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Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2. Biophys J 2019; 114:1858-1868. [PMID: 29694864 DOI: 10.1016/j.bpj.2018.02.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/05/2018] [Accepted: 02/20/2018] [Indexed: 11/22/2022] Open
Abstract
Phosphatidylinositol 4,5-bisphosphate (PIP2) acts as a signaling lipid, mediating membrane trafficking and recruitment of proteins to membranes. A key example is the PIP2-dependent regulation of the adhesion of L-selectin to the cytoskeleton adaptors of the N-terminal subdomain of ezrin-radixin-moesin (FERM). The molecular details of the mediating behavior of multivalent anionic PIP2 lipids in this process, however, remain unclear. Here, we use coarse-grained molecular dynamics simulation to explore the mechanistic details of PIP2 in the transformation, translocation, and association of the FERM/L-selectin complex. We compare membranes of different compositions and find that anionic phospholipids are necessary for both FERM and the cytoplasmic domain of L-selectin to absorb on the membrane surface. The subsequent formation of the FERM/L-selectin complex is strongly favored by the presence of PIP2, which clusters around both proteins and triggers a conformational transition in the cytoplasmic domain of L-selectin. We are able to quantify the effect of PIP2 on the association free energy of the complex by means of a potential of mean force. We conclude that PIP2 behaves as an adhesive agent to enhance the stability of the FERM/L-selectin complex and identify key residues involved. The molecular information revealed in this study highlights the specific role of membrane lipids such as PIP2 in protein translocation and potential signaling.
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Affiliation(s)
- Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, Biophysics Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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Mobarak E, Javanainen M, Kulig W, Honigmann A, Sezgin E, Aho N, Eggeling C, Rog T, Vattulainen I. How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:2436-2445. [PMID: 30028957 DOI: 10.1016/j.bbamem.2018.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 11/28/2022]
Abstract
Organic dye-tagged lipid analogs are essential for many fluorescence-based investigations of complex membrane structures, especially when using advanced microscopy approaches. However, lipid analogs may interfere with membrane structure and dynamics, and it is not obvious that the properties of lipid analogs would match those of non-labeled host lipids. In this work, we bridged atomistic simulations with super-resolution imaging experiments and biomimetic membranes to assess the performance of commonly used sphingomyelin-based lipid analogs. The objective was to compare, on equal footing, the relative strengths and weaknesses of acyl chain labeling, headgroup labeling, and labeling based on poly-ethyl-glycol (PEG) linkers in determining biomembrane properties. We observed that the most appropriate strategy to minimize dye-induced membrane perturbations and to allow consideration of Brownian-like diffusion in liquid-ordered membrane environments is to decouple the dye from a membrane by a PEG linker attached to a lipid headgroup. Yet, while the use of PEG linkers may sound a rational and even an obvious approach to explore membrane dynamics, the results also suggest that the dyes exploiting PEG linkers interfere with molecular interactions and their dynamics. Overall, the results highlight the great care needed when using fluorescent lipid analogs, in particular accurate controls.
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Affiliation(s)
- Edouard Mobarak
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland; Laboratory of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland
| | - Matti Javanainen
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland; Laboratory of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland; Laboratory of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland
| | - Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
| | - Noora Aho
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom; Institute of Applied Optics Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany; Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Tomasz Rog
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland; Laboratory of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland; Laboratory of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; MEMPHYS - Center for Biomembrane Physics (www.memphys.dk).
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Franco-Gonzalez JF, Rolland N, Zozoulenko IV. Substrate-Dependent Morphology and Its Effect on Electrical Mobility of Doped Poly(3,4-ethylenedioxythiophene) (PEDOT) Thin Films. ACS APPLIED MATERIALS & INTERFACES 2018; 10:29115-29126. [PMID: 30070463 DOI: 10.1021/acsami.8b08774] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Deposition dynamics, crystallization, molecular packing, and electronic mobility of poly(3,4-ethylenedioxythiophene) (PEDOT) thin films are affected by the nature of the substrate. Computational microscopy has been carried out to reveal the morphology-substrate dependence for PEDOT thin films doped with molecular tosylate deposited on different substrates including graphite, Si3N4, silicon, and amorphous SiO2. It is shown that the substrate is instrumental in formation of the lamellar structure. PEDOT films on the ordered substrates (graphite, Si3N4, and silicon) exhibit preferential face-on orientation, with graphite showing the most ordered and pronounced face-on packing. In contrast, PEDOT on amorphous SiO2 exhibits the dominant edge-on orientation, except in the dry state where both packings are equally presented. The role of water and the porosity of the substrate in formation of the edge-on structure on SiO2 is outlined. On the basis of the calculated morphology, the multiscale calculations of the electronic transport and percolative analysis are performed outlining how the character of the substrate affects the electron mobility. It is demonstrated that good crystallinity (PEDOT on graphite substrate) and high content of edge-on (PEDOT on SiO2 substrate) are not enough to achieve the highest electrical in-plane mobility. Instead, the least ordered material with lower degree of the edge-on content (PEDOT on silicon substrate) provides the highest mobility because it exhibits an efficient network of π-π stacked chain extending throughout the entire sample.
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Affiliation(s)
- Juan Felipe Franco-Gonzalez
- Laboratory of Organic Electronics, Department of Science and Technology , Linköping University , SE-601 74 Norrköping , Sweden
| | - Nicolas Rolland
- Laboratory of Organic Electronics, Department of Science and Technology , Linköping University , SE-601 74 Norrköping , Sweden
| | - Igor V Zozoulenko
- Laboratory of Organic Electronics, Department of Science and Technology , Linköping University , SE-601 74 Norrköping , Sweden
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Duncan AL, Reddy T, Koldsø H, Hélie J, Fowler PW, Chavent M, Sansom MSP. Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes. Sci Rep 2017; 7:16647. [PMID: 29192147 PMCID: PMC5709381 DOI: 10.1038/s41598-017-16865-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/15/2017] [Indexed: 01/07/2023] Open
Abstract
Cell membranes are crowded and complex environments. To investigate the effect of protein-lipid interactions on dynamic organization in mammalian cell membranes, we have performed coarse-grained molecular dynamics simulations containing >100 copies of an inwardly rectifying potassium (Kir) channel which forms specific interactions with the regulatory lipid phosphatidylinositol 4,5-bisphosphate (PIP2). The tendency of protein molecules to cluster has the effect of organizing the membrane into dynamic compartments. At the same time, the diversity of lipids present has a marked effect on the clustering behavior of ion channels. Sub-diffusion of proteins and lipids is observed. Protein crowding alters the sub-diffusive behavior of proteins and lipids such as PIP2 which interact tightly with Kir channels. Protein crowding also affects bilayer properties, such as membrane undulations and bending rigidity, in a PIP2-dependent manner. This interplay between the diffusion and the dynamic organization of Kir channels may have important implications for channel function.
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Affiliation(s)
- Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Tyler Reddy
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- T-6, MS K710, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- D. E. Shaw Research, 120 W 45th St., New York, NY, 10036, USA
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Semmle, Blue Boar Court, 9 Alfred St, Oxford, OX1 4EH, UK
| | - Philip W Fowler
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- IPBS-CNRS, Toulouse, Midi-Pyrénées, France
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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Sezgin E, Levental I, Mayor S, Eggeling C. The mystery of membrane organization: composition, regulation and roles of lipid rafts. Nat Rev Mol Cell Biol 2017; 18:361-374. [PMID: 28356571 PMCID: PMC5500228 DOI: 10.1038/nrm.2017.16] [Citation(s) in RCA: 1252] [Impact Index Per Article: 178.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cellular plasma membranes are laterally heterogeneous, featuring a variety of distinct subcompartments that differ in their biophysical properties and composition. A large number of studies have focused on understanding the basis for this heterogeneity and its physiological relevance. The membrane raft hypothesis formalized a physicochemical principle for a subtype of such lateral membrane heterogeneity, in which the preferential associations between cholesterol and saturated lipids drive the formation of relatively packed (or ordered) membrane domains that selectively recruit certain lipids and proteins. Recent studies have yielded new insights into this mechanism and its relevance in vivo, owing primarily to the development of improved biochemical and biophysical technologies.
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Affiliation(s)
- Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, 6431 Fannin Street, Houston, Texas 77030, USA
| | - Satyajit Mayor
- National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bellary Road, Bangalore 560065, India
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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Compartmentalization of the Cell Membrane. J Mol Biol 2016; 428:4739-4748. [DOI: 10.1016/j.jmb.2016.09.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 11/20/2022]
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Lin X, Lorent JH, Skinkle AD, Levental KR, Waxham MN, Gorfe AA, Levental I. Domain Stability in Biomimetic Membranes Driven by Lipid Polyunsaturation. J Phys Chem B 2016; 120:11930-11941. [PMID: 27797198 DOI: 10.1021/acs.jpcb.6b06815] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Biological membranes contain a broad variety of lipid species whose individual physicochemical properties and collective interactions ultimately determine membrane organization. A key aspect of the organization of cellular membranes is their lateral subdivision into domains of distinct structure and composition. The most widely studied membrane domains are lipid rafts, which are the biological manifestations of liquid-ordered phases that form in sterol-containing membranes. Detailed studies of biomimetic membrane mixtures have yielded wide-ranging insights into the physical principles behind lipid rafts; however, these simplified models do not fully capture the diversity and complexity of the mammalian lipidome, most notably in their exclusion of polyunsaturated lipids. Here, we assess the role of lipid acyl chain unsaturation as a driving force for phase separation using coarse-grained molecular dynamics (CGMD) simulations validated by model membrane experiments. The clear trends in our observations and good qualitative agreements between simulations and experiments support the conclusions that highly unsaturated lipids promote liquid-liquid domain stability by enhancing the differences in cholesterol content and lipid chain order between the coexisting domains. These observations reveal the important role of noncanonical biological lipids in the physical properties of membranes, showing that lipid polyunsaturation is a driving force for liquid-liquid phase separation.
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Affiliation(s)
- Xubo Lin
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - Joseph H Lorent
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - Allison D Skinkle
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - Kandice R Levental
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
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Vattulainen I, Róg T. Lipid membranes: Theory and simulations bridged to experiments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2251-2253. [PMID: 27316372 DOI: 10.1016/j.bbamem.2016.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Finland
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