1
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Litniewski M, Góźdź WT, Ciach A. Adsorption on a Spherical Colloidal Particle from a Mixture of Nanoparticles with Competing Interactions. Molecules 2024; 29:3170. [PMID: 38999122 PMCID: PMC11242970 DOI: 10.3390/molecules29133170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/13/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
Adsorption of nanoparticles on a spherical colloidal particle is studied by molecular dynamics simulations. We consider a generic model for a mixture of nanoparticles with energetically favored self-assembly into alternating layers of the two components. When both components are attracted to the colloidal particle, the adsorbed nanoparticles self-assemble either into alternating parallel tori and clusters at the two poles of the colloidal particle, or into alternating spirals wrapped around the spherical surface. The long-lived metastable states obtained in simulations follow from the spherical shape of the adsorbing surface and the requirement that the neighboring chains of the nanoparticles are composed of different components. A geometrical construction leading to all such patterns is presented. When the second component particles are repelled from the colloidal particle and the attraction of the first component is strong, the attracted particles form a monolayer at the surface of the colloidal particle that screens the repulsion of the second component. The subsequent adsorbed alternating spherical layers of the two components form together a thick shell. This structure leads to the adsorption that is larger than in the case of the same attraction of the two components to the colloidal particle.
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Affiliation(s)
- Marek Litniewski
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Wojciech T Góźdź
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Alina Ciach
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
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2
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Pantelopulos GA, Abraham CB, Straub JE. Cholesterol and Lipid Rafts in the Biogenesis of Amyloid-β Protein and Alzheimer's Disease. Annu Rev Biophys 2024; 53:455-486. [PMID: 38382114 DOI: 10.1146/annurev-biophys-062823-023436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Cholesterol has been conjectured to be a modulator of the amyloid cascade, the mechanism that produces the amyloid-β (Aβ) peptides implicated in the onset of Alzheimer's disease. We propose that cholesterol impacts the genesis of Aβ not through direct interaction with proteins in the bilayer, but indirectly by inducing the liquid-ordered phase and accompanying liquid-liquid phase separations, which partition proteins in the amyloid cascade to different lipid domains and ultimately to different endocytotic pathways. We explore the full process of Aβ genesis in the context of liquid-ordered phases induced by cholesterol, including protein partitioning into lipid domains, mechanisms of endocytosis experienced by lipid domains and secretases, and pH-controlled activation of amyloid precursor protein secretases in specific endocytotic environments. Outstanding questions on the essential role of cholesterol in the amyloid cascade are identified for future studies.
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Affiliation(s)
| | - Conor B Abraham
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
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3
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Cornet J, Coulonges N, Pezeshkian W, Penissat-Mahaut M, Desgrez-Dautet H, Marrink SJ, Destainville N, Chavent M, Manghi M. There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning. SOFT MATTER 2024; 20:4998-5013. [PMID: 38884641 DOI: 10.1039/d4sm00089g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
We describe a complete methodology to bridge the scales between nanoscale molecular dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species are furthermore embedded. To go from the molecular to the mesoscale, we notably appeal to physical renormalization arguments enabling us to rigorously infer the mesoscale interaction parameters from its molecular counterpart. We also explain how to deal with the physical timescales at stake at the mesoscale. Simulating the as-obtained mesoscale system enables us to equilibrate the long wavelengths of the vesicles of interest, up to the vesicle size. Conversely, we then backmap from the meso- to the nano-scale, which enables us to equilibrate in turn the short wavelengths down to the molecular length-scales. By applying our approach to the specific situation of patterning a vesicle membrane, we show that macroscopic membranes can thus be equilibrated at all length-scales in achievable computational time offering an original strategy to address the fundamental challenge of timescale in simulations of large bio-membrane systems.
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Affiliation(s)
- Julie Cornet
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
| | - Nelly Coulonges
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Maël Penissat-Mahaut
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Hermes Desgrez-Dautet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | | | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
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4
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Rouches MN, Machta BB. Polymer Collapse & Liquid-Liquid Phase-Separation are Coupled in a Generalized Prewetting Transition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591767. [PMID: 38746247 PMCID: PMC11092468 DOI: 10.1101/2024.04.29.591767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with particular sequences of DNA. At unphysiological concentrations many of these nuclear proteins can phase-separate in the absence of DNA, and it has been hypothesized that, in vivo, the thermodynamic forces driving these phases help determine chromosomal organization. However it is unclear how DNA, itself a long polymer subject to configurational transitions, interacts with three-dimensional protein phases. Here we show that a long compressible polymer can be coupled to interacting protein mixtures, leading to a generalized prewetting transition where polymer collapse is coincident with a locally stabilized liquid droplet. We use lattice Monte-Carlo simulations and a mean-field theory to show that these phases can be stable even in regimes where both polymer collapse and coexisting liquid phases are unstable in isolation, and that these new transitions can be either abrupt or continuous. For polymers with internal linear structure we further show that changes in the concentration of bulk components can lead to changes in three-dimensional polymer structure. In the nucleus there are many distinct proteins that interact with many different regions of chromatin, potentially giving rise to many different Prewet phases. The simple systems we consider here highlight chromatin's role as a lower-dimensional surface whose interactions with proteins are required for these novel phases.
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Affiliation(s)
- Mason N. Rouches
- Department of Molecular Biophysics & Biochemistry, Yale University and Quantitative Biology Institute, Yale University
| | - Benjamin B. Machta
- Department of Physics, Yale University and Quantitative Biology Institute, Yale University
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5
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Min S, Picou C, Jeong HJ, Bower A, Jeong K, Chung JK. Melittin-Phospholipase A 2 Synergism Is Mediated by Liquid-Liquid Miscibility Phase Transition in Giant Unilamellar Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7456-7462. [PMID: 38546877 DOI: 10.1021/acs.langmuir.3c03920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The primary constituents of honeybee venom, melittin and phospholipase A2 (PLA2), display toxin synergism in which the PLA2 activity is significantly enhanced by the presence of melittin. It has been shown previously that this is accomplished by the disruption in lipid packing, which allows PLA2 to become processive on the membrane surface. In this work, we show that melittin is capable of driving miscibility phase transition in giant unilamellar vesicles (GUVs) and that it raises the miscibility transition temperature (Tmisc) in a concentration-dependent manner. The induced phase separation enhances the processivity of PLA2, particularly at its boundaries, where a substantial difference in domain thickness creates a membrane discontinuity. The catalytic action of PLA2, in response, induces changes in the membrane, rendering it more conducive to melittin binding. This, in turn, facilitates further lipid phase separation and eventual vesicle lysis. Overall, our results show that melittin has powerful membrane-altering capabilities that activate PLA2 in various membrane contexts. More broadly, they exemplify how this biochemical system actively modulates and capitalizes on the spatial distribution of membrane lipids to efficiently achieve its objectives.
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Affiliation(s)
- Sein Min
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 United States
| | - Cyrus Picou
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 United States
| | - Hye Jin Jeong
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 United States
| | - Adam Bower
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 United States
| | - Keunhong Jeong
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 United States
| | - Jean K Chung
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 United States
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6
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Kim H, Juarez-Contreras I, Budin I. Using the yeast vacuole as a system to test the lipidic drivers of membrane heterogeneity in living cells. Methods Enzymol 2024; 700:77-104. [PMID: 38971613 DOI: 10.1016/bs.mie.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
The biophysical drivers of membrane lateral heterogeneity, often termed lipid rafts, have been largely explored using synthetic liposomes or mammalian plasma membrane-derived giant vesicles. Yeast vacuoles, an organelle comparable to mammalian lysosomes, is the only in vivo system that shows stable micrometer scale phase separation in unperturbed cells. The ease of manipulating lipid metabolism in yeast makes this a powerful system for identifying lipids involved in the onset of vacuole membrane heterogeneity. Vacuole domains are induced by stationary stage growth and nutritional starvation, during which they serve as a docking and internalization site for lipid droplet energy stores. Here we describe methods for characterizing vacuole phase separation, its physiological function, and its lipidic drivers. First, we detail methodologies for robustly inducing vacuole domain formation and quantitatively characterizing during live cell imaging experiments. Second, we detail a new protocol for biochemical isolation of stationary stage vacuoles, which allows for lipidomic dissection of membrane phase separation. Third, we describe biochemical techniques for analyzing lipid droplet internalization in vacuole domains. When combined with genetic or chemical perturbations to lipid metabolism, these methods allow for systematic dissection of lipid composition in the structure and function of ordered membrane domains in living cells.
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Affiliation(s)
- Hyesoo Kim
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States
| | - Israel Juarez-Contreras
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States
| | - Itay Budin
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States.
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7
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Henry WS, Müller S, Yang JS, Innes-Gold S, Das S, Reinhardt F, Sigmund K, Phadnis VV, Wan Z, Eaton E, Sampaio JL, Bell GW, Viravalli A, Hammond PT, Kamm RD, Cohen AE, Boehnke N, Hsu VW, Levental KR, Rodriguez R, Weinberg RA. Ether lipids influence cancer cell fate by modulating iron uptake. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585922. [PMID: 38562716 PMCID: PMC10983928 DOI: 10.1101/2024.03.20.585922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Cancer cell fate has been widely ascribed to mutational changes within protein-coding genes associated with tumor suppressors and oncogenes. In contrast, the mechanisms through which the biophysical properties of membrane lipids influence cancer cell survival, dedifferentiation and metastasis have received little scrutiny. Here, we report that cancer cells endowed with a high metastatic ability and cancer stem cell-like traits employ ether lipids to maintain low membrane tension and high membrane fluidity. Using genetic approaches and lipid reconstitution assays, we show that these ether lipid-regulated biophysical properties permit non-clathrin-mediated iron endocytosis via CD44, leading directly to significant increases in intracellular redox-active iron and enhanced ferroptosis susceptibility. Using a combination of in vitro three-dimensional microvascular network systems and in vivo animal models, we show that loss of ether lipids also strongly attenuates extravasation, metastatic burden and cancer stemness. These findings illuminate a mechanism whereby ether lipids in carcinoma cells serve as key regulators of malignant progression while conferring a unique vulnerability that can be exploited for therapeutic intervention.
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Affiliation(s)
- Whitney S Henry
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sebastian Müller
- Institut Curie, CNRS, INSERM, PSL Research University, Equipe Labellisée Ligue Contre le Cancer, Paris 75005, France
| | - Jia-Shu Yang
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, and Dept. of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Innes-Gold
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sunny Das
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ferenc Reinhardt
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kim Sigmund
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Vaishnavi V Phadnis
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Dept. of Biology, MIT, Cambridge, MA 02139, USA
| | - Zhengpeng Wan
- Dept. of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | - Elinor Eaton
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Julio L Sampaio
- Institut Curie, INSERM, Mines ParisTech, Paris 75005, France
| | - George W Bell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Amartya Viravalli
- Dept. of Chemical Engineering and Materials Science, University of Minnesota Minneapolis, MN 55455, USA
| | - Paula T Hammond
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
- Dept. of Chemical Engineering, MIT, Cambridge, MA 02139, USA
- Senior author
| | - Roger D Kamm
- Dept. of Biological Engineering, MIT, Cambridge, MA 02139, USA
- Dept. of Physics, Harvard University, Cambridge, MA 02138, USA
- Senior author
| | - Adam E Cohen
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Dept. of Physics, Harvard University, Cambridge, MA 02138, USA
- Senior author
| | - Natalie Boehnke
- Dept. of Chemical Engineering and Materials Science, University of Minnesota Minneapolis, MN 55455, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
- Senior author
| | - Victor W Hsu
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, and Dept. of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Senior author
| | - Kandice R Levental
- Dept. of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
- Senior author
| | - Raphaël Rodriguez
- Institut Curie, CNRS, INSERM, PSL Research University, Equipe Labellisée Ligue Contre le Cancer, Paris 75005, France
- Senior author
| | - Robert A Weinberg
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Dept. of Biology, MIT, Cambridge, MA 02139, USA
- Ludwig Center for Molecular Oncology, Cambridge, MA 02139, USA
- Senior author
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8
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Doherty W, Benson S, Pepdjonovic L, Koppes AN, Koppes RA. Cell Line and Media Composition Influence the Production of Giant Plasma Membrane Vesicles. ACS Biomater Sci Eng 2024; 10:1880-1891. [PMID: 38374716 PMCID: PMC10934252 DOI: 10.1021/acsbiomaterials.3c01596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
Giant plasma membrane vesicles (GPMVs) have been utilized as a model to study phase separation in the plasma membrane. Additionally, GPMVs have been employed as vehicle for delivering molecular cargo, including small molecule drugs and nanoparticles. Nearly all examples of GPMV production use a defined salt buffer that is a stark contrast to typical cell culture medium. In this study, we demonstrate that the addition of formaldehyde and dithiothreitol to a standard culture medium was capable of generating GPMVs at a concentration equal to or higher than the traditional production buffer. These methods were evaluated for two human cell lines: kidney endothelial and Schwann cells (SCs). Morphological properties of the resultant GPMVs exhibited no significant differences between the two formulations. Factors such as pH and seeding density significantly influenced the production of GPMVs in both mediums. The cell type and seeding density was shown to influence the number of GPMVs to the greatest extent. SCs yield more GPMVs at higher seeding densities compared to endothelial cells. Stability of the membrane of the GPMVs produced in both mediums was evaluated by monitoring passive diffusion of two fluorescently tagged dextrans (3 and 10 kDa). Regardless of the production formulation or cell type, approximately 85% GPMVs are impermeable to either dextran. Cold storage for on-demand use and shipping are essential for broader use of GPMVs. Toward this aim, we have evaluated the GMPV number and morphologies following storage at -80 °C and in liquid nitrogen. A significant loss of the GPMV number, ∼30%, was observed following storage across production formulations as well as cell types. Our results indicate that smaller GMPVs, <5 μm are more stable for preservation. In conclusion, GPMVs can be produced in a broad range of formulations, exhibit a high degree of stability, and can undergo cold storage for further adoption.
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Affiliation(s)
- William Doherty
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Sarah Benson
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Lisa Pepdjonovic
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Abigail N. Koppes
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Department
of Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Department
of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Ryan A. Koppes
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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9
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Yanagawa M, Shimobayashi SF. Multi-dimensional condensation of intracellular biomolecules. J Biochem 2024; 175:179-186. [PMID: 37993409 DOI: 10.1093/jb/mvad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023] Open
Abstract
Liquid-liquid phase separation has been recognized as universal mechanisms in living cells for the formation of RNA-protein condensates and ordered lipid domains. These biomolecular condensates or domains nucleate, diffuse and interact with each other across physical dimensions to perform their biological functions. Here we summarize key features of biophysical principles underlying the multi-dimensional condensation of RNA-protein condensates and ordered lipid domains, which are related to nuclear transcription, and signaling on cell membranes. Uncovering physicochemical factors that govern the spatiotemporal coupling of those condensates presents a new avenue in their functions and associated human diseases.
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Affiliation(s)
- Masataka Yanagawa
- Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shunsuke F Shimobayashi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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10
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Sakuma Y, Kayamori N, Tanaka J, Haga K, Imai M, Kawakatsu T. Effects of grafted polymers on the lipid membrane fluidity. Biophys J 2024; 123:489-501. [PMID: 38243595 PMCID: PMC10912922 DOI: 10.1016/j.bpj.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/27/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024] Open
Abstract
Since the membrane fluidity controls the cellular functions, it is important to identify the factors that determine the cell membrane viscosity. Cell membranes are composed of not only lipids and proteins but also polysaccharide chain-anchored molecules, such as glycolipids. To reveal the effects of grafted polymers on the membrane fluidity, in this study, we measured the membrane viscosity of polymer-grafted giant unilamellar vesicles (GUVs), which were prepared by introducing the poly (ethylene glycol) (PEG)-anchored lipids to the ternary GUVs composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and cholesterol. The membrane viscosity was obtained from the velocity field on the GUV generated by applying a point force, based on the hydrodynamic model proposed by Henle and Levine. The velocity field was visualized by a motion of the circular liquid ordered (Lo) domains formed by a phase separation. With increasing PEG density, the membrane viscosity of PEG-grafted GUVs increased gradually in the mushroom region and significantly in the brush region. We propose a hydrodynamic model that includes the excluded volume effect of PEG chains to explain the increase in membrane viscosity in the mushroom region. This work provides a basic understanding of how grafted polymers affect the membrane fluidity.
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Affiliation(s)
- Yuka Sakuma
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan.
| | - Nana Kayamori
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Julia Tanaka
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Kenya Haga
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Masayuki Imai
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Toshihiro Kawakatsu
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
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11
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Graf IR, Machta BB. A bifurcation integrates information from many noisy ion channels and allows for milli-Kelvin thermal sensitivity in the snake pit organ. Proc Natl Acad Sci U S A 2024; 121:e2308215121. [PMID: 38294944 PMCID: PMC10861916 DOI: 10.1073/pnas.2308215121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 12/10/2023] [Indexed: 02/02/2024] Open
Abstract
In various biological systems, information from many noisy molecular receptors must be integrated into a collective response. A striking example is the thermal imaging organ of pit vipers. Single nerve fibers in the organ reliably respond to milli-Kelvin (mK) temperature increases, a thousand times more sensitive than their molecular sensors, thermo-transient receptor potential (TRP) ion channels. Here, we propose a mechanism for the integration of this molecular information. In our model, amplification arises due to proximity to a dynamical bifurcation, separating a regime with frequent and regular action potentials (APs), from a regime where APs are irregular and infrequent. Near the transition, AP frequency can have an extremely sharp dependence on temperature, naturally accounting for the thousand-fold amplification. Furthermore, close to the bifurcation, most of the information about temperature available in the TRP channels' kinetics can be read out from the times between consecutive APs even in the presence of readout noise. A key model prediction is that the coefficient of variation in the distribution of interspike times decreases with AP frequency, and quantitative comparison with experiments indeed suggests that nerve fibers of snakes are located very close to the bifurcation. While proximity to such bifurcation points typically requires fine-tuning of parameters, we propose that having feedback act from the order parameter (AP frequency) onto the control parameter robustly maintains the system in the vicinity of the bifurcation. This robustness suggests that similar feedback mechanisms might be found in other sensory systems which also need to detect tiny signals in a varying environment.
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Affiliation(s)
| | - Benjamin B. Machta
- Department of Physics, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
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12
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Balakrishnan M, Kenworthy AK. Lipid Peroxidation Drives Liquid-Liquid Phase Separation and Disrupts Raft Protein Partitioning in Biological Membranes. J Am Chem Soc 2024; 146:1374-1387. [PMID: 38171000 PMCID: PMC10797634 DOI: 10.1021/jacs.3c10132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The peroxidation of membrane lipids by free radicals contributes to aging, numerous diseases, and ferroptosis, an iron-dependent form of cell death. Peroxidation changes the structure and physicochemical properties of lipids, leading to bilayer thinning, altered fluidity, and increased permeability of membranes in model systems. Whether and how lipid peroxidation impacts the lateral organization of proteins and lipids in biological membranes, however, remains poorly understood. Here, we employ cell-derived giant plasma membrane vesicles (GPMVs) as a model to investigate the impact of lipid peroxidation on ordered membrane domains, often termed membrane rafts. We show that lipid peroxidation induced by the Fenton reaction dramatically enhances the phase separation propensity of GPMVs into coexisting liquid-ordered (Lo) and liquid-disordered (Ld) domains and increases the relative abundance of the disordered phase. Peroxidation also leads to preferential accumulation of peroxidized lipids and 4-hydroxynonenal (4-HNE) adducts in the disordered phase, decreased lipid packing in both Lo and Ld domains, and translocation of multiple classes of raft proteins out of ordered domains. These findings indicate that the peroxidation of plasma membrane lipids disturbs many aspects of membrane rafts, including their stability, abundance, packing, and protein and lipid composition. We propose that these disruptions contribute to the pathological consequences of lipid peroxidation during aging and disease and thus serve as potential targets for therapeutic intervention.
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Affiliation(s)
- Muthuraj Balakrishnan
- Center
for Membrane and Cell Physiology, University
of Virginia, Charlottesville, Virginia 22903, United States
- Department
of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, United States
| | - Anne K. Kenworthy
- Center
for Membrane and Cell Physiology, University
of Virginia, Charlottesville, Virginia 22903, United States
- Department
of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, United States
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13
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Lipowsky R. Multispherical shapes of vesicles with intramembrane domains. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:4. [PMID: 38206459 PMCID: PMC10784401 DOI: 10.1140/epje/s10189-023-00399-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Phase separation of biomembranes into two fluid phases, a and b, leads to the formation of vesicles with intramembrane a- and b-domains. These vesicles can attain multispherical shapes consisting of several spheres connected by closed membrane necks. Here, we study the morphological complexity of these multispheres using the theory of curvature elasticity. Vesicles with two domains form two-sphere shapes, consisting of one a- and one b-sphere, connected by a closed ab-neck. The necks' effective mean curvature is used to distinguish positive from negative necks. Two-sphere shapes of two-domain vesicles can attain four different morphologies that are governed by two different stability conditions. The closed ab-necks are compressed by constriction forces which induce neck fission and vesicle division for large line tensions and/or large spontaneous curvatures. Multispherical shapes with one ab-neck and additional aa- and bb-necks involve several stability conditions, which act to reduce the stability regimes of the multispheres. Furthermore, vesicles with more than two domains form multispheres with more than one ab-neck. The multispherical shapes described here represent generalized constant-mean-curvature surfaces with up to four constant mean curvatures. These shapes are accessible to experimental studies using available methods for giant vesicles prepared from ternary lipid mixtures.
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Affiliation(s)
- Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany.
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14
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Lee Y, Park S, Yuan F, Hayden CC, Wang L, Lafer EM, Choi SQ, Stachowiak JC. Transmembrane coupling of liquid-like protein condensates. Nat Commun 2023; 14:8015. [PMID: 38049424 PMCID: PMC10696066 DOI: 10.1038/s41467-023-43332-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023] Open
Abstract
Liquid-liquid phase separation of proteins occurs on both surfaces of cellular membranes during diverse physiological processes. In vitro reconstitution could provide insight into the mechanisms underlying these events. However, most existing reconstitution techniques provide access to only one membrane surface, making it difficult to probe transmembrane phenomena. To study protein phase separation simultaneously on both membrane surfaces, we developed an array of freestanding planar lipid membranes. Interestingly, we observed that liquid-like protein condensates on one side of the membrane colocalized with those on the other side, resulting in transmembrane coupling. Our results, based on lipid probe partitioning and mobility of lipids, suggest that protein condensates locally reorganize membrane lipids, a process which could be explained by multiple effects. These findings suggest a mechanism by which signals originating on one side of a biological membrane, triggered by protein phase separation, can be transferred to the opposite side.
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Affiliation(s)
- Yohan Lee
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Sujin Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Feng Yuan
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Carl C Hayden
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Liping Wang
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Eileen M Lafer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Siyoung Q Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
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15
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Shelby SA, Veatch SL. The Membrane Phase Transition Gives Rise to Responsive Plasma Membrane Structure and Function. Cold Spring Harb Perspect Biol 2023; 15:a041395. [PMID: 37553204 PMCID: PMC10626261 DOI: 10.1101/cshperspect.a041395] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Several groups have recently reported evidence for the emergence of domains in cell plasma membranes when membrane proteins are organized by ligand binding or assembly of membrane proximal scaffolds. These domains recruit and retain components that favor the liquid-ordered phase, adding to a decades-old literature interrogating the contribution of membrane phase separation in plasma membrane organization and function. Here we propose that both past and present observations are consistent with a model in which membranes have a high compositional susceptibility, arising from their thermodynamic state in a single phase that is close to a miscibility phase transition. This rigorous framework naturally allows for both transient structure in the form of composition fluctuations and long-lived structure in the form of induced domains. In this way, the biological tuning of plasma membrane composition enables a responsive compositional landscape that facilitates and augments cellular biochemistry vital to plasma membrane functions.
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Affiliation(s)
- Sarah A Shelby
- Biochemistry & Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee 37996, USA
| | - Sarah L Veatch
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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16
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Mayor S, Bhat A, Kusumi A. A Survey of Models of Cell Membranes: Toward a New Understanding of Membrane Organization. Cold Spring Harb Perspect Biol 2023; 15:a041394. [PMID: 37643877 PMCID: PMC10547391 DOI: 10.1101/cshperspect.a041394] [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] [Indexed: 08/31/2023]
Abstract
The cell membrane, the boundary that separates living cells from their environment, has been the subject of study for over a century. The fluid-mosaic model of Singer and Nicolson in 1972 proposed the plasma membrane as a two-dimensional fluid composed of lipids and proteins. Fifty years hence, advances in biophysical and biochemical tools, particularly optical imaging techniques, have allowed for a better understanding of the physical nature, organization, and composition of cell membranes. This has been made possible by visualizing membrane heterogeneities and their dynamics and appreciating the asymmetrical arrangement of lipids in living cell membranes. Despite these advances, mechanisms underlying the local spatiotemporal organization of membrane components remain unclear. This review surveys various models of membrane organization, culminating in a new model that incorporates nonequilibrium processes and forces exerted by interactions with extramembrane elements such as the actin cytoskeleton. The proposed model provides a comprehensive understanding of membrane organization, taking into account the dynamic nature of the cell membrane and its interactions with its immediate environment.
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Affiliation(s)
- Satyajit Mayor
- National Centre for Biological Science, TIFR, Bangalore 560065, India
| | - Abrar Bhat
- National Centre for Biological Science, TIFR, Bangalore 560065, India
| | - Akihiro Kusumi
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
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17
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Balakrishnan M, Kenworthy AK. Lipid peroxidation drives liquid-liquid phase separation and disrupts raft protein partitioning in biological membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557355. [PMID: 37745342 PMCID: PMC10515805 DOI: 10.1101/2023.09.12.557355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The peroxidation of membrane lipids by free radicals contributes to aging, numerous diseases, and ferroptosis, an iron-dependent form of cell death. Peroxidation changes the structure, conformation and physicochemical properties of lipids, leading to major membrane alterations including bilayer thinning, altered fluidity, and increased permeability. Whether and how lipid peroxidation impacts the lateral organization of proteins and lipids in biological membranes, however, remains poorly understood. Here, we employ cell-derived giant plasma membrane vesicles (GPMVs) as a model to investigate the impact of lipid peroxidation on ordered membrane domains, often termed membrane rafts. We show that lipid peroxidation induced by the Fenton reaction dramatically enhances phase separation propensity of GPMVs into co-existing liquid ordered (raft) and liquid disordered (non-raft) domains and increases the relative abundance of the disordered, non-raft phase. Peroxidation also leads to preferential accumulation of peroxidized lipids and 4-hydroxynonenal (4-HNE) adducts in the disordered phase, decreased lipid packing in both raft and non-raft domains, and translocation of multiple classes of proteins out of rafts. These findings indicate that peroxidation of plasma membrane lipids disturbs many aspects of membrane rafts, including their stability, abundance, packing, and protein and lipid composition. We propose that these disruptions contribute to the pathological consequences of lipid peroxidation during aging and disease, and thus serve as potential targets for therapeutic intervention.
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Affiliation(s)
- Muthuraj Balakrishnan
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Anne K. Kenworthy
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
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18
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Sakamoto K, Akimoto T, Muramatsu M, Sansom MSP, Metzler R, Yamamoto E. Heterogeneous biological membranes regulate protein partitioning via fluctuating diffusivity. PNAS NEXUS 2023; 2:pgad258. [PMID: 37593200 PMCID: PMC10427746 DOI: 10.1093/pnasnexus/pgad258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/22/2023] [Accepted: 07/27/2023] [Indexed: 08/19/2023]
Abstract
Cell membranes phase separate into ordered L o and disordered L d domains depending on their compositions. This membrane compartmentalization is heterogeneous and regulates the localization of specific proteins related to cell signaling and trafficking. However, it is unclear how the heterogeneity of the membranes affects the diffusion and localization of proteins in L o and L d domains. Here, using Langevin dynamics simulations coupled with the phase-field (LDPF) method, we investigate several tens of milliseconds-scale diffusion and localization of proteins in heterogeneous biological membrane models showing phase separation into L o and L d domains. The diffusivity of proteins exhibits temporal fluctuations depending on the field composition. Increases in molecular concentrations and domain preference of the molecule induce subdiffusive behavior due to molecular collisions by crowding and confinement effects, respectively. Moreover, we quantitatively demonstrate that the protein partitioning into the L o domain is determined by the difference in molecular diffusivity between domains, molecular preference of domain, and molecular concentration. These results pave the way for understanding how biological reactions caused by molecular partitioning may be controlled in heterogeneous media. Moreover, the methodology proposed here is applicable not only to biological membrane systems but also to the study of diffusion and localization phenomena of molecules in various heterogeneous systems.
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Affiliation(s)
- Ken Sakamoto
- Department of System Design Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Takuma Akimoto
- Department of Physics, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Mayu Muramatsu
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, Potsdam-Golm 14476, Germany
- Asia Pacific Centre for Theoretical Physics, Pohang 37673, Republic of Korea
| | - Eiji Yamamoto
- Department of System Design Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
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19
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Rubio-Sánchez R, Mognetti BM, Cicuta P, Di Michele L. DNA-Origami Line-Actants Control Domain Organization and Fission in Synthetic Membranes. J Am Chem Soc 2023; 145:11265-11275. [PMID: 37163977 DOI: 10.1021/jacs.3c01493] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cells can precisely program the shape and lateral organization of their membranes using protein machinery. Aiming to replicate a comparable degree of control, here we introduce DNA-origami line-actants (DOLAs) as synthetic analogues of membrane-sculpting proteins. DOLAs are designed to selectively accumulate at the line-interface between coexisting domains in phase-separated lipid membranes, modulating the tendency of the domains to coalesce. With experiments and coarse-grained simulations, we demonstrate that DOLAs can reversibly stabilize two-dimensional analogues of Pickering emulsions on synthetic giant liposomes, enabling dynamic programming of membrane lateral organization. The control afforded over membrane structure by DOLAs extends to three-dimensional morphology, as exemplified by a proof-of-concept synthetic pathway leading to vesicle fission. With DOLAs we lay the foundations for mimicking, in synthetic systems, some of the critical membrane-hosted functionalities of biological cells, including signaling, trafficking, sensing, and division.
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Affiliation(s)
- Roger Rubio-Sánchez
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Bortolo Matteo Mognetti
- Interdisciplinary Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles (ULB), Campus Plaine, CP 231, Boulevard du Triomphe, B-1050 Brussels, Belgium
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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20
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Kim T, Yoo J, Do S, Hwang DS, Park Y, Shin Y. RNA-mediated demixing transition of low-density condensates. Nat Commun 2023; 14:2425. [PMID: 37105967 PMCID: PMC10140143 DOI: 10.1038/s41467-023-38118-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Biomolecular condensates play a key role in organizing cellular reactions by concentrating a specific set of biomolecules. However, whether condensate formation is accompanied by an increase in the total mass concentration within condensates or by the demixing of already highly crowded intracellular components remains elusive. Here, using refractive index imaging, we quantify the mass density of several condensates, including nucleoli, heterochromatin, nuclear speckles, and stress granules. Surprisingly, the latter two condensates exhibit low densities with a total mass concentration similar to the surrounding cyto- or nucleoplasm. Low-density condensates display higher permeability to cellular protein probes. We find that RNA tunes the biomolecular density of condensates. Moreover, intracellular structures such as mitochondria heavily influence the way phase separation proceeds, impacting the localization, morphology, and growth of condensates. These findings favor a model where segregative phase separation driven by non-associative or repulsive molecular interactions together with RNA-mediated selective association of specific components can give rise to low-density condensates in the crowded cellular environment.
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Affiliation(s)
- Taehyun Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jaeyoon Yoo
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sungho Do
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong Soo Hwang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, Daejeon, 34141, Republic of Korea
- Tomocube Inc, Daejeon, 34109, South Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Korea.
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21
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Feng S, Park S, Choi YK, Im W. CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. J Chem Theory Comput 2023; 19:2161-2185. [PMID: 37014931 PMCID: PMC10174225 DOI: 10.1021/acs.jctc.2c01246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
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Affiliation(s)
- Shasha Feng
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Yeol Kyo Choi
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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22
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Veatch SL, Rogers N, Decker A, Shelby SA. The plasma membrane as an adaptable fluid mosaic. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184114. [PMID: 36581017 PMCID: PMC9922517 DOI: 10.1016/j.bbamem.2022.184114] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022]
Abstract
The fluid mosaic model proposed by Singer and Nicolson established a powerful framework to interrogate biological membranes that has stood the test of time. They proposed that the membrane is a simple fluid, meaning that proteins and lipids are randomly distributed over distances larger than those dictated by direct interactions. Here we present an update to this model that describes a spatially adaptable fluid membrane capable of tuning local composition in response to forces originating outside the membrane plane. This revision is rooted in the thermodynamics of lipid mixtures, draws from recent experimental results, and suggests new modes of membrane function.
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Affiliation(s)
- Sarah L Veatch
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA.
| | - Nat Rogers
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Adam Decker
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Sarah A Shelby
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA.
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23
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Regulation of membrane protein structure and function by their lipid nano-environment. Nat Rev Mol Cell Biol 2023; 24:107-122. [PMID: 36056103 PMCID: PMC9892264 DOI: 10.1038/s41580-022-00524-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 129.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2022] [Indexed: 02/04/2023]
Abstract
Transmembrane proteins comprise ~30% of the mammalian proteome, mediating metabolism, signalling, transport and many other functions required for cellular life. The microenvironment of integral membrane proteins (IMPs) is intrinsically different from that of cytoplasmic proteins, with IMPs solvated by a compositionally and biophysically complex lipid matrix. These solvating lipids affect protein structure and function in a variety of ways, from stereospecific, high-affinity protein-lipid interactions to modulation by bulk membrane properties. Specific examples of functional modulation of IMPs by their solvating membranes have been reported for various transporters, channels and signal receptors; however, generalizable mechanistic principles governing IMP regulation by lipid environments are neither widely appreciated nor completely understood. Here, we review recent insights into the inter-relationships between complex lipidomes of mammalian membranes, the membrane physicochemical properties resulting from such lipid collectives, and the regulation of IMPs by either or both. The recent proliferation of high-resolution methods to study such lipid-protein interactions has led to generalizable insights, which we synthesize into a general framework termed the 'functional paralipidome' to understand the mutual regulation between membrane proteins and their surrounding lipid microenvironments.
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24
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Pattern Formation in Two-Component Monolayers of Particles with Competing Interactions. Molecules 2023; 28:molecules28031366. [PMID: 36771033 PMCID: PMC9920350 DOI: 10.3390/molecules28031366] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/04/2023] Open
Abstract
Competing interactions between charged inclusions in membranes of living organisms or charged nanoparticles in near-critical mixtures can lead to self-assembly into various patterns. Motivated by these systems, we developed a simple triangular lattice model for binary mixtures of oppositely charged particles with additional short-range attraction or repulsion between like or different particles, respectively. We determined the ground state for the system in contact with a reservoir of the particles for the whole chemical potentials plane, and the structure of self-assembled conglomerates for fixed numbers of particles. Stability of the low-temperature ordered patterns was verified by Monte Carlo simulations. In addition, we performed molecular dynamics simulations for a continuous model with interactions having similar features, but a larger range and lower strength than in the lattice model. Interactions with and without symmetry between different components were assumed. We investigated both the conglomerate formed in the center of a thin slit with repulsive walls, and the structure of a monolayer adsorbed at an attractive substrate. Both models give the same patterns for large chemical potentials or densities. For low densities, more patterns occur in the lattice model. Different phases coexist with dilute gas on the lattice and in the continuum, leading to different patterns in self-assembled conglomerates ('rafts').
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25
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Ko TH, Chen YF. Correlation between the In-Plane Critical Behavior and Out-of-Plane Interaction of Ternary Lipid Membranes. MEMBRANES 2022; 13:6. [PMID: 36676813 PMCID: PMC9860714 DOI: 10.3390/membranes13010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Liquid-liquid phase-separating lipid membranes belong to the 2-D Ising universality class. While their in-plane critical behaviors are well studied, how the behaviors modulate out-of-plane interactions is rarely explored, despite its profound implications for biomembranes and 2-D ferromagnets. Here, we examine how the interlayer interaction, manifested as membrane fusion, is affected by the membranes' critical fluctuations. Remarkably, the critical fluctuations suppress membrane fusion, suggesting a correlation between critical behaviors and interlayer interactions for 2-D Ising systems.
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26
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Ho PS, Kao TY, Li CC, Lan YJ, Lai YC, Chiang YW. Nanodisc Lipids Exhibit Singular Behaviors Implying Critical Phenomena. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15372-15383. [PMID: 36454955 DOI: 10.1021/acs.langmuir.2c02596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Nanodiscs are broadly used for characterization of membrane proteins as they are generally assumed to provide a near-native environment. In fact, it is an open question whether the physical properties of lipids in nanodiscs and membrane vesicles of the same lipid composition are identical. Here, we investigate the properties of lipids (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 1,2-dilauroyl-sn-glycero-3-phosphocholine, and their mixtures) in two different sample types, nanodiscs and multilamellar vesicles, by means of spin-label electron spin resonance techniques. Our results provide a quantitative description of lipid dynamics and ordering, elucidating the molecular details of how lipids in the two sample types behave differently in response to temperature and lipid composition. We show that the properties of lipids are altered in nanodiscs such that the dissimilarity of the fluid and gel lipid phases is reduced, and the first-order phase transitions are largely abolished in nanodiscs. We unveil that the ensemble of lipids in the middle of a nanodisc bilayer, as probed by the end-chain spin-label 16-PC, is promoted to a state close to a miscibility critical point, thereby rendering the phase transitions continuous. Critical phenomena have recently been proposed to explain features of the heterogeneity in native cell membranes. Our results lay the groundwork for how to establish a near-native environment in nanodiscs with simple organization of lipid components.
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Affiliation(s)
- Pei-Shan Ho
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Te-Yu Kao
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Chieh-Chin Li
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Yu-Jing Lan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Yei-Chen Lai
- Department of Chemistry, National Chung Hsing University, Taichung 402-002, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
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27
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Heberle FA, Welsch D, Scott HL, Waxham MN. Optimization of cryo-electron microscopy for quantitative analysis of lipid bilayers. BIOPHYSICAL REPORTS 2022; 3:100090. [PMID: 36593976 PMCID: PMC9804012 DOI: 10.1016/j.bpr.2022.100090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Cryogenic electron microscopy (cryo-EM) is among the most powerful tools available for interrogating nanoscale structure of biological materials. We recently showed that cryo-EM can be used to measure the bilayer thickness of lipid vesicles and biological membranes with subangstrom precision, resulting in the direct visualization of nanoscopic domains of different thickness in multicomponent lipid mixtures and giant plasma membrane vesicles. Despite the great potential of cryo-EM for revealing the lateral organization of biomembranes, a large parameter space of experimental conditions remains to be optimized. Here, we systematically investigate the influence of instrument parameters and image postprocessing steps on the ability to accurately measure bilayer thickness and discriminate regions of different thickness within unilamellar liposomes. This unique application of cryo-EM places particular demands on image acquisition optimization and analysis due to the facts that 1) each vesicle is a different size with different curvature, 2) the domains in each vesicle can be heterogenous in size, and 3) the random orientation of vesicles amplifies the variability of domain size in projected images. We also demonstrate a spatial autocorrelation analysis to extract additional information about lateral heterogeneity.
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Affiliation(s)
- Frederick A. Heberle
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee,Corresponding author
| | - Doug Welsch
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas
| | - Haden L. Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - M. Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas,Corresponding author
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28
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Role of the membrane anchor in the regulation of Lck activity. J Biol Chem 2022; 298:102663. [PMID: 36372231 PMCID: PMC9763865 DOI: 10.1016/j.jbc.2022.102663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Theoretical work suggests that collective spatiotemporal behavior of integral membrane proteins should be modulated by boundary lipids sheathing their membrane anchors. Here, we show evidence for this prediction while investigating the mechanism for maintaining a steady amount of the active form of integral membrane protein Lck kinase (LckA) by Lck trans-autophosphorylation regulated by the phosphatase CD45. We used super-resolution microscopy, flow cytometry, and pharmacological and genetic perturbation to gain insight into the spatiotemporal context of this process. We found that LckA is generated exclusively at the plasma membrane, where CD45 maintains it in a ceaseless dynamic equilibrium with its unphosphorylated precursor. Steady LckA shows linear dependence, after an initial threshold, over a considerable range of Lck expression levels. This behavior fits a phenomenological model of trans-autophosphorylation that becomes more efficient with increasing LckA. We then challenged steady LckA formation by genetically swapping the Lck membrane anchor with structurally divergent ones, such as that of Src or the transmembrane domains of LAT, CD4, palmitoylation-defective CD4 and CD45 that were expected to drastically modify Lck boundary lipids. We observed small but significant changes in LckA generation, except for the CD45 transmembrane domain that drastically reduced LckA due to its excessive lateral proximity to CD45. Comprehensively, LckA formation and maintenance can be best explained by lipid bilayer critical density fluctuations rather than liquid-ordered phase-separated nanodomains, as previously thought, with "like/unlike" boundary lipids driving dynamical proximity and remoteness of Lck with itself and with CD45.
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29
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Krasnobaev VD, Batishchev OV. The Role of Lipid Domains and Physical Properties of Membranes in the Development of Age-Related Neurodegenerative Diseases. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2022. [DOI: 10.1134/s199074782209001x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Abstract
Micromechanics techniques are playing an increasing role in characterization of biomembranes. The mechanical properties of membranes play an important role for a whole range of cellular processes. Lipid-protein biomembranes display lateral heterogeneity, domain formation, and morphological changes at mesoscopic and nanoscopic length scales. An attempt is made to introduce how membrane's material properties can be measured. Both fluctuation analysis and micro-pipette aspiration experiments have been used to quantify the micromechanics of membranes. The relationship between the structure and function of biomembranes is a critical concern in modern biology. This overview calls for a deeper understanding of how the cell complexity might be related to the mechanical properties of the lipid-protein membrane. Mechanical properties can influence cellular response to processes like adhesion, transport, differentiation, proliferation and migration.
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31
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Varma M, Deserno M. Distribution of cholesterol in asymmetric membranes driven by composition and differential stress. Biophys J 2022; 121:4001-4018. [PMID: 35927954 PMCID: PMC9674969 DOI: 10.1016/j.bpj.2022.07.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Many lipid membranes of eukaryotic cells are asymmetric, which means the two leaflets differ in at least one physical property, such as lipid composition or lateral stress. Maintaining this asymmetry is helped by the fact that ordinary phospholipids rarely transition between leaflets, but cholesterol is an exception: its flip-flop times are in the microsecond range, so that its distribution between leaflets is determined by a chemical equilibrium. In particular, preferential partitioning can draw cholesterol into a more saturated leaflet, and phospholipid number asymmetry can force it out of a compressed leaflet. Combining highly coarse-grained membrane simulations with theoretical modeling, we investigate how these two driving forces play against each other until cholesterol's chemical potential is equilibrated. The theory includes two coupled elastic sheets and a Flory-Huggins mixing free energy with a χ parameter. We obtain a relationship between χ and the interaction strength between cholesterol and lipids in either of the two leaflets, and we find that it depends, albeit weakly, on lipid number asymmetry. The differential stress measurements under various asymmetry conditions agree with our theoretical predictions. Using the two kinds of asymmetries in combination, we find that it is possible to counteract the phospholipid number bias, and the resultant stress in the membrane, via the control of cholesterol mixing in the leaflets.
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Affiliation(s)
- Malavika Varma
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania.
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32
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Doole FT, Kumarage T, Ashkar R, Brown MF. Cholesterol Stiffening of Lipid Membranes. J Membr Biol 2022; 255:385-405. [PMID: 36219221 PMCID: PMC9552730 DOI: 10.1007/s00232-022-00263-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022]
Abstract
Biomembrane order, dynamics, and other essential physicochemical parameters are controlled by cholesterol, a major component of mammalian cell membranes. Although cholesterol is well known to exhibit a condensing effect on fluid lipid membranes, the extent of stiffening that occurs with different degrees of lipid acyl chain unsaturation remains an enigma. In this review, we show that cholesterol locally increases the bending rigidity of both unsaturated and saturated lipid membranes, suggesting there may be a length-scale dependence of the bending modulus. We review our published data that address the origin of the mechanical effects of cholesterol on unsaturated and polyunsaturated lipid membranes and their role in biomembrane functions. Through a combination of solid-state deuterium NMR spectroscopy and neutron spin-echo spectroscopy, we show that changes in molecular packing cause the universal effects of cholesterol on the membrane bending rigidity. Our findings have broad implications for the role of cholesterol in lipid–protein interactions as well as raft-like mixtures, drug delivery applications, and the effects of antimicrobial peptides on lipid membranes.
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Affiliation(s)
- Fathima T Doole
- Deaprtment of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85712, USA
| | - Teshani Kumarage
- Department of Physics, Virginia Tech, Blacksburg, VA, 24061, USA.,Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA, 24061, USA. .,Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Michael F Brown
- Deaprtment of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85712, USA. .,Department of Physics, University of Arizona, Tucson, AZ, 85712, USA.
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33
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Yoda T. Phase Separation in Liposomes Determined by Ergosterol and Classified Using Machine Learning. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-8. [PMID: 36117262 DOI: 10.1017/s1431927622012521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Recent studies indicated that ergosterol (Erg) helps form strongly ordered lipid domains in membranes that depend on their chemical characters. However, direct evidence of concentration-dependent interaction of Erg with lipid membranes has not been reported. We studied the Erg concentration-dependent changes in the phase behaviors of membranes using cell-sized liposomes containing 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC)/1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). We observed the concentration range of phase separation in ternary membranes was significantly wider when Erg rather than cholesterol (Chol) was used as the sterol component. We used machine learning for the first time to analyze microscopic images of cell-sized liposomes and identify phase-separated structures. The automated method was successful in identifying homogeneous membranes but performance remained data-limited for the identification of phase separation domains characterized by more complex features.
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Affiliation(s)
- Tsuyoshi Yoda
- Aomori Prefectural Industrial Technology Research Center, Hachinohe Industrial Research Institute, Hachinohe City, Aomori 039-2245, Japan
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka City, Iwate 020-8550, Japan
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34
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Chai YJ, Cheng CY, Liao YH, Lin CH, Hsieh CL. Heterogeneous nanoscopic lipid diffusion in the live cell membrane and its dependency on cholesterol. Biophys J 2022; 121:3146-3161. [PMID: 35841144 PMCID: PMC9463655 DOI: 10.1016/j.bpj.2022.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/08/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022] Open
Abstract
Cholesterol plays a unique role in the regulation of membrane organization and dynamics by modulating the membrane phase transition at the nanoscale. Unfortunately, due to their small sizes and dynamic nature, the effects of cholesterol-mediated membrane nanodomains on membrane dynamics remain elusive. Here, using ultrahigh-speed single-molecule tracking with advanced optical microscope techniques, we investigate the diffusive motion of single phospholipids in the live cell plasma membrane at the nanoscale and its dependency on the cholesterol concentration. We find that both saturated and unsaturated phospholipids undergo anomalous subdiffusion on the length scale of 10-100 nm. The diffusion characteristics exhibit considerable variations in space and in time, indicating that the nanoscopic lipid diffusion is highly heterogeneous. Importantly, through the statistical analysis, apparent dual-mobility subdiffusion is observed from the mixed diffusion behaviors. The measured subdiffusion agrees well with the hop diffusion model that represents a diffuser moving in a compartmentalized membrane created by the cytoskeleton meshwork. Cholesterol depletion diminishes the lipid mobility with an apparently smaller compartment size and a stronger confinement strength. Similar results are measured with temperature reduction, suggesting that the more heterogeneous and restricted diffusion is connected to the nanoscopic membrane phase transition. Our conclusion supports the model that cholesterol depletion induces the formation of gel-phase, solid-like membrane nanodomains. These nanodomains undergo restricted diffusion and act as diffusion obstacles to the membrane molecules that are excluded from the nanodomains. This work provides the experimental evidence that the nanoscopic lipid diffusion in the cell plasma membrane is heterogeneous and sensitive to the cholesterol concentration and temperature, shedding new light on the regulation mechanisms of nanoscopic membrane dynamics.
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Affiliation(s)
- Yu-Jo Chai
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Ching-Ya Cheng
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Yi-Hung Liao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Chih-Hsiang Lin
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan.
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35
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Wongsirojkul N, Masuta A, Shimokawa N, Takagi M. Control of Line Tension at Phase-Separated Lipid Domain Boundaries: Monounsaturated Fatty Acids with Different Chain Lengths and Osmotic Pressure. MEMBRANES 2022; 12:membranes12080781. [PMID: 36005696 PMCID: PMC9415386 DOI: 10.3390/membranes12080781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/04/2022] [Accepted: 08/12/2022] [Indexed: 06/01/2023]
Abstract
Line tension at phase-separated lipid domain boundaries is an important factor that governs the stability of the phase separation. We studied the control of the line tension in lipid membranes composed of dioleoylphosphocholine (DOPC), dipalmitoylphosphocholine (DPPC), and cholesterol (Chol) by the addition of the following three monounsaturated fatty acids (MUFAs) with different chain lengths: palmitoleic acid (PaA), oleic acid (OA), and eicosenoic acid (EiA). In addition, we attempted to alter the line tension by applying osmotic pressure. The phase behavior of the MUFA-containing lipid membranes in the presence and absence of osmotic stress was observed by fluorescence and confocal laser scanning microscopy. The line tension was quantitatively measured from the domain boundary fluctuation by flicker spectroscopy, and the interactions between the lipids and MUFAs were examined by differential scanning calorimetry. PaA and OA, which are shorter MUFAs, decreased the line tension, whereas EiA changed the liquid domain to a solid domain. The osmotic pressure increased the line tension, even in the presence of MUFAs. It may be possible to control the line tension by combining the chemical approach of MUFA addition and the physical approach of applying osmotic pressure.
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Affiliation(s)
| | | | | | - Masahiro Takagi
- Correspondence: (N.S.); (M.T.); Tel.: +81-761-51-1650 (M.T.)
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36
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Graf IR, Machta BB. Thermodynamic stability and critical points in multicomponent mixtures with structured interactions. PHYSICAL REVIEW RESEARCH 2022; 4:033144. [PMID: 38343561 PMCID: PMC10857862 DOI: 10.1103/physrevresearch.4.033144] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Theoretical work has shed light on the phase behavior of idealized mixtures of many components with random interactions. However, typical mixtures interact through particular physical features, leading to a structured, nonrandom interaction matrix of lower rank. Here, we develop a theoretical framework for such mixtures and derive mean-field conditions for thermodynamic stability and critical behavior. Irrespective of the number of components and features, this framework allows for a generally lower-dimensional representation in the space of features and proposes a principled way to coarse-grain multicomponent mixtures as binary mixtures. Moreover, it suggests a way to systematically characterize different series of critical points and their codimensions in mean-field. Since every pairwise interaction matrix can be expressed in terms of features, our work is applicable to a broad class of mean-field models.
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Affiliation(s)
- Isabella R. Graf
- Department of Physics, Yale University, New Haven, Connecticut 06511, USA
| | - Benjamin B. Machta
- Department of Physics and Quantitative Biology Institute, Yale University, New Haven, Connecticut 06511, USA
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37
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Mendes A, Heil HS, Coelho S, Leterrier C, Henriques R. Mapping molecular complexes with super-resolution microscopy and single-particle analysis. Open Biol 2022; 12:220079. [PMID: 35892200 PMCID: PMC9326279 DOI: 10.1098/rsob.220079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Understanding the structure of supramolecular complexes provides insight into their functional capabilities and how they can be modulated in the context of disease. Super-resolution microscopy (SRM) excels in performing this task by resolving ultrastructural details at the nanoscale with molecular specificity. However, technical limitations, such as underlabelling, preclude its ability to provide complete structures. Single-particle analysis (SPA) overcomes this limitation by combining information from multiple images of identical structures and producing an averaged model, effectively enhancing the resolution and coverage of image reconstructions. This review highlights important studies using SRM-SPA, demonstrating how it broadens our knowledge by elucidating features of key biological structures with unprecedented detail.
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Affiliation(s)
| | | | - Simao Coelho
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras, Portugal,MRC Laboratory for Molecular Cell Biology, University College London, London, UK
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38
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Destainville N, Coulonges N. Boundary fluctuation dynamics of a phase-separated domain in planar geometry. Phys Rev E 2022; 105:064115. [PMID: 35854539 DOI: 10.1103/physreve.105.064115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Using phase-ordering kinetics and of renormalization group theories, we derive analytically the relaxation times of the long wavelength fluctuations of a phase-separated domain boundary in the vicinity of (and below) the critical temperature in the planar Ising universality class. For a conserved order parameter, the relaxation time grows like Λ^{3} at wavelength Λ and can be expressed in terms of parameters relevant at the microscopic scale: lattice spacing, bulk diffusion coefficient of the minority phase, and temperature. These results are supported by numerical simulations of 2D Ising models, enabling in addition calculating the nonuniversal numerical prefactor. We discuss the applications of these findings to the determination of the real timescale associated with elementary Monte Carlo moves from the measurement of long wavelength relaxation times on experimental systems or molecular dynamics simulations.
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Affiliation(s)
- Nicolas Destainville
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nelly Coulonges
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, Toulouse, France
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39
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Zapata-Mercado E, Azarova EV, Hristova K. Effect of reversible osmotic stress on live cell plasma membranes, probed via Laurdan general polarization measurements. Biophys J 2022; 121:2411-2418. [PMID: 35596525 DOI: 10.1016/j.bpj.2022.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/10/2021] [Accepted: 05/16/2022] [Indexed: 11/02/2022] Open
Abstract
Here we seek to gain insight into changes in the plasma membrane of live cells upon the application of osmotic stress using Laurdan, a fluorescent probe that reports on membrane organization, hydration, and dynamics. It is known that the application of osmotic stress to lipid vesicles causes a decrease in Laurdan's generalized polarization (GP), which has been interpreted as an indication of membrane stretching. In cells, we see the opposite effects, as GP increases when the osmolarity of the solution is decreased. This increase in GP is associated with the presence of caveolae, which are known to disassemble and flatten in response to osmotic stress.
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Affiliation(s)
- Elmer Zapata-Mercado
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Evgenia V Azarova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218.
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40
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Ureña J, Knight A, Lee IH. Membrane Cargo Density-Dependent Interaction between Protein and Lipid Domains on the Giant Unilamellar Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:4702-4712. [PMID: 35385290 DOI: 10.1021/acs.langmuir.2c00247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein cargos anchored on the lipid membrane can be segregated by fluidic domain phase separation. Lipid membranes at certain compositions may separate into lipid domains to segregate cargos, and protein cargos themselves may be involved in protein condensate domain formation with multivalent binding proteins to segregate cargos. Recent studies suggest that these two driving forces of phase separation closely interact on the lipid membranes to promote codomain formation. In this report, we studied the effect of cargo density on the outcome of the cargo phase separation on giant unilamellar vesicles. Proteins and lipids are connected only by the anchored cargos, so it was originally hypothesized that higher cargo density would increase the degree of interaction between the lipid and protein domains, promoting more phase separation. However, fluorescence image analysis on different cargo densities showed that the cooperative domain formation and steric pressure are at a tug of war opposing each other. Cooperative domain formation is dominant under lower anchor density conditions, and above a threshold density, steric pressure was dominant opposing the domain formation. The result suggests that the cargo density is a key parameter affecting the outcome of cargo organization on the lipid membranes by phase separation.
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Affiliation(s)
- Juan Ureña
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, United States
| | - Ashlynn Knight
- Department of Biology, Montclair State University, Montclair, New Jersey 07043, United States
| | - Il-Hyung Lee
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, United States
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41
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Sezgin E. Giant plasma membrane vesicles to study plasma membrane structure and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183857. [PMID: 34990591 DOI: 10.1016/j.bbamem.2021.183857] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/25/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022]
Abstract
The plasma membrane (PM) is a highly heterogenous structure intertwined with the cortical actin cytoskeleton and extracellular matrix. This complex architecture makes it difficult to study the processes taking place at the PM. Model membrane systems that are simple mimics of the PM overcome this bottleneck and allow us to study the biophysical principles underlying the processes at the PM. Among them, cell-derived giant plasma membrane vesicles (GPMVs) are considered the most physiologically relevant system, retaining the compositional complexity of the PM to a large extent. GPMVs have become a key tool in membrane research in the last few years. In this review, I will provide a brief overview of this system, summarize recent applications and discuss the limitations.
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Affiliation(s)
- Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden.
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42
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Fricke N, Raghunathan K, Tiwari A, Stefanski KM, Balakrishnan M, Waterson AG, Capone R, Huang H, Sanders CR, Bauer JA, Kenworthy AK. High-Content Imaging Platform to Discover Chemical Modulators of Plasma Membrane Rafts. ACS CENTRAL SCIENCE 2022; 8:370-378. [PMID: 35355811 PMCID: PMC8961798 DOI: 10.1021/acscentsci.1c01058] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 05/05/2023]
Abstract
Plasma membrane organization profoundly impacts cellular functionality. A well-known mechanism underlying this organization is through nanoscopic clustering of distinct lipids and proteins in membrane rafts. Despite their physiological importance, rafts remain a difficult-to-study aspect of membrane organization, in part because of the paucity of chemical tools to experimentally modulate their properties. Methods to selectively target rafts for therapeutic purposes are also currently lacking. To tackle these problems, we developed a high-throughput screen and an accompanying image analysis pipeline to identify small molecules that enhance or inhibit raft formation. Cell-derived giant plasma membrane vesicles were used as the experimental platform. A proof-of-principle screen using a bioactive lipid library demonstrates that this method is robust and capable of validating established raft modulators including C6- and C8-ceramide, miltefosine, and epigallocatechin gallate as well as identifying new ones. The platform we describe here represents a powerful tool to discover new chemical approaches to manipulate rafts and their components.
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Affiliation(s)
- Nico Fricke
- Department
of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Krishnan Raghunathan
- Department
of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Ajit Tiwari
- Department
of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Katherine M. Stefanski
- Department
of Biochemistry, Vanderbilt School of Medicine, Nashville, Tennessee 37240, United States
| | - Muthuraj Balakrishnan
- Center
for Membrane and Cell Physiology and Department of Molecular Physiology
and Biological Physics, University of Virginia
School of Medicine, Charlottesville, Virginia 22903, United States
| | - Alex G. Waterson
- Department
of Pharmacology, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Ricardo Capone
- Department
of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt School of Medicine, Nashville, Tennessee 37240, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt School of Medicine, Nashville, Tennessee 37240, United States
| | - Joshua A. Bauer
- Department
of Biochemistry, Vanderbilt School of Medicine, Nashville, Tennessee 37240, United States
- Vanderbilt
Institute of Chemical Biology, High-Throughput Screening Facility, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Anne K. Kenworthy
- Department
of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
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43
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Allender DW, Schick M. A Theoretical Basis for Nanodomains. J Membr Biol 2022; 255:451-460. [PMID: 35084528 DOI: 10.1007/s00232-021-00213-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/22/2021] [Indexed: 01/06/2023]
Abstract
We review the current theories of nanodomain, or "raft," formation. We emphasize that the idea that they are co-exisiting Lo and Ld phases is fraught with difficulties, as is the closely related idea that they are due to critical fluctuations. We then review an alternate theory that the plasma membrane is a two-dimensional microemulsion, and that the mechanism that drives to zero the line tension between Lo and Ld phases is the coupling of height and composition fluctuations. The theory yields rafts of SM and cholesterol in the outer leaf and POPS and POPC in the inner leaf. The "sea" between rafts consists of POPC in the outer leaf and POPE and cholesterol in the inner leaf. The characteristic size of the domain structures is tens of nanometers.
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Affiliation(s)
- D W Allender
- Department of Physics, University of Washington, Seattle, Washington, USA.,Department of Physics, Kent State University, Kent, OH, USA
| | - M Schick
- Department of Physics, University of Washington, Seattle, Washington, USA.
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44
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Truzzolillo D. Mixing-demixing transition and void formation in quasi-2D binary mixtures on a sphere. J Chem Phys 2022; 156:034904. [DOI: 10.1063/5.0080352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. Truzzolillo
- Laboratoire Charles Coulomb (L2C), UMR 5221 CNRS-Universitè de Montpellier, F-34095 Montpellier, France
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45
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Steinkühler J, Fonda P, Bhatia T, Zhao Z, Leomil FSC, Lipowsky R, Dimova R. Superelasticity of Plasma- and Synthetic Membranes Resulting from Coupling of Membrane Asymmetry, Curvature, and Lipid Sorting. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102109. [PMID: 34569194 PMCID: PMC8564416 DOI: 10.1002/advs.202102109] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Biological cells are contained by a fluid lipid bilayer (plasma membrane, PM) that allows for large deformations, often exceeding 50% of the apparent initial PM area. Isolated lipids self-organize into membranes, but are prone to rupture at small (<2-4%) area strains, which limits progress for synthetic reconstitution of cellular features. Here, it is shown that by preserving PM structure and composition during isolation from cells, vesicles with cell-like elasticity can be obtained. It is found that these plasma membrane vesicles store significant area in the form of nanotubes in their lumen. These act as lipid reservoirs and are recruited by mechanical tension applied to the outer vesicle membrane. Both in experiment and theory, it is shown that a "superelastic" response emerges from the interplay of lipid domains and membrane curvature. This finding allows for bottom-up engineering of synthetic biomaterials that appear one magnitude softer and with threefold larger deformability than conventional lipid vesicles. These results open a path toward designing superelastic synthetic cells possessing the inherent mechanics of biological cells.
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Affiliation(s)
- Jan Steinkühler
- Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park GolmPotsdam14424Germany
- Present address:
Department of Biomedical EngineeringNorthwestern UniversityEvanstonIL60657USA
| | - Piermarco Fonda
- Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park GolmPotsdam14424Germany
| | - Tripta Bhatia
- Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park GolmPotsdam14424Germany
- Department of Physical SciencesIndian Institute of Science Education and Research MohaliSector 81, Knowledge City, ManauliSAS NagarPunjab140306India
| | - Ziliang Zhao
- Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park GolmPotsdam14424Germany
- Present address:
Leibniz Institute of Photonic TechnologyJena07745Germany
| | - Fernanda S. C. Leomil
- Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park GolmPotsdam14424Germany
- Departamento de BiofísicaUniversidade Federal de São PauloSão Paulo043039‐032Brazil
| | - Reinhard Lipowsky
- Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park GolmPotsdam14424Germany
| | - Rumiana Dimova
- Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park GolmPotsdam14424Germany
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46
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Surface densities prewet a near-critical membrane. Proc Natl Acad Sci U S A 2021; 118:2103401118. [PMID: 34599097 DOI: 10.1073/pnas.2103401118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 11/18/2022] Open
Abstract
Recent work has highlighted roles for thermodynamic phase behavior in diverse cellular processes. Proteins and nucleic acids can phase separate into three-dimensional liquid droplets in the cytoplasm and nucleus and the plasma membrane of animal cells appears tuned close to a two-dimensional liquid-liquid critical point. In some examples, cytoplasmic proteins aggregate at plasma membrane domains, forming structures such as the postsynaptic density and diverse signaling clusters. Here we examine the physics of these surface densities, employing minimal simulations of polymers prone to phase separation coupled to an Ising membrane surface in conjunction with a complementary Landau theory. We argue that these surface densities are a phase reminiscent of prewetting, in which a molecularly thin three-dimensional liquid forms on a usually solid surface. However, in surface densities the solid surface is replaced by a membrane with an independent propensity to phase separate. We show that proximity to criticality in the membrane dramatically increases the parameter regime in which a prewetting-like transition occurs, leading to a broad region where coexisting surface phases can form even when a bulk phase is unstable. Our simulations naturally exhibit three-surface phase coexistence even though both the membrane and the polymer bulk only display two-phase coexistence on their own. We argue that the physics of these surface densities may be shared with diverse functional structures seen in eukaryotic cells.
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Haack F, Köster T, Uhrmacher AM. Receptor/Raft Ratio Is a Determinant for LRP6 Phosphorylation and WNT/β-Catenin Signaling. Front Cell Dev Biol 2021; 9:706731. [PMID: 34485292 PMCID: PMC8416303 DOI: 10.3389/fcell.2021.706731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
Abstract
Microdomains or lipid rafts greatly affect the distribution of proteins and peptides in the membrane and play a vital role in the formation and activation of receptor/protein complexes. A prominent example for the decisive impact of lipid rafts on signaling is LRP6, whose localization to the same lipid rafts domain as the kinase CK1γ is crucial for its successful phosphorylation and the subsequent activation of the signalosome, hence WNT/β-catenin signaling. However, according to various experimental measurements, approximately 25 to 35 % of the cell plasma membrane is covered by nanoscopic raft domains with diameters ranging between 10 to 200 nm. Extrapolating/Translating these values to the membrane of a “normal sized” cell yields a raft abundance, that, by far, outnumbers the membrane-associated pathway components of most individual signaling pathway, such as receptor and kinases. To analyze whether and how the quantitative ratio between receptor and rafts affects LRP6 phosphorylation and WNT/β-catenin pathway activation, we present a computational modeling study, that for the first time employs realistic raft numbers in a compartment-based pathway model. Our simulation experiments indicate, that for receptor/raft ratios smaller than 1, i.e., when the number of raft compartments clearly exceeds the number of pathway specific membrane proteins, we observe significant decrease in LRP6 phosphorylation and downstream pathway activity. Our results suggest that pathway specific targeting and sorting mechanism are required to significantly narrow down the receptor/raft ratio and to enable the formation of the LRP6 signalosome, hence signaling.
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Affiliation(s)
- Fiete Haack
- Modeling and Simulation Group, Institute for Visual and Analytic Computing, Institute of Electric Engineering and Computer Science, University of Rostock, Rostock, Germany
| | - Till Köster
- Modeling and Simulation Group, Institute for Visual and Analytic Computing, Institute of Electric Engineering and Computer Science, University of Rostock, Rostock, Germany
| | - Adelinde M Uhrmacher
- Modeling and Simulation Group, Institute for Visual and Analytic Computing, Institute of Electric Engineering and Computer Science, University of Rostock, Rostock, Germany
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Thallmair S, Javanainen M, Fábián B, Martinez-Seara H, Marrink SJ. Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations. J Phys Chem B 2021; 125:9537-9546. [PMID: 34398598 PMCID: PMC8404198 DOI: 10.1021/acs.jpcb.1c03665] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
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Molecular dynamics
(MD) simulations have become an indispensable
tool to investigate phase separation in model membrane systems. In
particular, simulations based on coarse-grained (CG) models have found
widespread use due to their increased computational efficiency, allowing
for simulations of multicomponent lipid bilayers undergoing phase
separation into liquid-ordered and liquid-disordered domains. Here,
we show that a significant temperature difference between molecule
types can artificially arise in CG MD membrane simulations with the
standard Martini simulation parameters in GROMACS. In particular,
the linear constraint solver (LINCS) algorithm does not converge with
its default settings, resulting in serious temperature differences
between molecules in a time step-dependent manner. We demonstrate
that the underlying reason for this behavior is the presence of highly
constrained moieties, such as cholesterol. Their presence can critically
impact numerous structural and dynamic membrane properties obtained
from such simulations. Furthermore, any preference of these molecules
toward a certain membrane phase can lead to spatial temperature gradients,
which can amplify the degree of phase separation or even induce it
in compositions that would otherwise mix well. We systematically investigated
the effect of the integration time step and LINCS settings on membrane
properties. Our data show that for cholesterol-containing membranes,
a time step of 20 fs should be combined with at least lincs_iter = 2 and lincs_order = 12, while using a time
step of 30 fs requires at least lincs_iter =
3 and lincs_order = 12 to bring the temperature
differences to a level where they do not perturb central membrane
properties. Moreover, we show that in cases where stricter LINCS settings
are computationally too demanding, coupling the lipids in multiple
groups to the temperature bath offers a practical workaround to the
problem, although the validity of this approach should be further
verified. Finally, we show that similar temperature gradients can
also emerge in atomistic simulations using the CHARMM force field
in combination with settings that allow for a 5 fs integration step.
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Affiliation(s)
- Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.,Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Balázs Fábián
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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49
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Ionic environment, thickness and line tension as determinants of phase separation in whole Purified Myelin Membranes monolayers. Colloids Surf B Biointerfaces 2021; 207:112027. [PMID: 34388613 DOI: 10.1016/j.colsurfb.2021.112027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/14/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
Purified myelin membranes (PMM) were spread as monomolecular films at the air/aqueous solution interface, and visualized by Brewster Angle Microscopy (BAM) at different lateral pressures (π) on three specific aqueous solutions: absence of salts, physiological conditions and presence of calcium. Coexistence of Liquid-Expanded (LE) and Liquid Ordered (LO) phases persisted up to collapse in the presence of salts, whereas monolayers became homogeneous at π ≥ 35-40 mN/m when salts are absent. This PMM phase-mixing behavior in monolayers is similar to the previously reported behavior of PMM multilamellar vesicles. Reflectivities (Rp) of p-polarized light from both phases were assessed throughout the whole π -range, and film thicknesses (t) were calculated from the Rp values and measured film refractive indices (n). The LO phase was found to be more reflective and thicker than the LE phase at π ≤ 15 mN/m, but less reflective and thinner at higher π. We also determined the line tension (λ) of PMM monolayers at the domain boundaries from the rate of domain shape relaxation, which turned out to be of the order of picoNewtons (pN) and decreased as π increased. A correlation between λ and thickness differences (Δt) was found, suggesting that Δt is a molecular determinant for λ in PMM monolayers. Both λ and Δt were found to increase markedly when calcium was present in the subphase. This result corroborates the concept of divalent cations as a stabilizing factor for phase separation, in line with earlier studies on this mixture forming multilamellar membrane arrangements.
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50
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Arumugam S, Schmieder S, Pezeshkian W, Becken U, Wunder C, Chinnapen D, Ipsen JH, Kenworthy AK, Lencer W, Mayor S, Johannes L. Ceramide structure dictates glycosphingolipid nanodomain assembly and function. Nat Commun 2021; 12:3675. [PMID: 34135326 PMCID: PMC8209009 DOI: 10.1038/s41467-021-23961-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 05/28/2021] [Indexed: 02/08/2023] Open
Abstract
Gangliosides in the outer leaflet of the plasma membrane of eukaryotic cells are essential for many cellular functions and pathogenic interactions. How gangliosides are dynamically organized and how they respond to ligand binding is poorly understood. Using fluorescence anisotropy imaging of synthetic, fluorescently labeled GM1 gangliosides incorporated into the plasma membrane of living cells, we found that GM1 with a fully saturated C16:0 acyl chain, but not with unsaturated C16:1 acyl chain, is actively clustered into nanodomains, which depends on membrane cholesterol, phosphatidylserine and actin. The binding of cholera toxin B-subunit (CTxB) leads to enlarged membrane domains for both C16:0 and C16:1, owing to binding of multiple GM1 under a toxin, and clustering of CTxB. The structure of the ceramide acyl chain still affects these domains, as co-clustering with the glycosylphosphatidylinositol (GPI)-anchored protein CD59 occurs only when GM1 contains the fully saturated C16:0 acyl chain, and not C16:1. Thus, different ceramide species of GM1 gangliosides dictate their assembly into nanodomains and affect nanodomain structure and function, which likely underlies many endogenous cellular processes.
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Affiliation(s)
- Senthil Arumugam
- Institut Curie, PSL Research University, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology unit, Paris, Cedex, France
- National Centre for Biological Sciences (NCBS), Bangalore, India
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC, Australia
- European Molecular Biological Laboratory Australia (EMBL Australia), Monash University, Clayton/ Melbourne, VIC, Australia
| | - Stefanie Schmieder
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Ulrike Becken
- Institut Curie, PSL Research University, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology unit, Paris, Cedex, France
| | - Christian Wunder
- Institut Curie, PSL Research University, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology unit, Paris, Cedex, France
| | - Dan Chinnapen
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - John Hjort Ipsen
- MEMPHYS/PhyLife, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Anne K Kenworthy
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, USA
| | - Wayne Lencer
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Harvard Digestive Diseases Center, Boston, MA, USA
| | - Satyajit Mayor
- National Centre for Biological Sciences (NCBS), Bangalore, India.
| | - Ludger Johannes
- Institut Curie, PSL Research University, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology unit, Paris, Cedex, France.
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