1
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Cui J, Jin H, Zhan W. Enzyme-Free Liposome Active Motion via Asymmetrical Lipid Efflux. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11468-11477. [PMID: 36084317 DOI: 10.1021/acs.langmuir.2c01866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As a class of biocompatible, water-dispersed colloids, liposomes have found widespread applications ranging from food to drug delivery. Adding mobility to these colloids, i.e., liposome micromotors, represents an attractive approach to next-generation liposome carriers with enhanced functionality and effectiveness. Currently, it remains unclear as to the scope of material features useful for building liposome micromotors or how they may differ functionally from their inorganic/polymer counterparts. In this work, we demonstrate liposome active motion taking advantage of mainly a pair of intrinsic material properties associated with these assemblies: lipid phase separation and extraction. We show that global phase separation of ternary lipid systems (such as DPPC/DOPC/cholesterol) within individual liposomes yields stable Janus particles with two distinctive liquid domains. While these anisotropic liposomes undergo pure Brownian diffusion in water, similar to their homogeneous analogues, adding extracting agents, cyclodextrins, to the system triggers asymmetrical cholesterol efflux about the liposomes, setting the latter into active motion. We present detailed analyses of liposome movement and cholesterol extraction kinetics to establish their correlation. We explore various experimental parameters as well as mechanistic details to account for such motion. Our results highlight the rich possibility to hierarchically design lipid-based artificial motors, from individual lipids, to their organization, surface chemistry, and interfacial mechanics.
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Affiliation(s)
- Jinyan Cui
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Hui Jin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Wei Zhan
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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2
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Sack S, Zucker B, Yecheskel Y, Zucker I. The role of size, charge, and cholesterol of cell membrane models in interactions with graphene oxide. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128661. [PMID: 35305415 DOI: 10.1016/j.jhazmat.2022.128661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/28/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
The growing in manufacturing and applications of graphene oxide (GO), a two-dimensional nanomaterial, highlights the need for a better understanding of its environmental impact and toxicity. This work investigates the interaction of GO with cell membrane models as an indication for GO's potential harmfulness. A wide range of biologically-relevant membrane parameters (size, charge and, cholesterol content) and simple optical techniques were used to evaluate the outcome of interactions of vesicular cell membrane models with GO. Loss of membrane integrity was found to be positively correlated with electrostatic attraction and negatively correlated with cholesterol content. The size of vesicle-GO aggregates increased as a function of initial vesicle size, while cholesterol content was found to have a negligible effect on aggregation. Interestingly, charged vesicles reduced vesicle-GO aggregate size either by electrostatic repulsion of negatively charge vesicles or by GO folding following attachment of positively charge vesicles. Overall, by examining how key biologically-relevant parameters of membrane models affect interactions with GO, we have augmented the understanding of the potential threats of GO towards biological cell and to the environment.
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Affiliation(s)
- Shaanan Sack
- School of Mechanical Engineering, Tel Aviv University, 69978, Israel
| | - Ben Zucker
- Sackler Faculty of Medicine, Tel Aviv University, 69978, Israel
| | - Yinon Yecheskel
- School of Mechanical Engineering, Tel Aviv University, 69978, Israel; The Porter School of Environmental and Earth Sciences, Tel Aviv University, 69978 Israel
| | - Ines Zucker
- School of Mechanical Engineering, Tel Aviv University, 69978, Israel; The Porter School of Environmental and Earth Sciences, Tel Aviv University, 69978 Israel.
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3
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Abstract
Invention of DNA origami has transformed the fabrication and application of biological nanomaterials. In this review, we discuss DNA origami nanoassemblies according to their four fundamental mechanical properties in response to external forces: elasticity, pliability, plasticity and stability. While elasticity and pliability refer to reversible changes in structures and associated properties, plasticity shows irreversible variation in topologies. The irreversible property is also inherent in the disintegration of DNA nanoassemblies, which is manifested by its mechanical stability. Disparate DNA origami devices in the past decade have exploited the mechanical regimes of pliability, elasticity, and plasticity, among which plasticity has shown its dominating potential in biomechanical and physiochemical applications. On the other hand, the mechanical stability of the DNA origami has been used to understand the mechanics of the assembly and disassembly of DNA nano-devices. At the end of this review, we discuss the challenges and future development of DNA origami nanoassemblies, again, from these fundamental mechanical perspectives.
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Affiliation(s)
- Jiahao Ji
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
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4
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Pandey S, Xiang Y, Walpita Kankanamalage DVD, Jayawickramarajah J, Leng Y, Mao H. Measurement of Single-Molecule Forces in Cholesterol and Cyclodextrin Host-Guest Complexes. J Phys Chem B 2021; 125:11112-11121. [PMID: 34523939 PMCID: PMC8788999 DOI: 10.1021/acs.jpcb.1c03916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Biological host molecules such as β-cyclodextrins (β-CDs) have been used to remove cholesterol guests from membranes and artery plaques. In this work, we calibrated the host-guest intermolecular mechanical forces (IMMFs) between cholesterol and cyclodextrin complexes by combining single-molecule force spectroscopy in optical tweezers and computational molecular simulations for the first time. Compared to native β-CD, methylated beta cyclodextrins complexed with cholesterols demonstrated higher mechanical stabilities due to the loss of more high-energy water molecules inside the methylated β-CD cavities. This result is consistent with the finding that methylated β-CD is more potent at solubilizing cholesterols than β-CD, suggesting that the IMMF can serve as a novel indicator to evaluate the solubility of small molecules such as cholesterols. Importantly, we found that the force spectroscopy measured in such biological host-guest complexes is direction-dependent: pulling from the alkyl end of the cholesterol molecule resulted in a larger IMMF than that from the hydroxyl end of the cholesterol molecule. Molecular dynamics coupled with umbrella sampling simulations further revealed that cholesterol molecules tend to enter or leave from the wide opening of cyclodextrins. Such an orientation rationalizes that cyclodextrins are rather efficient at extracting cholesterols from the phospholipid bilayer in which hydroxyl groups of cholesterols are readily exposed to the hydrophobic cavities of cyclodextrins. We anticipate that the IMMF measured by both experimental and computational force spectroscopy measurements help elucidate solubility mechanisms not only for cholesterols in different environments but also to host-guest systems in general, which have been widely exploited for their solubilization properties in drug delivery, for example.
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Affiliation(s)
- Shankar Pandey
- Department of Chemistry and Biochemistry, and Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, OH, 44242
| | - Yuan Xiang
- School of Engineering and Applied Science, The George Washington University, Washington, DC 20052, USA
| | | | | | - Yongsheng Leng
- School of Engineering and Applied Science, The George Washington University, Washington, DC 20052, USA
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, and Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, OH, 44242
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5
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Wang W, Arias DS, Deserno M, Ren X, Taylor RE. Emerging applications at the interface of DNA nanotechnology and cellular membranes: Perspectives from biology, engineering, and physics. APL Bioeng 2020; 4:041507. [PMID: 33344875 PMCID: PMC7725538 DOI: 10.1063/5.0027022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
DNA nanotechnology has proven exceptionally apt at probing and manipulating biological environments as it can create nanostructures of almost arbitrary shape that permit countless types of modifications, all while being inherently biocompatible. Emergent areas of particular interest are applications involving cellular membranes, but to fully explore the range of possibilities requires interdisciplinary knowledge of DNA nanotechnology, cell and membrane biology, and biophysics. In this review, we aim for a concise introduction to the intersection of these three fields. After briefly revisiting DNA nanotechnology, as well as the biological and mechanical properties of lipid bilayers and cellular membranes, we summarize strategies to mediate interactions between membranes and DNA nanostructures, with a focus on programmed delivery onto, into, and through lipid membranes. We also highlight emerging applications, including membrane sculpting, multicell self-assembly, spatial arrangement and organization of ligands and proteins, biomechanical sensing, synthetic DNA nanopores, biological imaging, and biomelecular sensing. Many critical but exciting challenges lie ahead, and we outline what strikes us as promising directions when translating DNA nanostructures for future in vitro and in vivo membrane applications.
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Affiliation(s)
- Weitao Wang
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - D. Sebastian Arias
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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6
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King GM, Kosztin I. Towards a Quantitative Understanding of Protein-Lipid Bilayer Interactions at the Single Molecule Level: Opportunities and Challenges. J Membr Biol 2020; 254:17-28. [PMID: 33196888 DOI: 10.1007/s00232-020-00151-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/04/2020] [Indexed: 11/28/2022]
Abstract
Protein-lipid interfaces are among the most fundamental in biology. Yet applying conventional techniques to study the biophysical attributes of these systems is challenging and has left many unknowns. For example, what is the kinetic pathway and energy landscape experienced by a polypeptide chain when in close proximity to a fluid lipid bilayer? Here we review the experimental and theoretical progress we have made in addressing this question from a single molecule perspective. Some remaining impediments are also discussed.
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Affiliation(s)
- Gavin M King
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, 65211, USA. .,Department of Biochemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA.
| | - Ioan Kosztin
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, 65211, USA.
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7
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Zhao B, Li N, Xie T, Bagheri Y, Liang C, Keshri P, Sun Y, You M. Quantifying tensile forces at cell-cell junctions with a DNA-based fluorescent probe. Chem Sci 2020; 11:8558-8566. [PMID: 34123115 PMCID: PMC8163409 DOI: 10.1039/d0sc01455a] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Cells are physically contacting with each other. Direct and precise quantification of forces at cell–cell junctions is still challenging. Herein, we have developed a DNA-based ratiometric fluorescent probe, termed DNAMeter, to quantify intercellular tensile forces. These lipid-modified DNAMeters can spontaneously anchor onto live cell membranes. The DNAMeter consists of two self-assembled DNA hairpins of different force tolerance. Once the intercellular tension exceeds the force tolerance to unfold a DNA hairpin, a specific fluorescence signal will be activated, which enables the real-time imaging and quantification of tensile forces. Using E-cadherin-modified DNAMeter as an example, we have demonstrated an approach to quantify, at the molecular level, the magnitude and distribution of E-cadherin tension among epithelial cells. Compatible with readily accessible fluorescence microscopes, these easy-to-use DNA tension probes can be broadly used to quantify mechanotransduction in collective cell behaviors. A DNA-based fluorescent probe to quantify the magnitude and distribution of tensile forces at cell–cell junctions.![]()
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Affiliation(s)
- Bin Zhao
- Department of Chemistry, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Ningwei Li
- Department of Mechanical & Industrial Engineering, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Tianfa Xie
- Department of Mechanical & Industrial Engineering, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Yousef Bagheri
- Department of Chemistry, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Chungwen Liang
- Computational and Modeling Core, Institute for Applied Life Sciences (IALS), University of Massachusetts Amherst Massachusetts 01003 USA
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Yubing Sun
- Department of Mechanical & Industrial Engineering, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts Amherst Massachusetts 01003 USA
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8
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Calcium-triggered fusion of lipid membranes is enabled by amphiphilic nanoparticles. Proc Natl Acad Sci U S A 2020; 117:18470-18476. [PMID: 32690682 DOI: 10.1073/pnas.1902597117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Lipid membrane fusion is an essential process for a number of critical biological functions. The overall process is thermodynamically favorable but faces multiple kinetic barriers along the way. Inspired by nature's engineered proteins such as SNAP receptor [soluble N-ethylmale-imide-sensitive factor-attachment protein receptor (SNARE)] complexes or viral fusogenic proteins that actively promote the development of membrane proximity, nucleation of a stalk, and triggered expansion of the fusion pore, here we introduce a synthetic fusogen that can modulate membrane fusion and equivalently prime lipid membranes for calcium-triggered fusion. Our fusogen consists of a gold nanoparticle functionalized with an amphiphilic monolayer of alkanethiol ligands that had previously been shown to fuse with lipid bilayers. While previous efforts to develop synthetic fusogens have only replicated the initial steps of the fusion cascade, we use molecular simulations and complementary experimental techniques to demonstrate that these nanoparticles can induce the formation of a lipid stalk and also drive its expansion into a fusion pore upon the addition of excess calcium. These results have important implications in general understanding of stimuli-triggered fusion and the development of synthetic fusogens for biomedical applications.
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9
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Ermilova I, Lyubartsev AP. Modelling of interactions between Aβ(25-35) peptide and phospholipid bilayers: effects of cholesterol and lipid saturation. RSC Adv 2020; 10:3902-3915. [PMID: 35492630 PMCID: PMC9048594 DOI: 10.1039/c9ra06424a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/14/2019] [Indexed: 11/25/2022] Open
Abstract
Aggregation of amyloid beta (Aβ) peptides in neuronal membranes is a known promoter of Alzheimer’s disease. To gain insight into the molecular details of Aβ peptide aggregation and its effect on model neuronal membranes, we carried out molecular dynamics simulations of the Aβ(25–35) fragment of the amyloid precursor protein in phospholipid bilayers composed of either fully saturated or highly unsaturated lipids, in the presence or absence of cholesterol. It was found that the peptide does not penetrate through any of the considered membranes, but can reside in the headgroup region and upper part of the lipid tails showing a clear preference to a polyunsaturated cholesterol-free membrane. Due to the ordering and condensing effect upon addition of cholesterol, membranes become more rigid facilitating peptide aggregation on the surface. Except for the case of the cholesterol-free saturated lipid bilayer, the peptides have a small effect on the membrane structure and ordering. It was also found that the most “active” amino-acid for peptide–lipid and peptide–cholesterol interaction is methionine-35, followed by asparagine-27 and serine-26, which form hydrogen bonds between peptides and polar atoms of lipid headgroups. These amino acids are also primarily responsible for peptide aggregation. This work will be relevant for designing strategies to develop drugs to combat Alzheimer’s disease. Molecular dynamics simulations of Aβ(25–35) peptides in phospholipid bilayers are carried out to investigate the effect of polyunsaturated lipids and cholesterol on aggregation of the peptides. ![]()
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Affiliation(s)
- Inna Ermilova
- Department of Materials and Environmental Chemistry, Stockholm University Stockholm Sweden +46 8161193
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University Stockholm Sweden +46 8161193
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10
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Norling K, Bernasconi V, Agmo Hernández V, Parveen N, Edwards K, Lycke NY, Höök F, Bally M. Gel Phase 1,2-Distearoyl- sn-glycero-3-phosphocholine-Based Liposomes Are Superior to Fluid Phase Liposomes at Augmenting Both Antigen Presentation on Major Histocompatibility Complex Class II and Costimulatory Molecule Display by Dendritic Cells in Vitro. ACS Infect Dis 2019; 5:1867-1878. [PMID: 31498993 DOI: 10.1021/acsinfecdis.9b00189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lipid-based nanoparticles have in recent years attracted increasing attention as pharmaceutical carriers. In particular, reports of them having inherent adjuvant properties combined with their ability to protect antigen from degradation make them suitable as vaccine vectors. However, the physicochemical profile of an ideal nanoparticle for vaccine delivery is still poorly defined. Here, we used an in vitro dendritic cell assay to assess the immunogenicity of a variety of liposome formulations as vaccine carriers and adjuvants. Using flow cytometry, we investigated liposome-assisted antigen presentation as well as the expression of relevant costimulatory molecules on the cell surface. Cytokine secretion was further evaluated with an enzyme-linked immunosorbent assay (ELISA). We show that liposomes can successfully enhance antigen presentation and maturation of dendritic cells, as compared to vaccine fusion protein (CTA1-3Eα-DD) administered alone. In particular, the lipid phase state of the membrane was found to greatly influence the vaccine antigen processing by dendritic cells. As compared to their fluid phase counterparts, gel phase liposomes were more efficient at improving antigen presentation. They were also superior at upregulating the costimulatory molecules CD80 and CD86 as well as increasing the release of the cytokines IL-6 and IL-1β. Taken together, we demonstrate that gel phase liposomes, while nonimmunogenic on their own, significantly enhance the antigen-presenting ability of dendritic cells and appear to be a promising way forward to improve vaccine immunogenicity.
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Affiliation(s)
- Karin Norling
- Division of Biological Physics, Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Valentina Bernasconi
- Mucosal Immunobiology and Vaccine Center (MIVAC), Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Víctor Agmo Hernández
- Department of Chemistry, BMC, Uppsala University, Box 599, 752 37 Uppsala, Sweden
- Department of Pharmacy, Uppsala University, Box 580, 751 23, Uppsala, Sweden
| | - Nagma Parveen
- Division of Biological Physics, Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Katarina Edwards
- Department of Chemistry, BMC, Uppsala University, Box 599, 752 37 Uppsala, Sweden
| | - Nils Y. Lycke
- Mucosal Immunobiology and Vaccine Center (MIVAC), Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Fredrik Höök
- Division of Biological Physics, Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Marta Bally
- Section of Virology, Department of Clinical Microbiology, Umeå University, 901 85 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, 901 85 Umeå, Sweden
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11
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Kolberg A, Wenzel C, Hackenstrass K, Schwarzl R, Rüttiger C, Hugel T, Gallei M, Netz RR, Balzer BN. Opposing Temperature Dependence of the Stretching Response of Single PEG and PNiPAM Polymers. J Am Chem Soc 2019; 141:11603-11613. [DOI: 10.1021/jacs.9b04383] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Adrianna Kolberg
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 23a, 79104 Freiburg, Germany
| | - Christiane Wenzel
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 23a, 79104 Freiburg, Germany
| | - Klara Hackenstrass
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 23a, 79104 Freiburg, Germany
| | - Richard Schwarzl
- Department Institute of Theoretical Bio- and Soft Matter Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Christian Rüttiger
- Ernst-Berl-Institute of Technical and Macromolecular Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 23a, 79104 Freiburg, Germany
- Cluster of Excellence livMatS@FIT, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Markus Gallei
- Ernst-Berl-Institute of Technical and Macromolecular Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
- Organic Macromolecular Chemistry, Saarland University, Campus Saarbrücken C4 2, 66123 Saarbrücken, Germany
| | - Roland R. Netz
- Department Institute of Theoretical Bio- and Soft Matter Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Bizan N. Balzer
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 23a, 79104 Freiburg, Germany
- Cluster of Excellence livMatS@FIT, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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12
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Brander S, Jank T, Hugel T. AFM Imaging Suggests Receptor-Free Penetration of Lipid Bilayers by Toxins. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:365-371. [PMID: 30565941 DOI: 10.1021/acs.langmuir.8b03146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A crucial step of exotoxin action is the attack on the membrane. Many exotoxins show an architecture following the AB model, where a binding subunit translocates an "action" subunit across a cell membrane. Atomic force microscopy is an ideal technique to study these systems because of its ability to provide structural as well as dynamic information at the same time. We report first images of toxins Photorhabdus luminescens TcdA1 and Clostridium difficile TcdB on a supported lipid bilayer. A significant amount of toxin binds to the bilayer at neutral pH in the absence of receptors. Lack of diffusion indicates that toxin particles penetrate the membrane. This observation is supported by fluorescence recovery after photobleaching measurements. We mimic endocytosis by acidification while imaging the particles over time; however, we see no large conformational change. We therefore conclude that the toxin particles we imaged in neutral conditions had already formed a pore and speculate that there is no "pre-pore" state in our imaging conditions (i.e., in the absence of receptor).
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13
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Ermilova I, Lyubartsev AP. Cholesterol in phospholipid bilayers: positions and orientations inside membranes with different unsaturation degrees. SOFT MATTER 2018; 15:78-93. [PMID: 30520494 DOI: 10.1039/c8sm01937a] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cholesterol is an essential component of all animal cell membranes and plays an important role in maintaining the membrane structure and physical-chemical properties necessary for correct cell functioning. The presence of cholesterol is believed to be responsible for domain formation (lipid rafts) due to different interactions of cholesterol with saturated and unsaturated lipids. In order to get detailed atomistic insight into the behaviour of cholesterol in bilayers composed of lipids with varying degrees of unsaturation, we have carried out a series of molecular dynamics simulations of saturated and polyunsaturated lipid bilayers with different contents of cholesterol, as well as well-tempered metadynamics simulations with a single cholesterol molecule in these bilayers. From these simulations we have determined distributions of cholesterol across the bilayer, its orientational properties, free energy profiles, and specific interactions of molecular groups able to form hydrogen bonds. Both molecular dynamics and metadynamics simulations showed that the most unsaturated bilayer with 22:6 fatty acid chains shows behaviour which is most different from other lipids. In this bilayer, cholesterol is relatively often found in a "flipped" configuration with the hydroxyl group oriented towards the membrane middle plane. This bilayer has also the highest (least negative) binding free energy among liquid phase bilayers, and the lowest reorientation barrier. Furthermore, cholesterol molecules in this bilayer are often found to form head-to-tail contacts which may lead to specific clustering behaviour. Overall, our simulations support ideas that there can be a subtle interconnection between the contents of highly unsaturated fatty acids and cholesterol, deficiency or excess of each of them is related to many human afflictions and diseases.
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Affiliation(s)
- Inna Ermilova
- Department of Materials and Environmental Chemistry, Stockholm Universtity, Stockholm, Sweden.
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm Universtity, Stockholm, Sweden.
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14
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Gurtovenko AA, Mukhamadiarov EI, Kostritskii AY, Karttunen M. Phospholipid–Cellulose Interactions: Insight from Atomistic Computer Simulations for Understanding the Impact of Cellulose-Based Materials on Plasma Membranes. J Phys Chem B 2018; 122:9973-9981. [DOI: 10.1021/acs.jpcb.8b07765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Andrey A. Gurtovenko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect V.O. 31, St. Petersburg, 199004 Russia
| | - Evgenii I. Mukhamadiarov
- Faculty of Physics, St. Petersburg State University, Ulyanovskaya str. 3, Petrodvorets, St. Petersburg, 198504 Russia
| | - Andrei Yu. Kostritskii
- Faculty of Physics, St. Petersburg State University, Ulyanovskaya str. 3, Petrodvorets, St. Petersburg, 198504 Russia
| | - Mikko Karttunen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect V.O. 31, St. Petersburg, 199004 Russia
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 3K7
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 5B7
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15
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Miller EJ, Voïtchovsky K, Staykova M. Substrate-led cholesterol extraction from supported lipid membranes. NANOSCALE 2018; 10:16332-16342. [PMID: 30132496 DOI: 10.1039/c8nr03399d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The lipid membrane is a principal building block in biology, technology and industry, where it often occurs supported by other hydrophilic structures. Interactions with the support can affect the physical behavior of the membrane from the local organization and diffusion of lipids and proteins, to phase transitions, and the local mechanical properties. In this study we show that supporting substrates textured with nanoscale hydrophilic and hydrophobic domains can modify the membrane's chemical composition by selectively extracting cholesterol molecules without affecting the remaining phospholipids. Using polydimethylsiloxane (PDMS) substrates with various degrees of plasma oxidation, we are able to trigger dramatic changes in the membrane morphology and biophysical properties, and relate them to the amount of extracted cholesterol. We also show that it is possible to control the cholesterol extraction through mechanical extension of the flexible PDMS support. Given the ubiquity of bio-substrates with textured surface properties and the wide use of PDMS we expect that our results will have implications not only in biological and chemical sciences but also in nanotechnologies such as organ on a chip technologies, biosensors, and stretchable bio-electronics.
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16
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Zhang Y, Chan C, Li Z, Ma J, Meng Q, Cheng X, Fan J. Lipid extraction by boron nitride nanosheets from liquid-ordered and liquid-disordered nanodomains. NANOSCALE 2018; 10:14073-14081. [PMID: 29999094 DOI: 10.1039/c8nr02018c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Atomically thin boron nitride nanosheets are important two-dimensional nanomaterials with great potential in biomedical applications. Understanding the basic interaction mechanisms between lipid domains and boron nitride nanosheets can help clarify the potential risks of these nanomaterials and thus provide guidance on the design of safe biomedical applications. Using molecular dynamics simulations, we demonstrate that the BNNS can disrupt the liquid disordered lipid bilayers much more easily compared to the liquid ordered phases. The potential of mean force profiles calculated from umbrella sampling further explain this adsorption preference. When the BNNS is placed at the boundary of the liquid ordered and liquid disordered nanodomains, disruption of the liquid ordered domains becomes much easier due to the presence of adjacent liquid disordered domains. Our findings provide new insights into the cytotoxicity of boron nitride nanosheets interacting with cellular membranes.
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Affiliation(s)
- Yonghui Zhang
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong, China.
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17
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Ikai A, Afrin R, Saito M, Watanabe-Nakayama T. Atomic force microscope as a nano- and micrometer scale biological manipulator: A short review. Semin Cell Dev Biol 2017; 73:132-144. [PMID: 28739341 DOI: 10.1016/j.semcdb.2017.07.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/16/2017] [Accepted: 07/19/2017] [Indexed: 11/27/2022]
Abstract
The amazing capacity of atomic force microscope to let us touch the molecular and cellular level samples with a sharp probe stimulated its application to bio-medical field among others. In addition to topographical imaging of the sample surface, a direct mechanical manipulation has attracted innovative minds to develop new methodologies aiming at direct handling of proteins, DNA/RNA, and cells. Measurement of their mechanical properties brought about a vivid picture of their physical nature. Direct handling of individual molecules and cells prompted development of nano-medical applications. This short review summarized recent application of AFM for measurement of mechanical properties of biological samples and attempts to perform direct manipulations of nano-medicine.
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Affiliation(s)
- Atsushi Ikai
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
| | - Rehana Afrin
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
| | - Masakazu Saito
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
| | - Takahiro Watanabe-Nakayama
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
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18
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Matin TR, Sigdel KP, Utjesanovic M, Marsh BP, Gallazzi F, Smith VF, Kosztin I, King GM. Single-Molecule Peptide-Lipid Affinity Assay Reveals Interplay between Solution Structure and Partitioning. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:4057-4065. [PMID: 28343391 DOI: 10.1021/acs.langmuir.7b00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Interactions between short protein segments and phospholipid bilayers dictate fundamental aspects of cellular activity and have important applications in biotechnology. Yet, the lack of a suitable methodology for directly probing these interactions has hindered the mechanistic understanding. We developed a precision atomic force microscopy-based single-molecule force spectroscopy assay and probed partitioning into lipid bilayers by measuring the mechanical force experienced by a peptide. Protein segments were constructed from the peripheral membrane protein SecA, a key ATPase in bacterial secretion. We focused on the first 10 amino-terminal residues of SecA (SecA2-11) that are lipophilic. In addition to the core SecA2-11 sequence, constructs with nearly identical chemical composition but with differing geometry were used: two copies of SecA2-11 linked in series and two copies SecA2-11 linked in parallel. Lipid bilayer partitioning interactions of peptides with differing structures were distinguished. To model the energetic landscape, a theory of diffusive barrier crossing was extended to incorporate a superposition of potential barriers with variable weights. Analysis revealed two dissociation pathways for the core SecA2-11 sequence with well-separated intrinsic dissociation rates. Molecular dynamics simulations showed that the three peptides had significant conformational differences in solution that correlated well with the measured variations in the propensity to partition into the bilayer. The methodology is generalizable and can be applied to other peptide and lipid species.
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Affiliation(s)
| | | | | | | | | | - Virginia F Smith
- Department of Chemistry, United States Naval Academy , Annapolis, Maryland 21402, United States
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19
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García-Arribas AB, Ahyayauch H, Sot J, López-González PL, Alonso A, Goñi FM. Ceramide-Induced Lamellar Gel Phases in Fluid Cell Lipid Extracts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:9053-9063. [PMID: 27486830 DOI: 10.1021/acs.langmuir.6b01579] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The effects of increasing amounts of palmitoylceramide (pCer) on human red blood cell lipid membranes have been studied using atomic force microscopy of supported lipid bilayers, in both imaging (bilayer thickness) and force-spectroscopy (nanomechanical resistance) modes. Membranes appeared homogeneous with pCer concentrations up to 10 mol % because of the high concentration of cholesterol (Chol) present in the membrane (∼45 mol %). However, the presence of pCer at 30 mol % gave rise to a clearly distinguishable segregated phase with a nanomechanical resistance 7-fold higher than the continuous phase. These experiments were validated using differential scanning calorimetry. Furthermore, Chol depletion of the bilayers caused lipid domain generation in the originally homogeneous samples, and Chol-depleted domain stiffness significantly increased with higher amounts of pCer. These results point to the possibility of different kinds of transient and noncompositionally constant, complex gel-like phases present in RBC lipid membranes rich in both pCer and Chol, in contrast to the widespread opinion about the displacements between pCer-enriched "gel-like" domains and liquid-ordered "raft-like" Chol-enriched phases. Changes in the biophysical properties of these complex gel-like phases governed by local modulation of pCer:Chol ratios could be a cell mechanism for fine-tuning the properties of membranes as required.
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Affiliation(s)
- Aritz B García-Arribas
- Biofisika Institute (CSIC, UPV/EHU) , 48940 Leioa, Spain
- Departamento de Bioquímica, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | - Hasna Ahyayauch
- Biofisika Institute (CSIC, UPV/EHU) , 48940 Leioa, Spain
- Departamento de Bioquímica, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
- Institut Supérieur Des Professions Infirmières Et Des Techniques De Santé Rabat, Km 4.5 route de Casa, Rabat, Morocco
| | - Jesús Sot
- Biofisika Institute (CSIC, UPV/EHU) , 48940 Leioa, Spain
- Departamento de Bioquímica, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | - Pablo L López-González
- Biofisika Institute (CSIC, UPV/EHU) , 48940 Leioa, Spain
- Departamento de Bioquímica, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | - Alicia Alonso
- Biofisika Institute (CSIC, UPV/EHU) , 48940 Leioa, Spain
- Departamento de Bioquímica, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | - Félix M Goñi
- Biofisika Institute (CSIC, UPV/EHU) , 48940 Leioa, Spain
- Departamento de Bioquímica, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
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20
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Stetter FWS, Kienle S, Krysiak S, Hugel T. Investigating single molecule adhesion by atomic force spectroscopy. J Vis Exp 2015:e52456. [PMID: 25867282 DOI: 10.3791/52456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.
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Affiliation(s)
- Frank W S Stetter
- Physik-Department E22a, Technische Universität München; IMETUM, Technische Universität München
| | - Sandra Kienle
- Physik-Department E22a, Technische Universität München; IMETUM, Technische Universität München
| | - Stefanie Krysiak
- Physik-Department E22a, Technische Universität München; IMETUM, Technische Universität München
| | - Thorsten Hugel
- Physik-Department E22a, Technische Universität München; IMETUM, Technische Universität München;
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Tych KM, Hughes ML, Bourke J, Taniguchi Y, Kawakami M, Brockwell DJ, Dougan L. Optimizing the calculation of energy landscape parameters from single-molecule protein unfolding experiments. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:012710. [PMID: 25679645 DOI: 10.1103/physreve.91.012710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Indexed: 06/04/2023]
Abstract
Single-molecule force spectroscopy using an atomic force microscope (AFM) can be used to measure the average unfolding force of proteins in a constant velocity experiment. In combination with Monte Carlo simulations and through the application of the Zhurkov-Bell model, information about the parameters describing the underlying unfolding energy landscape of the protein can be obtained. Using this approach, we have completed protein unfolding experiments on the polyprotein (I27)(5) over a range of pulling velocities. In agreement with previous work, we find that the observed number of protein unfolding events observed in each approach-retract cycle varies between one and five, due to the nature of the interactions between the polyprotein, the AFM tip, and the substrate, and there is an unequal unfolding probability distribution. We have developed a Monte Carlo simulation that incorporates the impact of this unequal unfolding probability distribution on the median unfolding force and the calculation of the protein unfolding energy landscape parameters. These results show that while there is a significant, unequal unfolding probability distribution, the unfolding energy landscape parameters obtained from use of the Zhurkov-Bell model are not greatly affected. This result is important because it demonstrates that the minimum acceptance criteria typically used in force extension experiments are justified and do not skew the calculation of the unfolding energy landscape parameters. We further validate this approach by determining the error in the energy landscape parameters for two extreme cases, and we provide suggestions for methods that can be employed to increase the level of accuracy in single-molecule experiments using polyproteins.
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Affiliation(s)
- Katarzyna M Tych
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Megan L Hughes
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - James Bourke
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yukinori Taniguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Masaru Kawakami
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lorna Dougan
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
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22
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Róg T, Vattulainen I. Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes? Chem Phys Lipids 2014; 184:82-104. [PMID: 25444976 DOI: 10.1016/j.chemphyslip.2014.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
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