1
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Birkenfeld KR, Gandhi TN, Simeral ML, Hafner JH. Cholesterol Conformational Structures in Phospholipid Membranes. J Phys Chem A 2024; 128:8002-8008. [PMID: 39228182 DOI: 10.1021/acs.jpca.4c02860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Cholesterol is a major component of biomembranes that impacts membrane order, permeability, and lateral organization, but the precise molecular mechanisms of cholesterol's actions are still under investigation. Density functional theory (DFT) calculations have opened the fingerprint vibration bands of large molecules to detailed spectral analysis. For cholesterol, Raman spectral interpretation for conformational structure and hydrogen bonding is now possible. Here, DFT calculations of cholesterol conformers identify 10 structure types that also have unique low-frequency Raman spectra. By fitting experimental spectra to these types, the distribution of cholesterol structures present in phospholipid (PL) membrane vesicles was measured. The distributions reveal that the cholesterol iso-octyl chain tends to align with saturated PL chains and shifts to a thermal distribution for unsaturated PL chains. The results agree with the templating effect of cholesterol on PL membranes and show that the top of the iso-octyl chain is rigid like the rings. It is also shown that the inclusion of water molecules hydrogen bonded to the cholesterol hydroxy group in the DFT calculations may improve the spectral fitting for future studies.
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Affiliation(s)
- Kyra R Birkenfeld
- Department of Physics & Astronomy, Rice University, Houston, Texas 77005, United States
| | - Tia N Gandhi
- Department of Physics & Astronomy, Rice University, Houston, Texas 77005, United States
| | - Mathieu L Simeral
- Department of Physics & Astronomy, Rice University, Houston, Texas 77005, United States
| | - Jason H Hafner
- Department of Physics & Astronomy, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
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2
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Lingwood C. Is cholesterol both the lock and key to abnormal transmembrane signals in Autism Spectrum Disorder? Lipids Health Dis 2024; 23:114. [PMID: 38643132 PMCID: PMC11032007 DOI: 10.1186/s12944-024-02075-3] [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] [Received: 12/12/2023] [Accepted: 03/08/2024] [Indexed: 04/22/2024] Open
Abstract
Disturbances in cholesterol homeostasis have been associated with ASD. Lipid rafts are central in many transmembrane signaling pathways (including mTOR) and changes in raft cholesterol content affect their order function. Cholesterol levels are controlled by several mechanisms, including endoplasmic reticulum associated degradation (ERAD) of the rate limiting HMGCoA reductase. A new approach to increase cholesterol via temporary ERAD blockade using a benign bacterial toxin-derived competitor for the ERAD translocon is suggested.A new lock and key model for cholesterol/lipid raft dependent signaling is proposed in which the rafts provide both the afferent and efferent 'tumblers' across the membrane to allow 'lock and key' receptor transmembrane signals.
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Affiliation(s)
- Clifford Lingwood
- Division of Molecular Medicine, Research Institute, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Departments of Biochemistry and Laboratory Medicine & Pathobiology, University of Toronto, Ontario, M5S 1A8, Canada.
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3
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Liu J, Arora N, Zhou Y. RAS GTPases and Interleaflet Coupling in the Plasma Membrane. Cold Spring Harb Perspect Biol 2023; 15:a041414. [PMID: 37463719 PMCID: PMC10513163 DOI: 10.1101/cshperspect.a041414] [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] [Indexed: 07/20/2023]
Abstract
RAS genes are frequently mutated in cancer. The primary signaling compartment of wild-type and constitutively active oncogenic mutant RAS proteins is the inner leaflet of the plasma membrane (PM). Thus, a better understanding of the unique environment of the PM inner leaflet is important to shed further light on RAS function. Over the past few decades, an integrated approach of superresolution imaging, molecular dynamic simulations, and biophysical assays has yielded new insights into the capacity of RAS proteins to sort lipids with specific headgroups and acyl chains, to assemble signaling nanoclusters on the inner PM. RAS proteins also sense and respond to changes in components of the outer PM leaflet, including glycophosphatidylinositol-anchored proteins, sphingophospholipids, glycosphingolipids, and galectins, as well as cholesterol that translocates between the two leaflets. Such communication between the inner and outer leaflets of the PM, called interleaflet coupling, allows RAS to potentially integrate extracellular mechanical and electrostatic information with intracellular biochemical signaling events, and reciprocally allows mutant RAS-transformed tumor cells to modify tumor microenvironments. Here, we review RAS-lipid interactions and speculate on potential mechanisms that allow communication between the opposing leaflets of the PM.
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Affiliation(s)
- Junchen Liu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Neha Arora
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
- Biochemistry and Cell Biology Program, Graduate School of Biomedical Sciences, MD Anderson Cancer Center and University of Texas, Houston, Texas 77030, USA
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4
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Lin X, Lin K, He S, Zhou Y, Li X, Lin X. Membrane Domain Anti-Registration Induces an Intrinsic Transmembrane Potential. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11621-11627. [PMID: 37563986 DOI: 10.1021/acs.langmuir.3c01137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Plasma membrane segregation into various nanoscale membrane domains is driven by distinct interactions between diverse lipids and proteins. Among them, liquid-ordered (Lo) membrane domains are defined as "lipid rafts" and liquid-disordered (Ld) ones as "lipid non-rafts". Using model membrane systems, both intra-leaflet and inter-leaflet dynamics of these membrane domains are widely studied. Nevertheless, the biological impact of the latter, which is accompanied by membrane domain registration/anti-registration, is far from clear. Hence, in this work, we studied the biological relevance of the membrane domain anti-registration using both all-atom molecular dynamics (MD) simulations and confocal fluorescence microscopy. All-atom MD simulations suggested an intrinsic transmembrane potential for the case of the membrane anti-registration (Lo/Ld). Meanwhile, confocal fluorescence microscopy experiments of HeLa and 293T cell lines indicated that membrane cholesterol depletion could significantly alter the transmembrane potential of cells. Considering differences in the cholesterol content between Lo and Ld membrane domains, our confocal fluorescence microscopy experiments are consistent with our all-atom MD simulations. In short, membrane domain anti-registration induces local membrane asymmetry and, thus, an intrinsic transmembrane potential.
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Affiliation(s)
- Xiaoqian Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
- Shen Yuan Honors College, Beihang University, Beijing 100191, China
| | - Kaidong Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Shiqi He
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yue Zhou
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xiu Li
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xubo Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
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5
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Li X, Zhou S, Lin X. Molecular View on the Impact of DHA Molecules on the Physical Properties of a Model Cell Membrane. J Chem Inf Model 2022; 62:2421-2431. [PMID: 35513897 DOI: 10.1021/acs.jcim.2c00074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Docosahexaenoic acid (DHA) is a ω-3 polyunsaturated fatty acid, which can be uptaken by cells and is essential for proper neuronal and retinal function. However, the detailed physical impact of DHA molecules on the plasma membrane is still unclear. Hence, in this work, we carried out μs-scale coarse-grained molecular dynamics (MD) simulations to reveal the interactions between DHA molecules and a model cell membrane. As is known, the cell membrane can segregate into liquid-ordered (Lo) and liquid-disordered (Ld) membrane domains due to the differential interactions between lipids and proteins. In order to capture this feature, we adopted the three-component phase-separated lipid membranes and considered both anionic and neutral DHA molecules in the current work. Our results showed that DHA molecules can spontaneously self-assemble into nanoclusters, fuse with lipid membranes, and localize preferably in Ld membrane domains. During the membrane fusion process, DHA molecules can change the intrinsic transmembrane potential of the lipid membrane, and the effects of anionic DHA molecules are much more significant. Besides, the presence of DHA molecules mainly in the Ld membrane domains could regulate the differences in the lipid chain order, membrane thickness, cholesterol preference, and cholesterol flip-flop basically in a concentration-dependent manner, which further promote the stability of the intraleaflet dynamics and inhibit the interleaflet dynamics (or promote membrane domain registration) of the membrane domains. In short, the impact of DHA molecules on the physical properties of a model cell membrane on the molecular level revealed in our work will provide useful insights for understanding the biological functions of DHA molecules.
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Affiliation(s)
- Xiu Li
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Shiying Zhou
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xubo Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
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6
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Lin X, Lin X. Designing amphiphilic Janus nanoparticles with tunable lipid raft affinity via molecular dynamics simulation. Biomater Sci 2021; 9:8249-8258. [PMID: 34757373 DOI: 10.1039/d1bm01364e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to the differential interactions among lipids and proteins, the plasma membrane can segregate into a series of functional nanoscale membrane domains ("lipid rafts"), which are essential in multiple biological processes such as signaling transduction, protein trafficking and endocytosis. On the other hand, Janus nanoparticles (NPs) have shown great promise in various biomedical applications due to their asymmetric characteristics and can integrate different surface properties and thus synergetic functions. Hence, in this work, we aim to design an amphiphilic Janus NP to target and regulate lipid rafts via tuning its surface ligand amphiphilicity using coarse-grained molecular dynamics (MD) simulations. Our μs-scale free coarse-grained MD simulations as well as umbrella sampling free energy calculations indicated that the hydrophobicity of the hydrophobic surface ligands not only determined the lateral membrane partitioning thermodynamics of Janus NPs in phase-separated lipid membranes, but also the difficulty in their insertion into different membrane domains of the lipid membrane. These two factors jointly regulated the lipid raft affinity of Janus NPs. Meanwhile, the hydrophilicity of the hydrophilic surface ligands could affect the insertion ability of Janus NPs. Besides, the ultra-small size could ensure the membrane-bound behavior of Janus NPs without disrupting the overall structure and phase separation kinetics of the lipid membrane. These results may provide valuable insights into the design of functional NPs targeting and controllably regulating lipid rafts.
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Affiliation(s)
- Xiaoqian Lin
- Institute of Single Cell Engineering, Key Laboratory of Ministry of Education for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China. .,Shen Yuan Honors College, Beihang University, Beijing 100191, China
| | - Xubo Lin
- Institute of Single Cell Engineering, Key Laboratory of Ministry of Education for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.
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7
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Lin X, Lin X. Surface ligand rigidity modulates lipid raft affinity of ultra-small hydrophobic nanoparticles: insights from molecular dynamics simulations. NANOSCALE 2021; 13:9825-9833. [PMID: 34032262 DOI: 10.1039/d1nr01563j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Differential preferences between lipids and proteins drive the formation of dynamical nanoscale membrane domains (lipid rafts), which play key roles in the proper functioning of cells. On the other hand, due to the potent physicochemical properties of nanoparticles (NPs), they have been widely used in drug delivery, bio-imaging and regulating various essential biological processes of the cells. Hence, in this work, we aim to design ultra-small hydrophobic NPs with tunable raft affinity, which is supposed to partition into the hydrophobic region of lipid membranes and be able to regulate the dynamics of the lipid raft domains. A series of μs-scale coarse-grained molecular dynamics simulations and umbrella sampling free energy calculations were performed to investigate the role of surface ligand rigidity of ultra-small hydrophobicNPs in their raft affinity. Our results indicated that the preferred localization of NPs can be tuned by adjusting their surface ligand rigidity. Generally, rigid NPs tended to target the raft domain, while soft NPs preferred the interface of the raft and non-raft domains. The free energy analysis further indicated that the surface ligand rigidity of NPs can enhance their targeting to lipid raft domains. Besides, we found that these ultra-small NPs had no significant effects on the phase separation of the lipid membrane although they might cause some local interference to surrounding lipids. These results indicate that the targeting to the lipid raft domain can be achieved by the surface ligand rigidity of NPs, which provides helpful insights for further regulations of lipid raft-mediated biological processes.
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Affiliation(s)
- Xiaoqian Lin
- Institute of Single Cell Engineering, Key Laboratory of Ministry of Education for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.
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8
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Dingjan T, Futerman AH. The fine-tuning of cell membrane lipid bilayers accentuates their compositional complexity. Bioessays 2021; 43:e2100021. [PMID: 33656770 DOI: 10.1002/bies.202100021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 01/17/2023]
Abstract
Cell membranes are now emerging as finely tuned molecular systems, signifying that re-evaluation of our understanding of their structure is essential. Although the idea that cell membrane lipid bilayers do little more than give shape and form to cells and limit diffusion between cells and their environment is totally passé, the structural, compositional, and functional complexity of lipid bilayers often catches cell and molecular biologists by surprise. Models of lipid bilayer structure have developed considerably since the heyday of the fluid mosaic model, principally by the discovery of the restricted diffusion of membrane proteins and lipids within the plane of the bilayer. In reviewing this field, we now suggest that further refinement of current models is necessary and propose that describing lipid bilayers as "finely-tuned molecular assemblies" best portrays their complexity and function. Also see the video abstract here: https://www.youtube.com/watch?v=ddkP-QRZTl8.
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Affiliation(s)
- Tamir Dingjan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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9
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Lorent JH, Levental KR, Ganesan L, Rivera-Longsworth G, Sezgin E, Doktorova M, Lyman E, Levental I. Plasma membranes are asymmetric in lipid unsaturation, packing and protein shape. Nat Chem Biol 2020; 16:644-652. [PMID: 32367017 DOI: 10.1101/698837] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 03/27/2020] [Indexed: 05/26/2023]
Abstract
A fundamental feature of cellular plasma membranes (PMs) is an asymmetric lipid distribution between the bilayer leaflets. However, neither the detailed, comprehensive compositions of individual PM leaflets nor how these contribute to structural membrane asymmetries have been defined. We report the distinct lipidomes and biophysical properties of both monolayers in living mammalian PMs. Phospholipid unsaturation is dramatically asymmetric, with the cytoplasmic leaflet being approximately twofold more unsaturated than the exoplasmic leaflet. Atomistic simulations and spectroscopy of leaflet-selective fluorescent probes reveal that the outer PM leaflet is more packed and less diffusive than the inner leaflet, with this biophysical asymmetry maintained in the endocytic system. The structural asymmetry of the PM is reflected in the asymmetric structures of protein transmembrane domains. These structural asymmetries are conserved throughout Eukaryota, suggesting fundamental cellular design principles.
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Affiliation(s)
- J H Lorent
- McGovern Medical School, Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - K R Levental
- McGovern Medical School, Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - L Ganesan
- McGovern Medical School, Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - E Sezgin
- John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- SciLifeLab, Karolinska Institute, Stockholm, Sweden
| | - M Doktorova
- McGovern Medical School, Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - E Lyman
- Department of Physics and Astronomy and Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - I Levental
- McGovern Medical School, Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA.
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10
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Lin X, Lin X, Gu N. Optimization of hydrophobic nanoparticles to better target lipid rafts with molecular dynamics simulations. NANOSCALE 2020; 12:4101-4109. [PMID: 32022059 DOI: 10.1039/c9nr09226a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Due to different interactions between lipids and proteins, a plasma membrane can segregate into different membrane domains. Among them, ordered functional membrane domains are defined as "lipid rafts", which play key roles in many biological processes (e.g., signal transduction, endocytosis, etc.) in the cell. Hence, it will be of much biological significance to monitor and even regulate the dynamics of lipid rafts. In this work, we designed a ligand-modified spherical nanoparticle with coarse-grained molecular dynamics simulations, which can be encapsulated into the hydrophobic region of the lipid membrane and specifically target either raft or non-raft membrane domains. The preferred localization of the nanoparticle can be tuned by adjusting ligand hydrophobicity, length and density. Generally, more hydrophobic nanoparticles tend to target the raft domain, while less hydrophobic nanoparticles prefer the non-raft domain. Besides, ligand length and density jointly determine the exposure of nanoparticle cores and thus affect the roles of ligands in nanoparticles' final localization. Our results may provide insights into the experimental design of functional nanoparticles, targeting the lipid raft and regulating its dynamics.
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Affiliation(s)
- Xiaoqian Lin
- Institute of Nanotechnology for Single Cell Analysis (INSCA), Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China. and School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xubo Lin
- Institute of Nanotechnology for Single Cell Analysis (INSCA), Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China. and School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Ning Gu
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Sciences & Medical Engineering, Southeast University, Nanjing 210096, China.
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11
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Zhang S, Lin X. Lipid Acyl Chain cis Double Bond Position Modulates Membrane Domain Registration/Anti-Registration. J Am Chem Soc 2019; 141:15884-15890. [DOI: 10.1021/jacs.9b06977] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Siya Zhang
- Institute of Nanotechnology for Single Cell Analysis (INSCA), Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China
- State Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Peking Union Medical College and Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Xubo Lin
- Institute of Nanotechnology for Single Cell Analysis (INSCA), Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
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12
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Guo J, Ho JCS, Chin H, Mark AE, Zhou C, Kjelleberg S, Liedberg B, Parikh AN, Cho NJ, Hinks J, Mu Y, Seviour T. Response of microbial membranes to butanol: interdigitation vs. disorder. Phys Chem Chem Phys 2019; 21:11903-11915. [PMID: 31125035 DOI: 10.1039/c9cp01469a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biobutanol production by fermentation is potentially a sustainable alternative to butanol production from fossil fuels. However, the toxicity of butanol to fermentative bacteria, resulting largely from cell membrane fluidization, limits production titers and is a major factor limiting the uptake of the technology. Here, studies were undertaken, in vitro and in silico, on the butanol effects on a representative bacterial (i.e. Escherichia coli) inner cell membrane. A critical butanol : lipid ratio for stability of 2 : 1 was observed, computationally, consistent with complete interdigitation. However, at this ratio the bilayer was ∼20% thicker than for full interdigitation. Furthermore, butanol intercalation induced acyl chain bending and increased disorder, measured as a 27% lateral diffusivity increase experimentally in a supported lipid bilayer. There was also a monophasic Tm reduction in butanol-treated large unilamellar vesicles. Both behaviours are inconsistent with an interdigitated gel. Butanol thus causes only partial interdigitation at physiological temperatures, due to butanol accumulating at the phospholipid headgroups. Acyl tail disordering (i.e. splaying and bending) fills the subsequent voids. Finally, butanol short-circuits the bilayer and creates a coupled system where interdigitated and splayed phospholipids coexist. These findings will inform the design of strategies targeting bilayer stability for increasing biobutanol production titers.
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Affiliation(s)
- Jingjing Guo
- Singapore Centre for Environmental Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
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13
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Lin X, Gorfe AA, Levental I. Protein Partitioning into Ordered Membrane Domains: Insights from Simulations. Biophys J 2019; 114:1936-1944. [PMID: 29694870 DOI: 10.1016/j.bpj.2018.03.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/09/2018] [Accepted: 03/22/2018] [Indexed: 11/24/2022] Open
Abstract
Cellular membranes are laterally organized into domains of distinct structures and compositions by the differential interaction affinities between various membrane lipids and proteins. A prominent example of such structures are lipid rafts, which are ordered, tightly packed domains that have been widely implicated in cellular processes. The functionality of raft domains is driven by their selective recruitment of specific membrane proteins to regulate their interactions and functions; however, there have been few general insights into the factors that determine the partitioning of membrane proteins between coexisting liquid domains. In this work, we used extensive coarse-grained and atomistic molecular dynamics simulations, potential of mean force calculations, and conceptual models to describe the partitioning dynamics and energetics of a model transmembrane domain from the linker of activation of T cells. We find that partitioning between domains is determined by an interplay between protein-lipid interactions and differential lipid packing between raft and nonraft domains. Specifically, we show that partitioning into ordered domains is promoted by preferential interactions between peptides and ordered lipids, mediated in large part by modification of the peptides by saturated fatty acids (i.e., palmitoylation). Ordered phase affinity is also promoted by elastic effects, specifically hydrophobic matching between the membrane and the peptide. Conversely, ordered domain partitioning is disfavored by the tight molecular packing of the lipids therein. The balance of these dominant drivers determines partitioning. In the case of the wild-type linker of activation of T cells transmembrane domain, these factors combine to yield enrichment of the peptide at Lo/Ld interfaces. These results define some of the general principles governing protein partitioning between coexisting membrane domains and potentially explain previous disparities among experiments and simulations across model systems.
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Affiliation(s)
- Xubo Lin
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas; School of Biological Science and Medical Engineering, Beihang University, Beijing, China; Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.
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14
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 432] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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15
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Lin X, Gorfe AA. Understanding Membrane Domain-Partitioning Thermodynamics of Transmembrane Domains with Potential of Mean Force Calculations. J Phys Chem B 2019; 123:1009-1016. [PMID: 30638009 DOI: 10.1021/acs.jpcb.8b10148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The transmembrane domain (TMD) of membrane proteins plays an essential role in their dynamics and functions. Certain properties of TMDs, such as raft affinity and orientation, have been studied extensively both experimentally and computationally. However, the extent to which specific physicochemical properties of TMDs determine their membrane domain-partitioning thermodynamics is still far from clear. In this work, we propose an approach based on umbrella sampling molecular dynamics simulations of model membranes and idealized TMDs to quantify the effect of TMD physicochemical properties, namely, length, degree of hydrophobicity, and size of TMDs, on their membrane domain-partitioning thermodynamics. The results, which are fully consistent with previous experimental and simulation data, indicate that the concept of "hydrophobic mismatch" should go beyond differences in hydrophobic thickness to include mismatch in the degree of hydrophobicity between the TMD and the surrounding hydrocarbon lipid chains. Our method provides quantitative insights into the role of specific physicochemical features of TMDs in membrane localization and orientation, which will be broadly useful for predicting the raft affinity and membrane partitioning of any transmembrane protein.
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Affiliation(s)
- Xubo Lin
- Beijing Advanced Innovation Center for Biomedical Engineering , Beihang University , Beijing 100083 , China.,Key Laboratory of Ministry of Education for Biomechanics and Mechanobiology, School of Biological Science and Medical Engineering , Beihang University , Beijing 100083 , China.,Department of Integrative Biology and Pharmacology, McGovern Medical School , The University of Texas Health Science Center at Houston , Houston , Texas 77030 , United States
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School , The University of Texas Health Science Center at Houston , Houston , Texas 77030 , United States
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16
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Thallmair S, Ingólfsson HI, Marrink SJ. Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models. J Phys Chem Lett 2018; 9:5527-5533. [PMID: 30192549 PMCID: PMC6151656 DOI: 10.1021/acs.jpclett.8b01877] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/07/2018] [Indexed: 05/25/2023]
Abstract
The plasma membrane is a highly complex multicomponent system that is central to the functioning of cells. Cholesterol, a key lipid component of the plasma membrane, promotes the formation of nanodomains. These nanodomains are often correlated across the two membrane leaflets, but the underlying physical mechanism remains unclear. Using coarse-grained molecular dynamics simulations, we investigate the influence of cholesterol flip-flop on membrane properties, in particular, the interleaflet coupling of cholesterol-enriched domains. We show that the cholesterol density correlation between the leaflets of an average mammalian plasma membrane is significantly reduced by suppressing interleaflet cholesterol population. Our results suggest an amplifying role of cholesterol in signal transduction across the leaflets.
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Affiliation(s)
- Sebastian Thallmair
- Groningen
Biomolecular Sciences and Biotechnology Institute and The Zernike
Institute for Advanced Material, University
of Groningen, Nijenborgh
7, 9747 AG Groningen, Netherlands
| | - Helgi I. Ingólfsson
- Groningen
Biomolecular Sciences and Biotechnology Institute and The Zernike
Institute for Advanced Material, University
of Groningen, Nijenborgh
7, 9747 AG Groningen, Netherlands
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, 94550 California, United States
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and The Zernike
Institute for Advanced Material, University
of Groningen, Nijenborgh
7, 9747 AG Groningen, Netherlands
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17
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Lin X, Wang H, Lou Z, Cao M, Zhang Z, Gu N. Roles of
PIP
2 in the membrane binding of
MIM
I‐
BAR
: insights from molecular dynamics simulations. FEBS Lett 2018; 592:2533-2542. [DOI: 10.1002/1873-3468.13186] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/01/2018] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Xubo Lin
- Beijing Advanced Innovation Center for Biomedical Engineering School of Biological Science and Medical Engineering Beihang University China
- State Key Laboratory of Bioelectronics Jiangsu Key Laboratory for Biomaterials and Devices School of Biological Sciences & Medical Engineering, Southeast University Nanjing China
| | - Hongyin Wang
- Department of Integrative Biology and Pharmacology McGovern Medical School The University of Texas Health Science Center at Houston TX USA
| | - Zhichao Lou
- State Key Laboratory of Bioelectronics Jiangsu Key Laboratory for Biomaterials and Devices School of Biological Sciences & Medical Engineering, Southeast University Nanjing China
- College of Materials Science and Engineering Nanjing Forestry University China
| | - Meng Cao
- State Key Laboratory of Bioelectronics Jiangsu Key Laboratory for Biomaterials and Devices School of Biological Sciences & Medical Engineering, Southeast University Nanjing China
- Collaborative Innovation Center of Suzhou Nano‐Science and Technology Suzhou Key Laboratory of Biomaterials and Technologies China
| | - Zuoheng Zhang
- State Key Laboratory of Bioelectronics Jiangsu Key Laboratory for Biomaterials and Devices School of Biological Sciences & Medical Engineering, Southeast University Nanjing China
- Collaborative Innovation Center of Suzhou Nano‐Science and Technology Suzhou Key Laboratory of Biomaterials and Technologies China
| | - Ning Gu
- State Key Laboratory of Bioelectronics Jiangsu Key Laboratory for Biomaterials and Devices School of Biological Sciences & Medical Engineering, Southeast University Nanjing China
- Collaborative Innovation Center of Suzhou Nano‐Science and Technology Suzhou Key Laboratory of Biomaterials and Technologies China
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18
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Wen PC, Mahinthichaichan P, Trebesch N, Jiang T, Zhao Z, Shinn E, Wang Y, Shekhar M, Kapoor K, Chan CK, Tajkhorshid E. Microscopic view of lipids and their diverse biological functions. Curr Opin Struct Biol 2018; 51:177-186. [PMID: 30048836 DOI: 10.1016/j.sbi.2018.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/27/2018] [Accepted: 07/05/2018] [Indexed: 12/21/2022]
Abstract
Biological membranes and their diverse lipid constituents play key roles in a broad spectrum of cellular and physiological processes. Characterization of membrane-associated phenomena at a microscopic level is therefore essential to our fundamental understanding of such processes. Due to the semi-fluid and dynamic nature of lipid bilayers, and their complex compositions, detailed characterization of biological membranes at an atomic scale has been refractory to experimental approaches. Computational modeling and simulation offer a highly complementary toolset with sufficient spatial and temporal resolutions to fill this gap. Here, we review recent molecular dynamics studies focusing on the diversity of lipid composition of biological membranes, or aiming at the characterization of lipid-protein interaction, with the overall goal of dissecting how lipids impact biological roles of the cellular membranes.
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Affiliation(s)
- Po-Chao Wen
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Noah Trebesch
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhiyu Zhao
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Eric Shinn
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuhang Wang
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mrinal Shekhar
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Karan Kapoor
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chun Kit Chan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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19
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Lorent JH, Diaz-Rohrer B, Lin X, Spring K, Gorfe AA, Levental KR, Levental I. Structural determinants and functional consequences of protein affinity for membrane rafts. Nat Commun 2017; 8:1219. [PMID: 29089556 PMCID: PMC5663905 DOI: 10.1038/s41467-017-01328-3] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 09/09/2017] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic plasma membranes are compartmentalized into functional lateral domains, including lipid-driven membrane rafts. Rafts are involved in most plasma membrane functions by selective recruitment and retention of specific proteins. However, the structural determinants of transmembrane protein partitioning to raft domains are not fully understood. Hypothesizing that protein transmembrane domains (TMDs) determine raft association, here we directly quantify raft affinity for dozens of TMDs. We identify three physical features that independently affect raft partitioning, namely TMD surface area, length, and palmitoylation. We rationalize these findings into a mechanistic, physical model that predicts raft affinity from the protein sequence. Application of these concepts to the human proteome reveals that plasma membrane proteins have higher raft affinity than those of intracellular membranes, consistent with raft-mediated plasma membrane sorting. Overall, our experimental observations and physical model establish general rules for raft partitioning of TMDs and support the central role of rafts in membrane traffic.
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Affiliation(s)
- Joseph H Lorent
- McGovern Medical School, University of Texas Health Science Center, Houston MSB 4.202A, 6431 Fannin St, Houston, TX, 77096, USA
| | - Blanca Diaz-Rohrer
- McGovern Medical School, University of Texas Health Science Center, Houston MSB 4.202A, 6431 Fannin St, Houston, TX, 77096, USA
| | - Xubo Lin
- McGovern Medical School, University of Texas Health Science Center, Houston MSB 4.202A, 6431 Fannin St, Houston, TX, 77096, USA
| | - Kevin Spring
- McGovern Medical School, University of Texas Health Science Center, Houston MSB 4.202A, 6431 Fannin St, Houston, TX, 77096, USA
| | - Alemayehu A Gorfe
- McGovern Medical School, University of Texas Health Science Center, Houston MSB 4.202A, 6431 Fannin St, Houston, TX, 77096, USA
| | - Kandice R Levental
- McGovern Medical School, University of Texas Health Science Center, Houston MSB 4.202A, 6431 Fannin St, Houston, TX, 77096, USA
| | - Ilya Levental
- McGovern Medical School, University of Texas Health Science Center, Houston MSB 4.202A, 6431 Fannin St, Houston, TX, 77096, USA.
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20
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Lin X, Lorent JH, Skinkle AD, Levental KR, Waxham MN, Gorfe AA, Levental I. Domain Stability in Biomimetic Membranes Driven by Lipid Polyunsaturation. J Phys Chem B 2016; 120:11930-11941. [PMID: 27797198 DOI: 10.1021/acs.jpcb.6b06815] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Biological membranes contain a broad variety of lipid species whose individual physicochemical properties and collective interactions ultimately determine membrane organization. A key aspect of the organization of cellular membranes is their lateral subdivision into domains of distinct structure and composition. The most widely studied membrane domains are lipid rafts, which are the biological manifestations of liquid-ordered phases that form in sterol-containing membranes. Detailed studies of biomimetic membrane mixtures have yielded wide-ranging insights into the physical principles behind lipid rafts; however, these simplified models do not fully capture the diversity and complexity of the mammalian lipidome, most notably in their exclusion of polyunsaturated lipids. Here, we assess the role of lipid acyl chain unsaturation as a driving force for phase separation using coarse-grained molecular dynamics (CGMD) simulations validated by model membrane experiments. The clear trends in our observations and good qualitative agreements between simulations and experiments support the conclusions that highly unsaturated lipids promote liquid-liquid domain stability by enhancing the differences in cholesterol content and lipid chain order between the coexisting domains. These observations reveal the important role of noncanonical biological lipids in the physical properties of membranes, showing that lipid polyunsaturation is a driving force for liquid-liquid phase separation.
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Affiliation(s)
- Xubo Lin
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - Joseph H Lorent
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - Allison D Skinkle
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - Kandice R Levental
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston , Houston, Texas 77030, United States
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