9080303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 02/05/2023] Open
Abstract
It is well known that the formation and spatial correlation of lipid domains in the two apposed leaflets of a bilayer are influenced by weak lipid–lipid interactions across the bilayer’s midplane. Transmembrane proteins span through both leaflets and thus offer an alternative domain coupling mechanism. Using a mean-field approximation of a simple bilayer-type lattice model, with two two-dimensional lattices stacked one on top of the other, we explore the role of this “structural” inter-leaflet coupling for the ability of a lipid membrane to phase separate and form spatially correlated domains. We present calculated phase diagrams for various effective lipid–lipid and lipid–protein interaction strengths in membranes that contain a binary lipid mixture in each leaflet plus a small amount of added transmembrane proteins. The influence of the transmembrane nature of the proteins is assessed by a comparison with “peripheral” proteins, which result from the separation of one single integral protein into two independent units that are no longer structurally connected across the bilayer. We demonstrate that the ability of membrane-spanning proteins to facilitate domain formation requires sufficiently strong lipid–protein interactions. Weak lipid–protein interactions generally tend to inhibit phase separation in a similar manner for transmembrane as for peripheral proteins.
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8
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 410] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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9
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Marson D, Guida F, Şologan M, Boccardo S, Pengo P, Perissinotto F, Iacuzzi V, Pellizzoni E, Polizzi S, Casalis L, Pasquato L, Pacor S, Tossi A, Posocco P. Mixed Fluorinated/Hydrogenated Self-Assembled Monolayer-Protected Gold Nanoparticles: In Silico and In Vitro Behavior. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900323. [PMID: 30941901 DOI: 10.1002/smll.201900323] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/18/2019] [Indexed: 05/23/2023]
Abstract
Gold nanoparticles (AuNPs) covered with mixtures of immiscible ligands present potentially anisotropic surfaces that can modulate their interactions at complex nano-bio interfaces. Mixed, self-assembled, monolayer (SAM)-protected AuNPs, prepared with incompatible hydrocarbon and fluorocarbon amphiphilic ligands, are used here to probe the molecular basis of surface phase separation and disclose the role of fluorinated ligands on the interaction with lipid model membranes and cells, by integrating in silico and experimental approaches. These results indicate that the presence of fluorinated amphiphilic ligands enhances the membrane binding ability and cellular uptake of gold nanoparticles with respect to those coated only with hydrogenated amphiphilic ligands. For mixed monolayers, computational results suggest that ligand phase separation occurs on the gold surface, and the resulting anisotropy affects the number of contacts and adhesion energies with a membrane bilayer. This reflects in a diverse membrane interaction for NPs with different surface morphologies, as determined by surface plasmon resonance, as well as differential effects on cells, as observed by flow cytometry and confocal microscopy. Overall, limited changes in monolayer features can significantly affect NP surface interfacial properties, which, in turn, affect the interaction of SAM-AuNPs with cellular membranes and subsequent effects on cells.
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Affiliation(s)
- Domenico Marson
- Department of Engineering and Architecture, University of Trieste, 34127, Trieste, Italy
| | - Filomena Guida
- Department of Engineering and Architecture, University of Trieste, 34127, Trieste, Italy
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Maria Şologan
- Department of Engineering and Architecture, University of Trieste, 34127, Trieste, Italy
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127, Trieste, Italy
| | - Silvia Boccardo
- Department of Engineering and Architecture, University of Trieste, 34127, Trieste, Italy
| | - Paolo Pengo
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127, Trieste, Italy
| | - Fabio Perissinotto
- NanoInnovation Laboratory, Elettra-Sincrotrone Trieste S.C.p.A, 34149, Basovizza, Italy
| | - Valentina Iacuzzi
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Elena Pellizzoni
- Department of Engineering and Architecture, University of Trieste, 34127, Trieste, Italy
| | - Stefano Polizzi
- Department of Molecular Science and Nanosystems, Ca' Foscari University, 30172, Venezia, Italy
- Centro di Microscopia Elettronica "G. Stevanato,", 30172, Venezia-Mestre, Italy
| | - Loredana Casalis
- NanoInnovation Laboratory, Elettra-Sincrotrone Trieste S.C.p.A, 34149, Basovizza, Italy
| | - Lucia Pasquato
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127, Trieste, Italy
| | - Sabrina Pacor
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Paola Posocco
- Department of Engineering and Architecture, University of Trieste, 34127, Trieste, Italy
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10
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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11
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Abstract
In the plasma membrane of eukaryotic cells, proteins and lipids are organized in clusters, the latter ones often called lipid domains or "lipid rafts." Recent findings highlight the dynamic nature of such domains and the key role of membrane geometry and spatial boundaries. In this study, we used porous substrates with different pore radii to address precisely the extent of the geometric constraint, permitting us to modulate and investigate the size and mobility of lipid domains in phase-separated continuous pore-spanning membranes (PSMs). Fluorescence video microscopy revealed two types of liquid-ordered (lo) domains in the freestanding parts of the PSMs: (i) immobile domains that were attached to the pore rims and (ii) mobile, round-shaped lo domains within the center of the PSMs. Analysis of the diffusion of the mobile lo domains by video microscopy and particle tracking showed that the domains' mobility is slowed down by orders of magnitude compared with the unrestricted case. We attribute the reduced mobility to the geometric confinement of the PSM, because the drag force is increased substantially due to hydrodynamic effects generated by the presence of these boundaries. Our system can serve as an experimental test bed for diffusion of 2D objects in confined geometry. The impact of hydrodynamics on the mobility of enclosed lipid domains can have great implications for the formation and lateral transport of signaling platforms.
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12
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Qiao CZ, Zhao SL, Liu HL, Dong W. Fluids in porous media. IV. Quench effect on chemical potential. J Chem Phys 2017. [PMID: 28641429 DOI: 10.1063/1.4984773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
It appears to be a common sense to measure the crowdedness of a fluid system by the densities of the species constituting it. In the present work, we show that this ceases to be valid for confined fluids under some conditions. A quite thorough investigation is made for a hard sphere (HS) fluid adsorbed in a hard sphere matrix (a quench-annealed system) and its corresponding equilibrium binary mixture. When fluid particles are larger than matrix particles, the quench-annealed system can appear much more crowded than its corresponding equilibrium binary mixture, i.e., having a much higher fluid chemical potential, even when the density of each species is strictly the same in both systems, respectively. We believe that the insight gained from this study should be useful for the design of functionalized porous materials.
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Affiliation(s)
- C Z Qiao
- Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon, Université Lyon 1, Laboratoire de Chimie, UMR 5182, 46, Allée d'Italie, 69364 Lyon Cedex 07, France
| | - S L Zhao
- School of Chemical Engineering and State Key Laboratory of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237 Shanghai, China
| | - H L Liu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, 200237 Shanghai, China
| | - W Dong
- Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon, Université Lyon 1, Laboratoire de Chimie, UMR 5182, 46, Allée d'Italie, 69364 Lyon Cedex 07, France
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13
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Sizes of lipid domains: What do we know from artificial lipid membranes? What are the possible shared features with membrane rafts in cells? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:789-802. [DOI: 10.1016/j.bbamem.2017.01.030] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/21/2017] [Accepted: 01/26/2017] [Indexed: 12/13/2022]
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14
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Cámara CI, Wilke N. Interaction of dextran derivatives with lipid monolayers and the consequential modulation of the film properties. Chem Phys Lipids 2017; 204:34-42. [DOI: 10.1016/j.chemphyslip.2017.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 12/23/2022]
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15
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Schmid F. Physical mechanisms of micro- and nanodomain formation in multicomponent lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:509-528. [PMID: 27823927 DOI: 10.1016/j.bbamem.2016.10.021] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/19/2016] [Accepted: 10/27/2016] [Indexed: 12/17/2022]
Abstract
This article summarizes a variety of physical mechanisms proposed in the literature, which can generate micro- and nanodomains in multicomponent lipid bilayers and biomembranes. It mainly focusses on lipid-driven mechanisms that do not involve direct protein-protein interactions. Specifically, it considers (i) equilibrium mechanisms based on lipid-lipid phase separation such as critical cluster formation close to critical points, and multiple domain formation in curved geometries, (ii) equilibrium mechanisms that stabilize two-dimensional microemulsions, such as the effect of linactants and the effect of curvature-composition coupling in bilayers and monolayers, and (iii) non-equilibrium mechanisms induced by the interaction of a biomembrane with the cellular environment, such as membrane recycling and the pinning effects of the cytoplasm. Theoretical predictions are discussed together with simulations and experiments. The presentation is guided by the theory of phase transitions and critical phenomena, and the appendix summarizes the mathematical background in a concise way within the framework of the Ginzburg-Landau theory. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Friederike Schmid
- Institute of Physics, Johannes Gutenberg University, 55099 Mainz, Germany
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16
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Koldsø H, Reddy T, Fowler PW, Duncan AL, Sansom MSP. Membrane Compartmentalization Reducing the Mobility of Lipids and Proteins within a Model Plasma Membrane. J Phys Chem B 2016; 120:8873-81. [PMID: 27483109 DOI: 10.1021/acs.jpcb.6b05846] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The cytoskeleton underlying cell membranes may influence the dynamic organization of proteins and lipids within the bilayer by immobilizing certain transmembrane (TM) proteins and forming corrals within the membrane. Here, we present coarse-grained resolution simulations of a biologically realistic membrane model of asymmetrically organized lipids and TM proteins. We determine the effects of a model of cytoskeletal immobilization of selected membrane proteins using long time scale coarse-grained molecular dynamics simulations. By introducing compartments with varying degrees of restraints within the membrane models, we are able to reveal how compartmentalization caused by cytoskeletal immobilization leads to reduced and anomalous diffusional mobility of both proteins and lipids. This in turn results in a reduced rate of protein dimerization within the membrane and of hopping of membrane proteins between compartments. These simulations provide a molecular realization of hierarchical models often invoked to explain single-molecule imaging studies of membrane proteins.
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Affiliation(s)
- Heidi Koldsø
- Department of Biochemistry, University of Oxford , South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Tyler Reddy
- Department of Biochemistry, University of Oxford , South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Philip W Fowler
- Department of Biochemistry, University of Oxford , South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford , South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, OX1 3QU Oxford, United Kingdom
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Santos G, Díaz M, Torres NV. Lipid Raft Size and Lipid Mobility in Non-raft Domains Increase during Aging and Are Exacerbated in APP/PS1 Mice Model of Alzheimer's Disease. Predictions from an Agent-Based Mathematical Model. Front Physiol 2016; 7:90. [PMID: 27014089 PMCID: PMC4791387 DOI: 10.3389/fphys.2016.00090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/25/2016] [Indexed: 12/13/2022] Open
Abstract
A connection between lipid rafts and Alzheimer's disease has been studied during the last decades. Mathematical modeling approaches have recently been used to correlate the effects of lipid composition changes in the physicochemical properties of raft-like membranes. Here we propose an agent based model to assess the effect of lipid changes in lipid rafts on the evolution and progression of Alzheimer's disease using lipid profile data obtained in an established model of familial Alzheimer's disease. We have observed that lipid raft size and lipid mobility in non-raft domains are two main factors that increase during age and are accelerated in the transgenic Alzheimer's disease mouse model. The consequences of these changes are discussed in the context of neurotoxic amyloid β production. Our agent based model predicts that increasing sterols (mainly cholesterol) and long-chain polyunsaturated fatty acids (LCPUFA) (mainly DHA, docosahexaenoic acid) proportions in the membrane composition might delay the onset and progression of the disease.
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Affiliation(s)
- Guido Santos
- Systems Biology and Mathematical Modelling Group, Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Instituto de Tecnologías Biomédicas, CIBICAN, Universidad de La Laguna San Cristóbal de La Laguna, Spain
| | - Mario Díaz
- Laboratorio de Fisiología y Biofísica de Membranas, Departamento de Biología Animal y Edafología y Geología, Facultad de Ciencias, Unidad Asociada de Investigación ULL-CSIC, Universidad de La Laguna San Cristóbal de La Laguna, Spain
| | - Néstor V Torres
- Systems Biology and Mathematical Modelling Group, Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Instituto de Tecnologías Biomédicas, CIBICAN, Universidad de La Laguna San Cristóbal de La Laguna, Spain
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18
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Kurtjak M, Urbic T. A simple water model in the presence of inert Lennard-Jones obstacles II: the hydrophobic effect. Mol Phys 2014. [DOI: 10.1080/00268976.2014.973919] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Sadeghi S, Müller M, Vink RLC. Raft formation in lipid bilayers coupled to curvature. Biophys J 2014; 107:1591-600. [PMID: 25296311 PMCID: PMC4190607 DOI: 10.1016/j.bpj.2014.07.072] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 07/09/2014] [Accepted: 07/15/2014] [Indexed: 11/05/2022] Open
Abstract
We present computer simulations of a membrane in which the local composition is coupled to the local membrane curvature. At high temperatures (i.e., above the temperature of macroscopic phase separation), finite-sized transient domains are observed, reminiscent of lipid rafts. The domain size is in the range of hundred nanometers, and set by the membrane elastic properties. These findings are in line with the notion of the membrane as a curvature-induced microemulsion. At low temperature, the membrane phase separates. The transition to the phase-separated regime is continuous and belongs to the two-dimensional Ising universality class when the coupling to curvature is weak, but becomes first-order for strong curvature-composition coupling.
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Affiliation(s)
- Sina Sadeghi
- Institute of Theoretical Physics, Georg-August-Universität Göttingen, Göttingen, Germany.
| | - Marcus Müller
- Institute of Theoretical Physics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Richard L C Vink
- Institute of Theoretical Physics, Georg-August-Universität Göttingen, Göttingen, Germany
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20
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Liang Q, Wu QY, Wang ZY. Effect of hydrophobic mismatch on domain formation and peptide sorting in the multicomponent lipid bilayers in the presence of immobilized peptides. J Chem Phys 2014; 141:074702. [DOI: 10.1063/1.4891931] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, People's Republic of China
- Department of Physics, Ningbo University, Ningbo 315211, People's Republic of China
| | - Qing-Yan Wu
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Zhi-Yong Wang
- School of Optoelectronic Information, Chongqing University of Technology, Chongqing 400054, People's Republic of China
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21
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Modeling the interplay between protein and lipid aggregation in supported membranes. Chem Phys Lipids 2014; 185:141-52. [PMID: 24968242 DOI: 10.1016/j.chemphyslip.2014.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/26/2014] [Accepted: 06/20/2014] [Indexed: 12/16/2022]
Abstract
We present a theoretical model that deals with the complex interplay between lipid segregation and the self-aggregation of lipid-attached proteins. The model, in contrast to previous ones that consider proteins only as passive elements affecting the lipid distribution, describes the system including three terms: the dynamic interactions between protein monomers, the interactions between lipid components, and a mixed term considering protein-lipid interactions. It is used to explain experimental results performed on a well-defined system in which a self-aggregating soluble bacterial cytoskeletal protein polymerizes on a lipid bilayer containing two lipid components. All the elements considered in a previously described protein model, including torsion of the monomers within the filament, are needed to account for the observed filament shapes. The model also points out that lipid segregation can affect the length and curvature of the filaments and that the dynamic behavior of the lipids and proteins can have different time scales, giving rise to memory effects. This simple model that considers a dynamic protein assembly on a fluid and active lipid surface can be easily extended to other biologically relevant situations in which the interplay between protein and lipid aggregation is needed to fully describe the system.
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23
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Palmieri B, Safran SA. Hybrid lipids increase nanoscale fluctuation lifetimes in mixed membranes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:032708. [PMID: 24125295 DOI: 10.1103/physreve.88.032708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 08/22/2013] [Indexed: 06/02/2023]
Abstract
A recently proposed ternary mixture model is used to predict fluctuation domain lifetimes in the one phase region. The membrane is made of saturated, unsaturated, and hybrid lipids that have one saturated and one unsaturated hydrocarbon chain. The hybrid lipid is a natural linactant which can reduce the packing incompatibility between saturated and unsaturated lipids. The fluctuation lifetimes are predicted as a function of the hybrid lipid fraction and the fluctuation domain size. These lifetimes can be increased by up to three orders of magnitude compared to the case of no hybrids. With hybrid, small length scale fluctuations have sizable amplitudes even close to the critical temperature and, hence, benefit from enhanced critical slowing down. The increase in lifetime is particularly important for nanometer scale fluctuation domains where the hybrid orientation and the other lipids composition are highly coupled.
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Affiliation(s)
- Benoit Palmieri
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel
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24
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Li H, Gorfe AA. Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: simulations with the MARTINI force field. PLoS One 2013; 8:e71018. [PMID: 23923044 PMCID: PMC3724741 DOI: 10.1371/journal.pone.0071018] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/28/2013] [Indexed: 11/25/2022] Open
Abstract
Lipid-anchored Ras oncoproteins assemble into transient, nano-sized substructures on the plasma membrane. These substructures, called nanoclusters, were proposed to be crucial for high-fidelity signal transmission in cells. However, the molecular basis of Ras nanoclustering is poorly understood. In this work, we used coarse-grained (CG) molecular dynamics simulations to investigate the molecular mechanism by which full-length H-ras proteins form nanoclusters in a model membrane. We chose two different conformations of H-ras that were proposed to represent the active and inactive state of the protein, and a domain-forming model bilayer made up of di16:0-PC (DPPC), di18:2-PC (DLiPC) and cholesterol. We found that, irrespective of the initial conformation, Ras molecules assembled into a single large aggregate. However, the two binding modes, which are characterized by the different orientation of the G-domain with respect to the membrane, differ in dynamics and organization during and after aggregation. Some of these differences involve regions of Ras that are important for effector/modulator binding, which may partly explain observed differences in the ability of active and inactive H-ras nanoclusters to recruit effectors. The simulations also revealed some limitations in the CG force field to study protein assembly in solution, which we discuss in the context of proposed potential avenues of improvement.
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Affiliation(s)
- Hualin Li
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, Houston, Texas, United States of America
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, Houston, Texas, United States of America
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26
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Speck T, Vink RLC. Random pinning limits the size of membrane adhesion domains. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:031923. [PMID: 23030960 DOI: 10.1103/physreve.86.031923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 08/24/2012] [Indexed: 06/01/2023]
Abstract
Theoretical models describing specific adhesion of membranes predict (for certain parameters) a macroscopic phase separation of bonds into adhesion domains. We show that this behavior is fundamentally altered if the membrane is pinned randomly due to, e.g., proteins that anchor the membrane to the cytoskeleton. Perturbations which locally restrict membrane height fluctuations induce quenched disorder of the random-field type. This rigorously prevents the formation of macroscopic adhesion domains following the Imry-Ma argument [Imry and Ma, Phys. Rev. Lett. 35, 1399 (1975)]. Our prediction of random-field disorder follows from analytical calculations and is strikingly confirmed in large-scale Monte Carlo simulations. These simulations are based on an efficient composite Monte Carlo move, whereby membrane height and bond degrees of freedom are updated simultaneously in a single move. The application of this move should prove rewarding for other systems also.
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Affiliation(s)
- Thomas Speck
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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