1
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Kumar J, Chng CP, Huang C. Hydrophobic Matching Dictates over the Linear Rule of Mixtures in Binary Lipid Membranes. J Phys Chem B 2023; 127:7946-7954. [PMID: 37674349 DOI: 10.1021/acs.jpcb.3c04502] [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: 09/08/2023]
Abstract
Biological membranes feature heterogeneous mixtures of lipids with different head and tail characteristics. Their biophysical properties are dictated by the intimate interaction among different constituent lipids. Previous studies suggest that the membrane area-per-lipid (APL) deviates from the linear rule of mixtures (LRM) for binary lipid membranes, but the underlying mechanism remains elusive. Our molecular dynamics (MD) simulations of binary lipid membranes consisting of lipids with different tail characteristics reveal a competitive mechanism whereby lipids tend to deform each other to minimize the hydrophobic mismatch between their tails. Depending on the relative tail lengths and saturation levels, this may result in an either positive or negative deviation of APL from the LRM. As lipid packing plays an essential role in membrane fusion and peptide-membrane binding, our findings may help guide the selection of lipids for the effective rational design of nanoliposomes and membrane-targeting peptides.
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Affiliation(s)
- Jatin Kumar
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| | - Choon-Peng Chng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| | - Changjin Huang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
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2
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Santos G, Díaz M. Dimensional Changes in Lipid Rafts from Human Brain Cortex Associated to Development of Alzheimer's Disease. Predictions from an Agent-Based Mathematical Model. Int J Mol Sci 2021; 22:ijms222212181. [PMID: 34830060 PMCID: PMC8620379 DOI: 10.3390/ijms222212181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/02/2021] [Accepted: 11/07/2021] [Indexed: 11/30/2022] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease caused by abnormal functioning of critical physiological processes in nerve cells and aberrant accumulation of protein aggregates in the brain. The initial cause remains elusive—the only unquestionable risk factor for the most frequent variant of the disease is age. Lipid rafts are microdomains present in nerve cell membranes and they are known to play a significant role in the generation of hallmark proteinopathies associated to AD, namely senile plaques, formed by aggregates of amyloid β peptides. Recent studies have demonstrated that human brain cortex lipid rafts are altered during early neuropathological phases of AD as defined by Braak and Braak staging. The lipid composition and physical properties of these domains appear altered even before clinical symptoms are detected. Here, we use a coarse grain molecular dynamics mathematical model to predict the dimensional evolution of these domains using the experimental data reported by our group in human frontal cortex. The model predicts significant size and frequency changes which are detectable at the earliest neuropathological stage (ADI/II) of Alzheimer’s disease. Simulations reveal a lower number and a larger size in lipid rafts from ADV/VI, the most advanced stage of AD. Paralleling these changes, the predictions also indicate that non-rafts domains undergo simultaneous alterations in membrane peroxidability, which support a link between oxidative stress and AD progression. These synergistic changes in lipid rafts dimensions and non-rafts peroxidability are likely to become part of a positive feedback loop linked to an irreversible amyloid burden and neuronal death during the evolution of AD neuropathology.
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Affiliation(s)
- Guido Santos
- Systems Biology and Mathematical Modelling Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Biology Section, Science School, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain
- Correspondence:
| | - Mario Díaz
- Laboratory of Membrane Physiology and Biophysics, Department of Animal Biology, Edaphology and Geology, Biology Section, Science School, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain;
- IUETSP (Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias), Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain
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3
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Carmona-Salazar L, Cahoon RE, Gasca-Pineda J, González-Solís A, Vera-Estrella R, Treviño V, Cahoon EB, Gavilanes-Ruiz M. Plasma and vacuolar membrane sphingolipidomes: composition and insights on the role of main molecular species. PLANT PHYSIOLOGY 2021; 186:624-639. [PMID: 33570616 PMCID: PMC8154057 DOI: 10.1093/plphys/kiab064] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/24/2021] [Indexed: 05/04/2023]
Abstract
Lipid structures affect membrane biophysical properties such as thickness, stability, permeability, curvature, fluidity, asymmetry, and interdigitation, contributing to membrane function. Sphingolipids are abundant in plant endomembranes and plasma membranes (PMs) and comprise four classes: ceramides, hydroxyceramides, glucosylceramides, and glycosylinositolphosphoceramides (GIPCs). They constitute an array of chemical structures whose distribution in plant membranes is unknown. With the aim of describing the hydrophobic portion of sphingolipids, 18 preparations from microsomal (MIC), vacuolar (VM), PM, and detergent-resistant membranes (DRM) were isolated from Arabidopsis (Arabidopsis thaliana) leaves. Sphingolipid species, encompassing pairing of long-chain bases and fatty acids, were identified and quantified in these membranes. Sphingolipid concentrations were compared using univariate and multivariate analysis to assess sphingolipid diversity, abundance, and predominance across membranes. The four sphingolipid classes were present at different levels in each membrane: VM was enriched in glucosylceramides, hydroxyceramides, and GIPCs; PM in GIPCs, in agreement with their key role in signal recognition and sensing; and DRM in GIPCs, as reported by their function in nanodomain formation. While a total of 84 sphingolipid species was identified in MIC, VM, PM, and DRM, only 34 were selectively distributed in the four membrane types. Conversely, every membrane contained a different number of predominant species (11 in VM, 6 in PM, and 17 in DRM). This study reveals that MIC, VM, PM, and DRM contain the same set of sphingolipid species but every membrane source contains its own specific assortment based on the proportion of sphingolipid classes and on the predominance of individual species.
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Affiliation(s)
- Laura Carmona-Salazar
- Dpto. de Bioquímica, Facultad de Química, Conj. E. Universidad Nacional Autónoma de México, UNAM. Cd. Universitaria, Coyoacán. 04510, Cd. de México, México
| | - Rebecca E Cahoon
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, NE 68588–0665, USA
| | - Jaime Gasca-Pineda
- UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, UNAM, 54090, Estado de México, México
| | - Ariadna González-Solís
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, NE 68588–0665, USA
| | - Rosario Vera-Estrella
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM. Cuernavaca, Morelos, México
| | - Victor Treviño
- Tecnológico de Monterrey, Escuela de Medicina, 64710 Monterrey, Nuevo León, México
| | - Edgar B Cahoon
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, NE 68588–0665, USA
| | - Marina Gavilanes-Ruiz
- Dpto. de Bioquímica, Facultad de Química, Conj. E. Universidad Nacional Autónoma de México, UNAM. Cd. Universitaria, Coyoacán. 04510, Cd. de México, México
- Author for communication:
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4
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Lipid interactions of an actinoporin pore-forming oligomer. Biophys J 2021; 120:1357-1366. [PMID: 33617834 DOI: 10.1016/j.bpj.2021.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/16/2021] [Accepted: 02/11/2021] [Indexed: 12/16/2022] Open
Abstract
The actinoporins are cytolytic toxins produced by sea anemones. Upon encountering a membrane, preferably containing sphingomyelin, they oligomerize and insert their N-terminal helix into the membrane, forming a pore. Whether sphingomyelin is specifically recognized by the protein or simply induces phase coexistence in the membrane has been debated. Here, we perform multi-microsecond molecular dynamics simulations of an octamer of fragaceatoxin C, a member of the actinoporin family, in lipid bilayers containing either pure 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) or a 1:1 mixture of DOPC and palmitoyl sphingomyelin (PSM). The complex is highly stable in both environments, with only slight fraying of the inserted helices near their N-termini. Analyzing the structural parameters of the mixed membrane in the course of the simulation, we see signs of a phase transition for PSM in the inner leaflet of the bilayer. In both leaflets, cross-interactions between lipids of different type decrease over time. Surprisingly, the aromatic loop thought to be responsible for sphingomyelin recognition interacts more with DOPC than PSM by the end of the simulation. These results support the notion that the key membrane property that actinoporins recognize is lipid phase coexistence.
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5
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Wang R, Zhu W, Peng J, Li K, Li C. Lipid rafts as potential mechanistic targets underlying the pleiotropic actions of polyphenols. Crit Rev Food Sci Nutr 2020; 62:311-324. [PMID: 32951435 DOI: 10.1080/10408398.2020.1815171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Polyphenols have attracted a lot of global attention due to their diverse biological actions against cancer, obesity, and cardiovascular diseases. Although extensive research has been carried out to elucidate the mechanisms of pleiotropic actions of polyphenols, this remains unclear. Lipid rafts are distinct nanodomains enriched in cholesterol and sphingolipids, present in the inner and outer leaflets of cell membranes, forming functional platforms for the regulation of cellular processes and diseases. Recent studies focusing on the interaction between polyphenols and cellular lipid rafts shed new light on the pleiotropic actions of polyphenols. Polyphenols are postulated to interact with lipid rafts in two ways: first, they interfere with the structural integrity of lipid rafts, by disrupting their structure and clustering of the ordered domains; second, they modulate the downstream signaling pathways mediated by lipid rafts, by binding to receptor proteins associated with lipid rafts, such as the 67 kDa laminin receptor (67LR), epidermal growth factor receptor (EGFR), and others. This study aims to elaborate the mechanism of interaction between polyphenols and lipid rafts, and describe pleiotropic preventive effects of polyphenols.
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Affiliation(s)
- Ruifeng Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wei Zhu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinming Peng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kaikai Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chunmei Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Environment Correlative Food Science, Huazhong Agricultural University, Ministry of Education, Wuhan, China
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6
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Zapata-Morin PA, Sierra-Valdez FJ, Ruiz-Suárez JC. The cut-off effect of n-alcohols in lipid rafts: A lipid-dependent phenomenon ☆. J Mol Graph Model 2020; 101:107732. [PMID: 32920240 DOI: 10.1016/j.jmgm.2020.107732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
n-Aliphatic alcohols act as anesthetics only up to a certain chain length, beyond which its biological activity disappears. This is known as the 'cut-off' phenomenon. Although the most accepted explanation is based on action sites in membrane proteins, it is not well understood why alcohols alter their functions. The structural dependence of these protein receptors to lipid domains known as 'lipid rafts', suggests a new approach to tackle the puzzling phenomenon. In this work, by performing molecular dynamic simulations (MDS) to explore the lipid role, we provide relevant molecular details about the membrane-alcohol interaction at the cut-off point regime. Since the high variability of the cut-off points found on protein receptors in neurons may be a consequence of differences in the lipid composition surrounding such proteins, our results could have a clear-cut importance.
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Affiliation(s)
- Patricio A Zapata-Morin
- Facultad de Ciencias Biológicas, Laboratorio de Micología y Fitopatología, Universidad Autónoma de Nuevo León, San Nicolás de Los Garza, Nuevo León, 66455, Mexico
| | - F J Sierra-Valdez
- Centro de Investigación Biomédica, Hospital Zambrano Hellion, TecSalud, Ave. Batallón de San Patricio 112, San Pedro Garza García, 66278, Nuevo León, Mexico; Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo León, 64849, Mexico
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7
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Satish S, Perlin DS. Echinocandin Resistance in Aspergillus fumigatus Has Broad Implications for Membrane Lipid Perturbations That Influence Drug-Target Interactions. Microbiol Insights 2019; 12:1178636119897034. [PMID: 35185336 PMCID: PMC8855445 DOI: 10.1177/1178636119897034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/13/2019] [Indexed: 01/13/2023] Open
Abstract
Echinocandin drugs target the fungal enzyme β-(1,3)-glucan synthase (GS), which is required for the synthesis of cell wall component β-(1,3)-d-glucan. They are first-line therapy for Candida infections but are increasingly used as second-line therapy for Aspergillus infections. Resistance to echinocandins has been mainly studied in Candida and occurs due to mutations in FKS genes encoding GS. In our recent report, we identified a novel mechanism of echinocandin resistance in Aspergillus fumigatus. We showed that caspofungin exposure modifies GS, rendering it insensitive to echinocandins. This mechanism of resistance involved alteration of the GS lipid microenvironment and was mediated via an off-target effect on mitochondria leading to increased reactive oxygen species (ROS). We hypothesized that caspofungin-induced ROS alters the lipid composition around GS, changing its conformation and making it insensitive to echinocandins. In this commentary, we review both fks1-dependent and fks1-independent mechanisms of echinocandin resistance in A fumigatus. We believe this new resistance mechanism is also conserved among Candida spp. with implications for drug tolerance and/or resistance. Furthermore, we propose that ROS acts as a signaling molecule regulating lipid biogenesis, which impacts the structure-function of membrane proteins with implications for other types of drug-target interactions.
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Affiliation(s)
- Shruthi Satish
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
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8
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Meinhardt S, Schmid F. Structure of lateral heterogeneities in a coarse-grained model for multicomponent membranes. SOFT MATTER 2019; 15:1942-1952. [PMID: 30662989 DOI: 10.1039/c8sm02261e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We study the lateral domain structure in a coarse-grained molecular model for multicomponent lipid bilayers by semi-grandcanonical Monte Carlo simulations. The membranes are filled with liquid ordered (lo) domains surrounded by a liquid disordered (ld) matrix. Depending on the membrane composition and temperature, we identify different morphological regimes: one regime (I) where the lo domains are small and relatively compact, and two regimes (II, II') where they are larger and often interconnected. In the latter two regimes, the ld matrix forms a network of disordered trenches separating the lo domains, with a relatively high content of interdigitated line defects. Since such defects are also a structural element of the modulated ripple phase in one component membranes, we argue that the regimes II, II' may be amorphous equivalents of the ripple phase in multicomponent membranes. We also analyze the local structure and provide evidence that the domains in regime I are stabilized by a monolayer curvature mechanism postulated in earlier work [S. Meinhardt et al., PNAS, 2013, 110, 4476].
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Affiliation(s)
- Sebastian Meinhardt
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, USA
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9
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Kristanc L, Božič B, Jokhadar ŠZ, Dolenc MS, Gomišček G. The pore-forming action of polyenes: From model membranes to living organisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:418-430. [DOI: 10.1016/j.bbamem.2018.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/04/2018] [Accepted: 11/14/2018] [Indexed: 01/05/2023]
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10
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Vázquez RF, Daza Millone MA, Pavinatto FJ, Fanani ML, Oliveira ON, Vela ME, Maté SM. Impact of sphingomyelin acyl chain (16:0 vs 24:1) on the interfacial properties of Langmuir monolayers: A PM-IRRAS study. Colloids Surf B Biointerfaces 2019; 173:549-556. [DOI: 10.1016/j.colsurfb.2018.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 09/28/2018] [Accepted: 10/09/2018] [Indexed: 11/17/2022]
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11
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Bera I, Klauda JB. Molecular Simulations of Mixed Lipid Bilayers with Sphingomyelin, Glycerophospholipids, and Cholesterol. J Phys Chem B 2017; 121:5197-5208. [DOI: 10.1021/acs.jpcb.7b00359] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Indrani Bera
- Department
of Chemical and Biomolecular Engineering and ‡Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery B. Klauda
- Department
of Chemical and Biomolecular Engineering and ‡Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
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12
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Kurniawan J, Ventrici J, Kittleson G, Kuhl TL. Interaction Forces between Lipid Rafts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:382-387. [PMID: 28001077 DOI: 10.1021/acs.langmuir.6b03717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cellular membranes containing sphingolipids and cholesterol have been shown to self-organize into lipid rafts-specialized domains that host integral membrane proteins and modulate the bioactivity of cells. In this work, force-distance profiles between raft membranes in the liquid-ordered phase consisting of singly unsaturated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a complex mixture of brain sphingomyelin (BSM), and cholesterol were measured using the surface force apparatus (SFA). Two distinct force profiles were detected corresponding to uniform raft membranes and raft membranes with a higher level of topological membrane defects (heterogeneous) as corroborated by atomic force microscopy (AFM) scans. In all cases a weak, long-range electrostatic repulsion was observed with some variation in the surface charge density. The variation in electrostatic repulsion was attributed to charged lipid species primarily from the constituent lipids in the BSM mixture. The adhesion between the uniform raft membranes was comparable to our previous work with pure component, liquid-ordered POPC-DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine)-cholesterol membranes. Raft membranes with more topological defects adhered more strongly owing to hydrophobic attraction between exposed acyl chains. Even though the rafts were in the liquid-ordered phase and membrane defects were present in the contact region, the raft membranes were stable, and no structural rearrangement was observed throughout the measurements. Our findings demonstrate that liquid-ordered membranes are stable to mechanical loading and not particularly sensitive to compositional variation.
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Affiliation(s)
- James Kurniawan
- Department of Chemical Engineering, ‡Department of Chemistry, and §Department of Biomedical Engineering, University of California , Davis 95616, United States
| | - João Ventrici
- Department of Chemical Engineering, ‡Department of Chemistry, and §Department of Biomedical Engineering, University of California , Davis 95616, United States
| | - Gregory Kittleson
- Department of Chemical Engineering, ‡Department of Chemistry, and §Department of Biomedical Engineering, University of California , Davis 95616, United States
| | - Tonya L Kuhl
- Department of Chemical Engineering, ‡Department of Chemistry, and §Department of Biomedical Engineering, University of California , Davis 95616, United States
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13
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Schmid F. Physical mechanisms of micro- and nanodomain formation in multicomponent lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:509-528. [PMID: 27823927 DOI: 10.1016/j.bbamem.2016.10.021] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/19/2016] [Accepted: 10/27/2016] [Indexed: 12/17/2022]
Abstract
This article summarizes a variety of physical mechanisms proposed in the literature, which can generate micro- and nanodomains in multicomponent lipid bilayers and biomembranes. It mainly focusses on lipid-driven mechanisms that do not involve direct protein-protein interactions. Specifically, it considers (i) equilibrium mechanisms based on lipid-lipid phase separation such as critical cluster formation close to critical points, and multiple domain formation in curved geometries, (ii) equilibrium mechanisms that stabilize two-dimensional microemulsions, such as the effect of linactants and the effect of curvature-composition coupling in bilayers and monolayers, and (iii) non-equilibrium mechanisms induced by the interaction of a biomembrane with the cellular environment, such as membrane recycling and the pinning effects of the cytoplasm. Theoretical predictions are discussed together with simulations and experiments. The presentation is guided by the theory of phase transitions and critical phenomena, and the appendix summarizes the mathematical background in a concise way within the framework of the Ginzburg-Landau theory. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Friederike Schmid
- Institute of Physics, Johannes Gutenberg University, 55099 Mainz, Germany
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14
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Di Meo F, Fabre G, Berka K, Ossman T, Chantemargue B, Paloncýová M, Marquet P, Otyepka M, Trouillas P. In silico pharmacology: Drug membrane partitioning and crossing. Pharmacol Res 2016; 111:471-486. [PMID: 27378566 DOI: 10.1016/j.phrs.2016.06.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 01/09/2023]
Abstract
Over the past decade, molecular dynamics (MD) simulations have become particularly powerful to rationalize drug insertion and partitioning in lipid bilayers. MD simulations efficiently support experimental evidences, with a comprehensive understanding of molecular interactions driving insertion and crossing. Prediction of drug partitioning is discussed with respect to drug families (anesthetics; β-blockers; non-steroidal anti-inflammatory drugs; antioxidants; antiviral drugs; antimicrobial peptides). To accurately evaluate passive permeation coefficients turned out to be a complex theoretical challenge; however the recent methodological developments based on biased MD simulations are particularly promising. Particular attention is paid to membrane composition (e.g., presence of cholesterol), which influences drug partitioning and permeation. Recent studies concerning in silico models of membrane proteins involved in drug transport (influx and efflux) are also reported here. These studies have allowed gaining insight in drug efflux by, e.g., ABC transporters at an atomic resolution, explicitly accounting for the mandatory forces induced by the surrounded lipid bilayer. Large-scale conformational changes were thoroughly analyzed.
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Affiliation(s)
- Florent Di Meo
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Gabin Fabre
- LCSN, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Karel Berka
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Tahani Ossman
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Benjamin Chantemargue
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France; Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Markéta Paloncýová
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Pierre Marquet
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Michal Otyepka
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Patrick Trouillas
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France; Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic.
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15
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Javanainen M, Martinez-Seara H. Efficient preparation and analysis of membrane and membrane protein systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2468-2482. [PMID: 26947184 DOI: 10.1016/j.bbamem.2016.02.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 11/25/2022]
Abstract
Molecular dynamics (MD) simulations have become a highly important technique to consider lipid membrane systems, and quite often they provide considerable added value to laboratory experiments. Rapid development of both software and hardware has enabled the increase of time and size scales reachable by MD simulations to match those attainable by several accurate experimental techniques. However, until recently, the quality and maturity of software tools available for building membrane models for simulations as well as analyzing the results of these simulations have seriously lagged behind. Here, we discuss the recent developments of such tools from the end-users' point of view. In particular, we review the software that can be employed to build lipid bilayers and other related structures with or without embedded membrane proteins to be employed in MD simulations. Additionally, we provide a brief critical insight into force fields and MD packages commonly used for membrane and membrane protein simulations. Finally, we list analysis tools that can be used to study the properties of membrane and membrane protein systems. In all these points we comment on the respective compatibility of the covered tools. We also share our opinion on the current state of the available software. We briefly discuss the most commonly employed tools and platforms on which new software can be built. We conclude the review by providing a few ideas and guidelines on how the development of tools can be further boosted to catch up with the rapid pace at which the field of membrane simulation progresses. This includes improving the compatibility between software tools and promoting the openness of the codes on which these applications rely. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Matti Javanainen
- Department of Physics, Tampere University of Technology, Tampere, Finland.
| | - Hector Martinez-Seara
- Department of Physics, Tampere University of Technology, Tampere, Finland; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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16
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Ogawa Y, Tanaka M. A fluorescent cholesterol analogue for observation of free cholesterol in the plasma membrane of live cells. Anal Biochem 2016; 492:49-55. [DOI: 10.1016/j.ab.2015.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/14/2015] [Accepted: 09/03/2015] [Indexed: 01/16/2023]
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17
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Abstract
The fundamental mechanisms of protein and lipid organization at the plasma membrane have continued to engage researchers for decades. Among proposed models, one idea has been particularly successful which assumes that sterol-dependent nanoscopic phases of different lipid chain order compartmentalize proteins, thereby modulating protein functionality. This model of membrane rafts has sustainably sparked the fields of membrane biophysics and biology, and shifted membrane lipids into the spotlight of research; by now, rafts have become an integral part of our terminology to describe a variety of cell biological processes. But is the evidence clear enough to continue supporting a theoretical concept which has resisted direct proof by observation for nearly twenty years? In this essay, we revisit findings that gave rise to and substantiated the raft hypothesis, discuss its impact on recent studies, and present alternative mechanisms to account for plasma membrane heterogeneity.
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Affiliation(s)
- Eva Sevcsik
- Institute of Applied Physics, Vienna University of Technology, Vienna, Austria
| | - Gerhard J Schütz
- Institute of Applied Physics, Vienna University of Technology, Vienna, Austria
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18
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Effects of Stretching Speed on Mechanical Rupture of Phospholipid/Cholesterol Bilayers: Molecular Dynamics Simulation. Sci Rep 2015; 5:15369. [PMID: 26471872 PMCID: PMC4607938 DOI: 10.1038/srep15369] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/24/2015] [Indexed: 11/09/2022] Open
Abstract
Rupture of biological cell membrane under mechanical stresses is critical for cell viability. It is triggered by local rearrangements of membrane molecules. We investigated the effects of stretching speed on mechanical rupture of phospholipid/cholesterol bilayers using unsteady molecular dynamics simulations. We focused on pore formation, the trigger of rupture, in a 40 mol% cholesterol-including bilayer. The unsteady stretching was modeled by proportional and temporal scaling of atom positions at stretching speeds from 0.025 to 30 m/s. The effects of the stretching speed on the critical areal strain, where the pore forms, is composed of two regimes. At low speeds (<1.0 m/s), the critical areal strain is insensitive to speed, whereas it significantly increases at higher speeds. Also, the strain is larger than that of a pure bilayer, regardless of the stretching speeds, which qualitatively agrees with available experimental data. Transient recovery of the cholesterol and phospholipid molecular orientations was evident at lower speeds, suggesting the formation of a stretch-induced interdigitated gel-like phase. However, this recovery was not confirmed at higher speeds or for the pure bilayer. The different responses of the molecular orientations may help explain the two regimes for the effect of stretching speed on pore formation.
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19
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Lorent JH, Levental I. Structural determinants of protein partitioning into ordered membrane domains and lipid rafts. Chem Phys Lipids 2015; 192:23-32. [PMID: 26241883 DOI: 10.1016/j.chemphyslip.2015.07.022] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/27/2015] [Accepted: 07/29/2015] [Indexed: 11/16/2022]
Abstract
Increasing evidence supports the existence of lateral nanoscopic lipid domains in plasma membranes, known as lipid rafts. These domains preferentially recruit membrane proteins and lipids to facilitate their interactions and thereby regulate transmembrane signaling and cellular homeostasis. The functionality of raft domains is intrinsically dependent on their selectivity for specific membrane components; however, while the physicochemical determinants of raft association for lipids are known, very few systematic studies have focused on the structural aspects that guide raft partitioning of proteins. In this review, we describe biophysical and thermodynamic aspects of raft-mimetic liquid ordered phases, focusing on those most relevant for protein partitioning. Further, we detail the variety of experimental models used to study protein-raft interactions. Finally, we review the existing literature on mechanisms for raft targeting, including lipid post-translational modifications, lipid binding, and transmembrane domain features. We conclude that while protein palmitoylation is a clear raft-targeting signal, few other general structural determinants for raft partitioning have been revealed, suggesting that many discoveries lie ahead in this burgeoning field.
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Affiliation(s)
- Joseph Helmuth Lorent
- Department for Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, USA
| | - Ilya Levental
- Department for Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, USA.
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20
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Kalli AC, Sansom MSP, Reithmeier RAF. Molecular dynamics simulations of the bacterial UraA H+-uracil symporter in lipid bilayers reveal a closed state and a selective interaction with cardiolipin. PLoS Comput Biol 2015; 11:e1004123. [PMID: 25729859 PMCID: PMC4346270 DOI: 10.1371/journal.pcbi.1004123] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/09/2015] [Indexed: 11/25/2022] Open
Abstract
The Escherichia coli UraA H+-uracil symporter is a member of the nucleobase/ascorbate transporter (NAT) family of proteins, and is responsible for the proton-driven uptake of uracil. Multiscale molecular dynamics simulations of the UraA symporter in phospholipid bilayers consisting of: 1) 1-palmitoyl 2-oleoyl-phosphatidylcholine (POPC); 2) 1-palmitoyl 2-oleoyl-phosphatidylethanolamine (POPE); and 3) a mixture of 75% POPE, 20% 1-palmitoyl 2-oleoyl-phosphatidylglycerol (POPG); and 5% 1-palmitoyl 2-oleoyl-diphosphatidylglycerol/cardiolipin (CL) to mimic the lipid composition of the bacterial inner membrane, were performed using the MARTINI coarse-grained force field to self-assemble lipids around the crystal structure of this membrane transport protein, followed by atomistic simulations. The overall fold of the protein in lipid bilayers remained similar to the crystal structure in detergent on the timescale of our simulations. Simulations were performed in the absence of uracil, and resulted in a closed state of the transporter, due to relative movement of the gate and core domains. Anionic lipids, including POPG and especially CL, were found to associate with UraA, involving interactions between specific basic residues in loop regions and phosphate oxygens of the CL head group. In particular, three CL binding sites were identified on UraA: two in the inner leaflet and a single site in the outer leaflet. Mutation of basic residues in the binding sites resulted in the loss of CL binding in the simulations. CL may play a role as a “proton trap” that channels protons to and from this transporter within CL-enriched areas of the inner bacterial membrane. Symporters are proteins that are responsible for the co-transport of ions and small molecule solutes across cell membranes. UraA is an example of a symporter, and is responsible for the proton-driven uptake of uracil in bacteria like E. coli. Despite its importance as a member of a large family of nucleobase/ascorbate transporters (NAT) and the existence of structural and functional data, the mechanism by which UraA transports uracil across the bacterial membrane, and in particular the role of its diverse and complex lipid environment in the transport mechanism, remains elusive. In this study, we have used a multiscale computational methodology to examine the dynamics of UraA and to elucidate its interactions with lipids that resemble its native environment in the bacterial inner membrane. Our results demonstrate that negatively-charged lipids in the membrane (phosphatidylglycerol and cardiolipin) associate preferentially with UraA and may play a role in its function. Additionally, our simulations resulted in a closed state of UraA, a likely intermediate in the transport mechanism that may not be readily accessible by experimental methods.
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Affiliation(s)
- Antreas C. Kalli
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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21
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Carmona-Salazar L, El Hafidi M, Gutiérrez-Nájera N, Noyola-Martínez L, González-Solís A, Gavilanes-Ruíz M. Fatty acid profiles from the plasma membrane and detergent resistant membranes of two plant species. PHYTOCHEMISTRY 2015; 109:25-35. [PMID: 25457489 DOI: 10.1016/j.phytochem.2014.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 05/17/2014] [Accepted: 10/16/2014] [Indexed: 06/04/2023]
Abstract
It is essential to establish the composition of the plant plasma membrane in order to understand its organization and behavior under continually changing environments. Knowledge of the lipid phase, in particular the fatty acid (FA) complex repertoire, is important since FAs determine many of the physical-chemical membrane properties. FAs are constituents of the membrane glycerolipid and sphingolipid backbones and can also be linked to some sterols. In addition, FAs are components of complex lipids that can constitute membrane micro-domains, and the use of detergent-resistant membranes is a common approach to study their composition. The diversity and cellular allocation of the membrane lipids containing FAs are very diverse and the approaches to analyze them provide only general information. In this work, a detailed FA analysis was performed using highly purified plasma membranes from bean leaves and germinating maize embryos and their respective detergent-resistant membrane preparations. The analyses showed the presence of a significant amount of very long chain FAs (containing 28C, 30C and 32C), in both plasma membrane preparations from bean and maize, that have not been previously reported. Herein is demonstrated that a significant enrichment of very long chain saturated FAs and saturated FAs can occur in detergent-resistant membrane preparations, as compared to the plasma membranes from both plant species. Considering that a thorough analysis of FAs is rarely performed in purified plasma membranes and detergent-resistant membranes, this work provides qualitative and quantitative evidence on the contributions of the length and saturation of FAs to the organization of the plant plasma membrane and detergent-resistant membranes.
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Affiliation(s)
- Laura Carmona-Salazar
- Dpto. de Bioquímica, Edif. E, Facultad de Química, UNAM. Ciudad Universitaria, Coyoacán, 04510 Mexico, D.F., Mexico
| | - Mohammed El Hafidi
- Dpto. de Biomedicina Cardiovascular, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Tlalpan, 14080 México, D.F., Mexico
| | - Nora Gutiérrez-Nájera
- Laboratorio de Bioquímica, Instituto Nacional de Medicina Genómica, Periférico Sur No. Col. Arenal Tepepan, Tlalpan, México, D.F., Mexico
| | - Liliana Noyola-Martínez
- Dpto. de Bioquímica, Edif. E, Facultad de Química, UNAM. Ciudad Universitaria, Coyoacán, 04510 Mexico, D.F., Mexico
| | - Ariadna González-Solís
- Dpto. de Bioquímica, Edif. E, Facultad de Química, UNAM. Ciudad Universitaria, Coyoacán, 04510 Mexico, D.F., Mexico
| | - Marina Gavilanes-Ruíz
- Dpto. de Bioquímica, Edif. E, Facultad de Química, UNAM. Ciudad Universitaria, Coyoacán, 04510 Mexico, D.F., Mexico.
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22
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Basu I, Mukhopadhyay C. In silico phase separation in the presence of GM1 in ternary and quaternary lipid bilayers. Phys Chem Chem Phys 2015; 17:17130-9. [DOI: 10.1039/c5cp01970b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using coarse grain molecular dynamics simulations, the spontaneous phase separation in the ternary (POPC [1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine]/cholesterol/GM1) and quaternary (POPC/PSM[palmitoyl sphingomyelin]/cholesterol/GM1) lipid bilayers into liquid ordered (Lo) and liquid disordered (Ld) domains, due to self-aggregation of GM1 molecules and co-localization of cholesterol with GM1 in accordance with experiments, is studied.
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Affiliation(s)
- Ipsita Basu
- Department of Chemistry
- University of Calcutta
- India
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23
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Molecular dynamics simulations of pore formation in stretched phospholipid/cholesterol bilayers. Chem Phys Lipids 2014; 183:43-9. [DOI: 10.1016/j.chemphyslip.2014.05.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/13/2014] [Accepted: 05/15/2014] [Indexed: 11/21/2022]
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24
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Guixà-González R, Ramírez-Anguita JM, Kaczor AA, Selent J. Simulating G protein-coupled receptors in native-like membranes: from monomers to oligomers. Methods Cell Biol 2014; 117:63-90. [PMID: 24143972 DOI: 10.1016/b978-0-12-408143-7.00004-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
G protein-coupled receptors (GPCRs) are one of the most relevant superfamilies of transmembrane proteins as they participate in an important variety of biological events. Recently, the scientific community is witnessing an advent of a GPCR crystallization age along with impressive improvements achieved in the field of computer simulations during the last two decades. Computer simulation techniques such as molecular dynamics (MD) simulations are now frequent tools to study the dynamic behavior of GPCRs and, more importantly, to model the complex membrane environment where these proteins spend their lifetime. Thanks to these tools, GPCRs can be simulated not only longer but also in a more "physiological" fashion. In this scenario, scientists are taking advantage of such advances to approach certain phenomena such as GPCR oligomerization occurring only at timescales not reachable until now. Thus, despite current MD simulations having important limitations today, they have become an essential tool to study key biophysical properties of GPCRs and GPCR oligomers.
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Affiliation(s)
- Ramon Guixà-González
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra/IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader, Barcelona, Spain
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25
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Sphingolipids as modulators of membrane proteins. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:665-70. [PMID: 24201378 DOI: 10.1016/j.bbalip.2013.10.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/22/2013] [Accepted: 10/28/2013] [Indexed: 12/13/2022]
Abstract
The diversity of the transmembranome of higher eukaryotes is matched by an enormous diversity of sphingolipid classes and molecular species. The intrinsic properties of sphingolipids are not only suited for orchestrating lateral architectures of biological membranes, but their molecular distinctions also allow for the evolution of protein motifs specifically recognising and interacting with individual lipids. Although various reports suggest a role of sphingolipids in membrane protein function, only a few cases have determined the specificity of these interactions. In this review we discuss examples of specific protein-sphingolipid interactions for which a modulator-like dependency on sphingolipids was assigned to specific proteins. These novel functions of sphingolipids in specific protein-lipid assemblies contribute to the complexity of the sphingolipid classes and other molecular species observed in animal cells. This article is part of a Special Issue entitled New Frontiers in Sphingolipid Biology.
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26
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Bennett WD, Tieleman DP. Computer simulations of lipid membrane domains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1765-76. [DOI: 10.1016/j.bbamem.2013.03.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 10/27/2022]
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27
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Petruk AA, Varriale S, Coscia MR, Mazzarella L, Merlino A, Oreste U. The structure of the CD3 ζζ transmembrane dimer in POPC and raft-like lipid bilayer: a molecular dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2637-45. [PMID: 23896554 DOI: 10.1016/j.bbamem.2013.07.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 07/05/2013] [Accepted: 07/16/2013] [Indexed: 12/15/2022]
Abstract
Plasma membrane lipids significantly affect assembly and activity of many signaling networks. The present work is aimed at analyzing, by molecular dynamics simulations, the structure and dynamics of the CD3 ζζ dimer in palmitoyl-oleoyl-phosphatidylcholine bilayer (POPC) and in POPC/cholesterol/sphingomyelin bilayer, which resembles the raft membrane microdomain supposed to be the site of the signal transducing machinery. Both POPC and raft-like environment produce significant alterations in structure and flexibility of the CD3 ζζ with respect to nuclear magnetic resonance (NMR) model: the dimer is more compact, its secondary structure is slightly less ordered, the arrangement of the Asp6 pair, which is important for binding to the Arg residue in the alpha chain of the T cell receptor (TCR), is stabilized by water molecules. Different interactions of charged residues with lipids at the lipid-cytoplasm boundary occur when the two environments are compared. Furthermore, in contrast to what is observed in POPC, in the raft-like environment correlated motions between transmembrane and cytoplasmic regions are observed. Altogether the data suggest that when the TCR complex resides in the raft domains, the CD3 ζζ dimer assumes a specific conformation probably necessary to the correct signal transduction.
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Affiliation(s)
- Ariel Alcides Petruk
- Instituto Superior de Investigaciones Biológicas (INSIBIO-CONICET), Chacabuco 461, S. M. de Tucumán, Tucumán T4000ILI, Argentina
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28
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Petruzielo RS, Heberle FA, Drazba P, Katsaras J, Feigenson GW. Phase behavior and domain size in sphingomyelin-containing lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1828:1302-13. [PMID: 23337475 PMCID: PMC3582766 DOI: 10.1016/j.bbamem.2013.01.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 11/15/2022]
Abstract
Membrane raft size measurements are crucial to understanding the stability and functionality of rafts in cells. The challenge of accurately measuring raft size is evidenced by the disparate reports of domain sizes, which range from nanometers to microns for the ternary model membrane system sphingomyelin (SM)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/cholesterol (Chol). Using Förster resonance energy transfer (FRET) and differential scanning calorimetry (DSC), we established phase diagrams for porcine brain SM (bSM)/dioleoyl-sn-glycero-3-phosphocholine (DOPC)/Chol and bSM/POPC/Chol at 15 and 25°C. By combining two techniques with different spatial sensitivities, namely FRET and small-angle neutron scattering (SANS), we have significantly narrowed the uncertainty in domain size estimates for bSM/POPC/Chol mixtures. Compositional trends in FRET data revealed coexisting domains at 15 and 25°C for both mixtures, while SANS measurements detected no domain formation for bSM/POPC/Chol. Together these results indicate that liquid domains in bSM/POPC/Chol are between 2 and 7nm in radius at 25°C: that is, domains must be on the order of the 2-6nm Förster distance of the FRET probes, but smaller than the ~7nm minimum cluster size detectable with SANS. However, for palmitoyl SM (PSM)/POPC/Chol at a similar composition, SANS detected coexisting liquid domains. This increase in domain size upon replacing the natural SM component (which consists of a mixture of chain lengths) with synthetic PSM, suggests a role for SM chain length in modulating raft size in vivo.
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Affiliation(s)
| | - Frederick A. Heberle
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6100, USA
| | - Paul Drazba
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, TN, 37996-1200, USA
| | - John Katsaras
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6100, USA
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, TN, 37996-1200, USA
- Canadian Neutron Beam Centre, National Research Council, Chalk River, Ontario, Canada K0J 1J0
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6453, USA
| | - Gerald W. Feigenson
- Department of Molecular Biology and Genetics, Field of Biophysics, Cornell University, Ithaca, NY, 14853 USA
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29
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Abstract
How mechanical forces are sensed remains largely mysterious. The forces that gate prokaryotic and several eukaryotic channels were found to come from the lipid membrane. Our survey of animal cells found that membrane force foci all have cholesterol-gathering proteins and are reinforced with cholesterol. This result is evident in overt force sensors at the tips of stereocilia for vertebrate hearing and the touch receptor of Caenorhabditis elegans and mammalian neurons. For less specialized cells, cadherins sustain the force between neighboring cells and integrins between cells and matrix. These tension bearers also pass through and bind to a cholesterol-enriched platform before anchoring to cytoskeleton through other proteins. Cholesterol, in alliance with sphingomyelin and specialized proteins, enforces a more ordered structure in the bilayer. Such a stiffened platform can suppress mechanical noise, redirect, rescale, and confine force. We speculate that such platforms may be dynamic. The applied force may allow disordered-phase lipids to enter the platform-staging channel opening in the thinner mobile neighborhood. The platform may also contain specialized protein/lipid subdomains enclosing mechanosensitive channels to open with localized tension. Such a dynamic stage can mechanically operate structurally disparate channels or enzymes without having to tie them directly to cadherin, integrin, or other protein tethers.
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30
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Baoukina S, Mendez-Villuendas E, Bennett WFD, Tieleman DP. Computer simulations of the phase separation in model membranes. Faraday Discuss 2013; 161:63-75; discussion 113-50. [DOI: 10.1039/c2fd20117h] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Computational Studies of Biomembrane Systems: Theoretical Considerations, Simulation Models, and Applications. FROM SINGLE MOLECULES TO NANOSCOPICALLY STRUCTURED MATERIALS 2013. [DOI: 10.1007/12_2013_258] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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32
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Ernst AM, Contreras FX, Thiele C, Wieland F, Brügger B. Mutual recognition of sphingolipid molecular species in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2616-22. [DOI: 10.1016/j.bbamem.2012.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 06/04/2012] [Indexed: 01/11/2023]
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33
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Matsumori N, Yasuda T, Okazaki H, Suzuki T, Yamaguchi T, Tsuchikawa H, Doi M, Oishi T, Murata M. Comprehensive Molecular Motion Capture for Sphingomyelin by Site-Specific Deuterium Labeling. Biochemistry 2012; 51:8363-70. [DOI: 10.1021/bi3009399] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nobuaki Matsumori
- Department of Chemistry, Graduate
School of Science, Osaka University, Toyonaka,
Osaka 560-0043, Japan
| | - Tomokazu Yasuda
- Department of Chemistry, Graduate
School of Science, Osaka University, Toyonaka,
Osaka 560-0043, Japan
| | - Hiroki Okazaki
- Department of Chemistry, Graduate
School of Science, Osaka University, Toyonaka,
Osaka 560-0043, Japan
| | - Takashi Suzuki
- Department of Chemistry, Graduate
School of Science, Osaka University, Toyonaka,
Osaka 560-0043, Japan
| | - Toshiyuki Yamaguchi
- Department of Chemistry, Graduate
School of Science, Osaka University, Toyonaka,
Osaka 560-0043, Japan
- ERATO,
Lipid Active Structure
Project, Japan Science and Technology Agency, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate
School of Science, Osaka University, Toyonaka,
Osaka 560-0043, Japan
| | - Mototsugu Doi
- Department of Chemistry, Graduate
School of Science, Osaka University, Toyonaka,
Osaka 560-0043, Japan
| | - Tohru Oishi
- Department of Chemistry, Graduate
School of Sciences, Kyushu University,
Higashi-ku, Fukuoka 812-8581, Japan
| | - Michio Murata
- Department of Chemistry, Graduate
School of Science, Osaka University, Toyonaka,
Osaka 560-0043, Japan
- ERATO,
Lipid Active Structure
Project, Japan Science and Technology Agency, Toyonaka, Osaka 560-0043, Japan
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34
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Łach A, Grzybek M, Heger E, Korycka J, Wolny M, Kubiak J, Kolondra A, Bogusławska DM, Augoff K, Majkowski M, Podkalicka J, Kaczor J, Stefanko A, Kuliczkowski K, Sikorski AF. Palmitoylation of MPP1 (membrane-palmitoylated protein 1)/p55 is crucial for lateral membrane organization in erythroid cells. J Biol Chem 2012; 287:18974-84. [PMID: 22496366 DOI: 10.1074/jbc.m111.332981] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
S-Acylation of proteins is a ubiquitous post-translational modification and a common signal for membrane association. The major palmitoylated protein in erythrocytes is MPP1, a member of the MAGUK family and an important component of the ternary complex that attaches the spectrin-based skeleton to the plasma membrane. Here we show that DHHC17 is the only acyltransferase present in red blood cells (RBC). Moreover, we give evidence that protein palmitoylation is essential for membrane organization and is crucial for proper RBC morphology, and that the effect is specific for MPP1. Our observations are based on the clinical cases of two related patients whose RBC had no palmitoylation activity, caused by a lack of DHHC17 in the membrane, which resulted in a strong decrease of the amount of detergent-resistant membrane (DRM) material. We confirmed that this loss of detergent-resistant membrane was due to the lack of palmitoylation by treatment of healthy RBC with 2-bromopalmitic acid (2-BrP, common palmitoylation inhibitor). Concomitantly, fluorescence lifetime imaging microscopy (FLIM) analyses of an order-sensing dye revealed a reduction of membrane order after chemical inhibition of palmitoylation in erythrocytes. These data point to a pathophysiological relationship between the loss of MPP1-directed palmitoylation activity and perturbed lateral membrane organization.
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Affiliation(s)
- Agnieszka Łach
- Laboratory of Cytobiochemistry, Biotechnology Faculty, University of Wrocław, Przybyszewskiego 63/77, 51-148 Wrocław, Poland
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35
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Alwarawrah M, Dai J, Huang J. Modification of Lipid Bilayer Structure by Diacylglycerol: A Comparative Study of Diacylglycerol and Cholesterol. J Chem Theory Comput 2012; 8:749-758. [PMID: 22389636 PMCID: PMC3289152 DOI: 10.1021/ct200790q] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diacylglycerols (DAGs) are important second messengers in biomembranes, and they can activate protein kinase C and many other enzymes and receptors. However, their interactions with cholesterol and other lipids have not been previously studied using molecular dynamics (MD) simulation. In this study, nine independent atomistic MD simulations were performed to specifically investigate the interactions between di16:0DAG, 16:0,18:1-phosphatidylcholine (POPC), and cholesterol. Despite of their substantial differences in chemical structure, DAG and cholesterol produce some very similar effects in POPC bilayers: increasing acyl chain order and bilayer thickness, reducing volume-per-lipid, and decreasing lateral diffusion of molecules. More significantly, DAG also produces a strong "condensing effect" in PC bilayers. In comparison, cholesterol is more effective than DAG in producing the above effects. The driving force for the condensing effect is their molecular shape: DAG and cholesterol both have small polar headgroups and large hydrophobic bodies. In a lipid bilayer, in order to avoid the unfavorable exposure of their hydrophobic parts to water, neighboring phospholipid headgroups move toward cholesterol or DAG to provide cover. Thus, seemingly complex interactions between DAG, cholesterol and phospholipid can be clearly explained using the Umbrella Model. Our simulations confirmed the hypothesis that DAG increases the spacing between phospholipid headgroups, which is important for activating protein kinase C and other enzymes. Interestingly, our simulations also show that the conventional wisdom that the spacing created by a DAG is directly above the DAG molecule is incorrect; instead, the largest spacing usually occurs between the first and the second nearest-neighbor PC headgroups from a DAG, due to the umbrella effect.
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Affiliation(s)
| | - Jian Dai
- Department of Physics Texas Tech University Lubbock, Texas 79409
| | - Juyang Huang
- Department of Physics Texas Tech University Lubbock, Texas 79409
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36
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Bennett WFD, Tieleman DP. Molecular simulation of rapid translocation of cholesterol, diacylglycerol, and ceramide in model raft and nonraft membranes. J Lipid Res 2012; 53:421-429. [PMID: 22246847 DOI: 10.1194/jlr.m022491] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The translocation of lipids across membranes (flip-flop) is an important biological process. Slow exchange on a physiological timescale allows the creation of asymmetric distributions of lipids across cellular membranes. The location of lipids and their rate of exchange have important biological consequences, especially for lipids involved in cellular signaling. We investigated the translocation of cholesterol, ceramide, and diacylglycerol in two model bilayers using molecular dynamics simulations. We estimate half times for flip-flop for cholesterol, diacylglycerol, and ceramide of 20 μs, 30 μs, and 10 ms in a POPC bilayer, compared with approximately 30 min, 30 ms, and 30 s in a model raft bilayer (1:1:1 PSM, POPC, and cholesterol). Cholesterol has a large (54 kJ/mol) free energy of exchange between the POPC and raft bilayer, and therefore, it strongly prefers the more ordered and rigid raft bilayer over the more liquid POPC bilayer. Ceramide and diacylglycerol have relatively small free energies of exchange, suggesting nearly equal preference for both bilayers. This unexpected result may have implications for ceramide and diacylglycerol signaling and membrane localization.
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Affiliation(s)
- W F Drew Bennett
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - D Peter Tieleman
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
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37
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Herrera FE, Pantano S. Structure and dynamics of nano-sized raft-like domains on the plasma membrane. J Chem Phys 2012; 136:015103. [DOI: 10.1063/1.3672704] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Shintani M, Matsuo Y, Sakuraba S, Matubayasi N. Interaction of naphthalene derivatives with lipids in membranes studied by the 1H-nuclear Overhauser effect and molecular dynamics simulation. Phys Chem Chem Phys 2012; 14:14049-60. [DOI: 10.1039/c2cp41984j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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39
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Saito H, Shinoda W. Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers: A Molecular Dynamics Study. J Phys Chem B 2011; 115:15241-50. [DOI: 10.1021/jp201611p] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hiroaki Saito
- Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
- CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Wataru Shinoda
- Nanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan
- CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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40
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Orešič M, Hyötyläinen T, Herukka SK, Sysi-Aho M, Mattila I, Seppänan-Laakso T, Julkunen V, Gopalacharyulu PV, Hallikainen M, Koikkalainen J, Kivipelto M, Helisalmi S, Lötjönen J, Soininen H. Metabolome in progression to Alzheimer's disease. Transl Psychiatry 2011; 1:e57. [PMID: 22832349 PMCID: PMC3309497 DOI: 10.1038/tp.2011.55] [Citation(s) in RCA: 197] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mild cognitive impairment (MCI) is considered as a transition phase between normal aging and Alzheimer's disease (AD). MCI confers an increased risk of developing AD, although the state is heterogeneous with several possible outcomes, including even improvement back to normal cognition. We sought to determine the serum metabolomic profiles associated with progression to and diagnosis of AD in a prospective study. At the baseline assessment, the subjects enrolled in the study were classified into three diagnostic groups: healthy controls (n=46), MCI (n=143) and AD (n=47). Among the MCI subjects, 52 progressed to AD in the follow-up. Comprehensive metabolomics approach was applied to analyze baseline serum samples and to associate the metabolite profiles with the diagnosis at baseline and in the follow-up. At baseline, AD patients were characterized by diminished ether phospholipids, phosphatidylcholines, sphingomyelins and sterols. A molecular signature comprising three metabolites was identified, which was predictive of progression to AD in the follow-up. The major contributor to the predictive model was 2,4-dihydroxybutanoic acid, which was upregulated in AD progressors (P=0.0048), indicating potential involvement of hypoxia in the early AD pathogenesis. This was supported by the pathway analysis of metabolomics data, which identified upregulation of pentose phosphate pathway in patients who later progressed to AD. Together, our findings primarily implicate hypoxia, oxidative stress, as well as membrane lipid remodeling in progression to AD. Establishment of pathogenic relevance of predictive biomarkers such as ours may not only facilitate early diagnosis, but may also help identify new therapeutic avenues.
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Affiliation(s)
- M Orešič
- VTT Technical Research Centre of Finland, Espoo, Finland.
| | - T Hyötyläinen
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - S-K Herukka
- Department of Neurology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - M Sysi-Aho
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - I Mattila
- VTT Technical Research Centre of Finland, Espoo, Finland
| | | | - V Julkunen
- Department of Neurology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | | | - M Hallikainen
- Department of Neurology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - J Koikkalainen
- VTT Technical Research Centre of Finland, Tampere, Finland
| | - M Kivipelto
- Aging Research Center, Karolinska Institute, Stockholm, Sweden
| | - S Helisalmi
- Department of Neurology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - J Lötjönen
- VTT Technical Research Centre of Finland, Tampere, Finland
| | - H Soininen
- Department of Neurology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
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41
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Kaiser HJ, Surma MA, Mayer F, Levental I, Grzybek M, Klemm RW, Da Cruz S, Meisinger C, Müller V, Simons K, Lingwood D. Molecular convergence of bacterial and eukaryotic surface order. J Biol Chem 2011; 286:40631-7. [PMID: 21965671 DOI: 10.1074/jbc.m111.276444] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The conservation of fluidity is a theme common to all cell membranes. In this study, an analysis of lipid packing was conducted via C-laurdan spectroscopy of cell surface membranes prepared from representative species of Bacteria and Eukarya. We found that despite their radical differences in composition (namely the presence and absence of membrane-rigidifying sterol) the membrane order of all taxa converges on a remarkably similar level. To understand how this similarity is constructed, we reconstituted membranes with either bacterial or eukaryotic components. We found that transmembrane segments of proteins have an important role in buffering lipid-mediated packing. This buffering ensures that sterol-free and sterol-containing membranes exhibit similar barrier properties.
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Affiliation(s)
- Hermann-Josef Kaiser
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
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42
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Liu Y, Chipot C, Shao X, Cai W. The effects of 7-dehydrocholesterol on the structural properties of membranes. Phys Biol 2011; 8:056005. [DOI: 10.1088/1478-3975/8/5/056005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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43
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Qiu L, Buie C, Reay A, Vaughn MW, Cheng KH. Molecular dynamics simulations reveal the protective role of cholesterol in β-amyloid protein-induced membrane disruptions in neuronal membrane mimics. J Phys Chem B 2011; 115:9795-812. [PMID: 21740063 PMCID: PMC3163122 DOI: 10.1021/jp2012842] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Interactions of β-amyloid (Aβ) peptides with neuronal membranes have been associated with the pathogenesis of Alzheimer's disease (AD); however, the molecular details remain unclear. We used atomistic molecular dynamics (MD) simulations to study the interactions of Aβ(40) and Aβ(42) with model neuronal membranes. The differences between cholesterol-enriched and depleted lipid domains were investigated by the use of model phosphatidylcholine (PC) lipid bilayers with and without 40 mol % cholesterol. A total of 16 independent 200 ns simulation replicates were investigated. The surface area per lipid, bilayer thickness, water permeability barrier, and lipid order parameter, which are sensitive indicators of membrane disruption, were significantly altered by the inserted state of the protein. We conclude that cholesterol protects Aβ-induced membrane disruption and inhibits β-sheet formation of Aβ on the lipid bilayer. The latter could represent a two-dimensional (2D) seeding template for the formation of toxic oligomeric Aβ in the pathogenesis of AD.
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Affiliation(s)
- Liming Qiu
- Department of Physics, Texas Tech University, Lubbock, Texas 79409
| | - Creighton Buie
- Department of Physics, Texas Tech University, Lubbock, Texas 79409
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409
| | - Andrew Reay
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409
| | - Mark W. Vaughn
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409
| | - Kwan Hon Cheng
- Department of Physics, Texas Tech University, Lubbock, Texas 79409
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44
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Matsumori N, Tanada N, Nozu K, Okazaki H, Oishi T, Murata M. Design and synthesis of sphingomyelin-cholesterol conjugates and their formation of ordered membranes. Chemistry 2011; 17:8568-75. [PMID: 21728198 DOI: 10.1002/chem.201100849] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Indexed: 12/11/2022]
Abstract
A lipid raft is a cholesterol (Chol)-rich microdomain floating in a sea of lipid bilayers. Although Chol is thought to interact preferentially with sphingolipids such as sphingomyelin (SM), rather than with glycerophospholipids, the origin of the specific interaction has remained unresolved, primarily because of the high mobility of lipid molecules and weak intermolecular interactions. In this study, we synthesized SM-Chol conjugates with functionally designed linker portions to restrain Chol mobility and examined their formation of ordered membranes by a detergent insolubility assay, fluorescence anisotropy experiments, and fluorescence-quenching assay. In all of the tests, membranes prepared from the conjugates showed properties of ordered domains comparable to a SM-Chol (1:1) membrane. To gain insight into the structure of bilayers composed from the conjugates, we performed molecular dynamics simulations with 64 molecules of the conjugates, which suggested that the conjugates form a stable bilayer structure by bending at the linker portion and, mostly, reproduce the hydrogen bonds between the SM and Chol portions. These results imply that the molecular recognition between SM and Chol in an ordered domain is essentially reproduced by the conjugated molecules and, thus, demonstrates that these conjugate molecules could potentially serve as molecular probes for understanding molecular recognition in lipid rafts.
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Affiliation(s)
- Nobuaki Matsumori
- Department of Chemistry, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
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45
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Matsumori N, Okazaki H, Nomura K, Murata M. Fluorinated cholesterol retains domain-forming activity in sphingomyelin bilayers. Chem Phys Lipids 2011; 164:401-8. [DOI: 10.1016/j.chemphyslip.2011.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 05/21/2011] [Accepted: 05/24/2011] [Indexed: 01/02/2023]
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46
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Contreras FX, Ernst AM, Wieland F, Brügger B. Specificity of intramembrane protein-lipid interactions. Cold Spring Harb Perspect Biol 2011; 3:cshperspect.a004705. [PMID: 21536707 DOI: 10.1101/cshperspect.a004705] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Our concept of biological membranes has markedly changed, from the fluid mosaic model to the current model that lipids and proteins have the ability to separate into microdomains, differing in their protein and lipid compositions. Since the breakthrough in crystallizing membrane proteins, the most powerful method to define lipid-binding sites on proteins has been X-ray and electron crystallography. More recently, chemical biology approaches have been developed to analyze protein-lipid interactions. Such methods have the advantage of providing highly specific cellular probes. With the advent of novel tools to study functions of individual lipid species in membranes together with structural analysis and simulations at the atomistic resolution, a growing number of specific protein-lipid complexes are defined and their functions explored. In the present article, we discuss the various modes of intramembrane protein-lipid interactions in cellular membranes, including examples for both annular and nonannular bound lipids. Furthermore, we will discuss possible functional roles of such specific protein-lipid interactions as well as roles of lipids as chaperones in protein folding and transport.
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47
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Structure and Dynamics of Glycosphingolipids in Lipid Bilayers: Insights from Molecular Dynamics Simulations. ACTA ACUST UNITED AC 2011. [DOI: 10.1155/2011/950256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Glycolipids are important constituents of biological membranes, and understanding their structure and dynamics in lipid bilayers provides insights into their physiological and pathological roles. Experimental techniques have provided details into their behavior at model and biological membranes; however, computer simulations are needed to gain atomic level insights. This paper summarizes the insights obtained from MD simulations into the conformational and orientational dynamics of glycosphingolipids and their exposure, hydration, and hydrogen-bonding interactions in membrane environment. The organization of glycosphingolipids in raft-like membranes and their modulation of lipid membrane structure are also reviewed.
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48
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49
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Coppock PS, Kindt JT. Determination of Phase Transition Temperatures for Atomistic Models of Lipids from Temperature-Dependent Stripe Domain Growth Kinetics. J Phys Chem B 2010; 114:11468-73. [DOI: 10.1021/jp104529m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick S. Coppock
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322
| | - James T. Kindt
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322
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50
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Gurtovenko AA, Anwar J, Vattulainen I. Defect-Mediated Trafficking across Cell Membranes: Insights from in Silico Modeling. Chem Rev 2010; 110:6077-103. [DOI: 10.1021/cr1000783] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Andrey A. Gurtovenko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
| | - Jamshed Anwar
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
| | - Ilpo Vattulainen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
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