1
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Blake MJ, Castillo HB, Curtis AE, Calhoun TR. Facilitating flip-flop: Structural tuning of molecule-membrane interactions in living bacteria. Biophys J 2023; 122:1735-1747. [PMID: 37041744 PMCID: PMC10209030 DOI: 10.1016/j.bpj.2023.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/17/2023] [Accepted: 04/04/2023] [Indexed: 04/13/2023] Open
Abstract
The first barrier that a small molecule must overcome before trespassing into a living cell is the lipid bilayer surrounding the intracellular content. It is imperative, therefore, to understand how the structure of a small molecule influences its fate in this region. Through the use of second harmonic generation, we show how the differing degrees of ionic headgroups, conjugated system, and branched hydrocarbon tail disparities of a series of four styryl dye molecules influence the propensity to "flip-flop" or to be further organized in the outer leaflet by the membrane. We show here that initial adsorption experiments match previous studies on model systems; however, more complex dynamics are observed over time. Aside from probe molecule structure, these dynamics also vary between cell species and can deviate from trends reported based on model membranes. Specifically, we show here that the membrane composition is an important factor to consider for headgroup-mediated small-molecule dynamics. Overall, the findings presented here on how structural variability of small molecules impacts their initial adsorption and eventual destinations within membranes in the context of living cells could have practical applications in antibiotic and drug adjuvant design.
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Affiliation(s)
- Marea J Blake
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee
| | - Hannah B Castillo
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee
| | - Anna E Curtis
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee
| | - Tessa R Calhoun
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee.
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2
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Anderson RH, Sochacki KA, Vuppula H, Scott BL, Bailey EM, Schultz MM, Kerkvliet JG, Taraska JW, Hoppe AD, Francis KR. Sterols lower energetic barriers of membrane bending and fission necessary for efficient clathrin-mediated endocytosis. Cell Rep 2021; 37:110008. [PMID: 34788623 PMCID: PMC8620193 DOI: 10.1016/j.celrep.2021.110008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/03/2021] [Accepted: 10/26/2021] [Indexed: 01/16/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) is critical for cellular signal transduction, receptor recycling, and membrane homeostasis in mammalian cells. Acute depletion of cholesterol disrupts CME, motivating analysis of CME dynamics in the context of human disorders of cholesterol metabolism. We report that inhibition of post-squalene cholesterol biosynthesis impairs CME. Imaging of membrane bending dynamics and the CME pit ultrastructure reveals prolonged clathrin pit lifetimes and shallow clathrin-coated structures, suggesting progressive impairment of curvature generation correlates with diminishing sterol abundance. Sterol structural requirements for efficient CME include 3′ polar head group and B-ring conformation, resembling the sterol structural prerequisites for tight lipid packing and polarity. Furthermore, Smith-Lemli-Opitz fibroblasts with low cholesterol abundance exhibit deficits in CME-mediated transferrin internalization. We conclude that sterols lower the energetic costs of membrane bending during pit formation and vesicular scission during CME and suggest that reduced CME activity may contribute to cellular phenotypes observed within disorders of cholesterol metabolism. Anderson et al. demonstrate that sterol abundance and identity play a dominant role in facilitating clathrin-mediated endocytosis. Detailed analyses of clathrin-coated pits under sterol depletion support a requirement for sterol-mediated membrane bending during multiple stages of endocytosis, implicating endocytic dysfunction within the pathogenesis of disorders of cholesterol metabolism.
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Affiliation(s)
- Ruthellen H Anderson
- Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA; Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Kem A Sochacki
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Harika Vuppula
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA
| | - Brandon L Scott
- Nanoscience and Nanoengineering, South Dakota School of Mines & Technology, Rapid City, SD 57701, USA
| | - Elizabeth M Bailey
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA
| | - Maycie M Schultz
- Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Jason G Kerkvliet
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA
| | - Justin W Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Adam D Hoppe
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA.
| | - Kevin R Francis
- Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD 57104, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA.
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3
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Dos Santos Cavaleiro RM, da Silva Arouche T, Martins Tanoue PS, Sá Pereira TS, de Carvalho Junior RN, Paranhos Costa FL, de Andrade Filho TS, Dos Santos Borges R, de Jesus Chaves Neto AM. Hormones Nanofiltration in Carbon Nanotubes and Boron Nitride Nanotubes Using Uniform External Electric Field Through Molecular Dynamics. JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY 2021; 21:5499-5509. [PMID: 33980360 DOI: 10.1166/jnn.2021.19467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hormones are a dangerous group of molecules that can cause harm to humans. This study based on classical molecular dynamics proposes the nanofiltration of wastewater contaminated by hormones from a computer simulation study, in which the water and the hormone were filtered in two single-walled nanotube compositions. The calculations were carried out by changing the intensities of the electric field that acted as a force exerting pressure on the filtration along the nanotube, in the simulation time of 100 ps. The hormones studied were estrone, estradiol, estriol, progesterone, ethinylestradiol, diethylbestrol, and levonorgestrel in carbon nanotubes (CNTs) and boron nitride (BNNTs). The most efficient nanofiltrations were for fields with low intensities in the order of 10-8 au and 10-7 au. The studied nanotubes can be used in membranes for nanofiltration in water treatment plants due to the evanescent field potential caused by the action of the electric field inside. Our data showed that the action of EF in conjunction with the van der Walls forces of the nanotubes is sufficient to generate the attractive potential. Evaluating the transport of water molecules in CNTs and BNNTs, under the influence of the electric field, a sequence of simulations with the same boundary conditions was carried out, seeking to know the percentage of water molecules filtered in the nanotubes.
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Affiliation(s)
| | - Tiago da Silva Arouche
- Laboratory for Preparation and Computing of Nanomaterials (LPCN), Federal University of Pará, 66075-110, Belém, PA, Brazil
| | - Phelipe Seiichi Martins Tanoue
- Laboratory for Preparation and Computing of Nanomaterials (LPCN), Federal University of Pará, 66075-110, Belém, PA, Brazil
| | - Tais Souza Sá Pereira
- Laboratory for Preparation and Computing of Nanomaterials (LPCN), Federal University of Pará, 66075-110, Belém, PA, Brazil
| | | | - Fabio Luiz Paranhos Costa
- Federal University of Goiás, Campus Jataí. Rodovia BR-364, Setor Francisco Antônio, 75801615 - Jataí, GO - Brazil
| | - Tarciso Silva de Andrade Filho
- Federal University of the South and Southeast of Pará, Campus de Marabá. FL 17, QD 04, LT Especial Nova Marabá 68505080 - Maraba, PA - Brazil
| | - Rosivaldo Dos Santos Borges
- Federal University of Pará, Department of Pharmacy. Rua Augusto Correa, SN Pharmaceutical Chemistry Laboratory Guarna 66075-110 - Belem, PA - Brazil
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4
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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5
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Smith P, Lorenz CD. LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations. J Chem Theory Comput 2021; 17:5907-5919. [PMID: 34450002 DOI: 10.1021/acs.jctc.1c00447] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations are now widely used to study emergent phenomena in lipid membranes with complex compositions. Here, we present LiPyphilic-a fast, fully tested, and easy-to-install Python package for analyzing such simulations. Analysis tools in LiPyphilic include the identification of cholesterol flip-flop events, the classification of local lipid environments, and the degree of interleaflet registration. LiPyphilic is both force field- and resolution-agnostic, and by using the powerful atom selection language of MDAnalysis, it can handle membranes with highly complex compositions. LiPyphilic also offers two on-the-fly trajectory transformations to (i) fix membranes split across periodic boundaries and (ii) perform nojump coordinate unwrapping. Our implementation of nojump unwrapping accounts for fluctuations in the box volume under the NPT ensemble-an issue that most current implementations have overlooked. The full documentation of LiPyphilic, including installation instructions and links to interactive online tutorials, is available at https://lipyphilic.readthedocs.io/en/latest.
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Affiliation(s)
- Paul Smith
- Department of Physics, King's College London, London WC2R 2LS, U.K
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6
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Interfacial hydration determines orientational and functional dimorphism of sterol-derived Raman tags in lipid-coated nanoparticles. Proc Natl Acad Sci U S A 2021; 118:2105913118. [PMID: 34389679 DOI: 10.1073/pnas.2105913118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Lipid-coated noble metal nanoparticles (L-NPs) combine the biomimetic surface properties of a self-assembled lipid membrane with the plasmonic properties of a nanoparticle (NP) core. In this work, we investigate derivatives of cholesterol, which can be found in high concentrations in biological membranes, and other terpenoids, as tunable, synthetic platforms to functionalize L-NPs. Side chains of different length and polarity, with a terminal alkyne group as Raman label, are introduced into cholesterol and betulin frameworks. The synthesized tags are shown to coexist in two conformations in the lipid layer of the L-NPs, identified as "head-out" and "head-in" orientations, whose relative ratio is determined by their interactions with the lipid-water hydrogen-bonding network. The orientational dimorphism of the tags introduces orthogonal functionalities into the NP surface for selective targeting and plasmon-enhanced Raman sensing, which is utilized for the identification and Raman imaging of epidermal growth factor receptor-overexpressing cancer cells.
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7
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Shen H, Wu Z, Zhao K, Yang H, Deng M, Wen S. Effect of Cholesterol and 6-Ketocholestanol on Membrane Dipole Potential and Sterol Flip-Flop Motion in Bilayer Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11232-11241. [PMID: 31373497 DOI: 10.1021/acs.langmuir.9b01802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A variety of experimental and theoretical approaches have been employed to investigate the sterol flip-flop motion in lipid bilayer membranes. However, the sterol effect on the dipole potential of lipid bilayer membranes is less well studied and the influence of dipole potential on sterol flip-flop motion in lipid bilayer membranes is less well understood. In our previous works, we have demonstrated the performance of our coarse-grained (CG) model in the computation of the dipole potential. In this work, five 30 μs CG simulations of dimyristoylphosphatidylcholine (DMPC) bilayers were carried out at different sterol concentrations (in a range from 10 to 50% mole fraction). Then, a comparison was made between the effects of cholesterol (CHOL) and 6-ketocholestanol (6-KC) on the dipole potential of DMPC lipid bilayers as well as the sterol flip-flop motion. Our CG simulations show that the membrane dipole potential is impacted more significantly by 6-KC than by CHOL. This finding is consistent with recent experimental studies. Meanwhile, our work suggests that the sterol-sterol interactions (in particular, electrostatic interactions) should be critical to the formation of sterol-sterol clusters, which would hinder the sterol flip-flop motion inside the lipid bilayers. This is in support of the recent experimental study on the sterol transportation in lipid bilayer membranes.
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Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology , Guizhou Education University , No. 115, Gaoxin Road , Guiyang , Guizhou 550018 , P. R. China
- School of Information , Guizhou University of Finance and Economics , University City of Huaxi District, Guiyang , Guizhou 550025 , P. R. China
| | - Zhenhua Wu
- School of Information , Guizhou University of Finance and Economics , University City of Huaxi District, Guiyang , Guizhou 550025 , P. R. China
| | - Kun Zhao
- School of Information , Guizhou University of Finance and Economics , University City of Huaxi District, Guiyang , Guizhou 550025 , P. R. China
| | - Hengxiu Yang
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology , Guizhou Education University , No. 115, Gaoxin Road , Guiyang , Guizhou 550018 , P. R. China
| | - Mingsen Deng
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology , Guizhou Education University , No. 115, Gaoxin Road , Guiyang , Guizhou 550018 , P. R. China
- School of Information , Guizhou University of Finance and Economics , University City of Huaxi District, Guiyang , Guizhou 550025 , P. R. China
| | - Shuiguo Wen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology , Guizhou Education University , No. 115, Gaoxin Road , Guiyang , Guizhou 550018 , P. R. China
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8
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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9
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Manna M, Nieminen T, Vattulainen I. Understanding the Role of Lipids in Signaling Through Atomistic and Multiscale Simulations of Cell Membranes. Annu Rev Biophys 2019; 48:421-439. [DOI: 10.1146/annurev-biophys-052118-115553] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell signaling controls essentially all cellular processes. While it is often assumed that proteins are the key architects coordinating cell signaling, recent studies have shown more and more clearly that lipids are also involved in signaling processes in a number of ways. Lipids do, for instance, act as messengers, modulate membrane receptor conformation and dynamics, and control membrane receptor partitioning. Further, through structural modifications such as oxidation, the functions of lipids as part of signaling processes can be modified. In this context, in this article we discuss the understanding recently revealed by atomistic and coarse-grained computer simulations of nanoscale processes and underlying physicochemical principles related to lipids’ functions in cellular signaling.
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Affiliation(s)
- Moutusi Manna
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462 066, India
| | - Tuomo Nieminen
- Computational Physics Laboratory, Tampere University, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Computational Physics Laboratory, Tampere University, FI-33014 Tampere, Finland
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
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10
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Influence of 7α-hydroxycholesterol on sphingomyelin and sphingomyelin/phosphatidylcholine films - The Langmuir monolayer study complemented with theoretical calculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:861-870. [DOI: 10.1016/j.bbamem.2019.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/29/2022]
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11
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Boonnoy P, Karttunen M, Wong-ekkabut J. Does α-Tocopherol Flip-Flop Help to Protect Membranes Against Oxidation? J Phys Chem B 2018; 122:10362-10370. [DOI: 10.1021/acs.jpcb.8b09064] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Jirasak Wong-ekkabut
- Thailand Center of Excellence in Physics, Commission on Higher Education, Bangkok 10400, Thailand
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12
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Interaction of gabaergic ketones with model membranes: A molecular dynamics and experimental approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1563-1570. [DOI: 10.1016/j.bbamem.2018.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 01/28/2023]
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13
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Tse CH, Comer J, Wang Y, Chipot C. Link between Membrane Composition and Permeability to Drugs. J Chem Theory Comput 2018; 14:2895-2909. [PMID: 29771515 DOI: 10.1021/acs.jctc.8b00272] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Prediction of membrane permeability to small molecules represents an important aspect of drug discovery. First-principles calculations of this quantity require an accurate description of both the thermodynamics and kinetics that underlie translocation of the permeant across the lipid bilayer. In this contribution, the membrane permeability to three drugs, or drug-like molecules, namely, 9-anthroic acid (ANA), 2',3'-dideoxyadenosine (DDA), and hydrocortisone (HYL), are estimated in a pure 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) and in a POPC:cholesterol (2:1) mixture. On the basis of independent 2-5-μs free-energy calculations combined with a time-fractional Smoluchowski determination of the diffusivity, the estimated membrane permeabilities to these chemically diverse permeants fall within an order of magnitude from the experimental values obtained in egg-lecithin bilayers, with the exception of HYL in pure POPC. This exception is particularly interesting because the calculated permeability of the sterol-rich bilayer to HYL, in close agreement with the experimental value, is about 600 times lower than that of the pure POPC bilayer to HYL. In contrast, the permeabilities to ANA and DDA differ by less than a factor of 10 between the pure POPC and POPC:cholesterol bilayers. The unusual behavior of HYL, a large, amphiphilic compound, may be linked with the longer range perturbation of the lipid bilayer it induces, compared to ANA and DDA, suggestive of a possibly different translocation mechanism. We find that the tendency of lower permeabilities of the POPC:cholesterol bilayer relative to those of the pure POPC one is a consequence of increased free-energy barriers. Beyond reporting accurate estimates of the membrane permeability, the present contribution also demonstrates that rigorous free-energy calculations and a fractional-diffusion model are key in revealing the molecular phenomena linking the composition of a membrane to its permeability to drugs.
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Affiliation(s)
- Chi Hang Tse
- Shenzhen Research Institute , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China.,Department of Physics , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine and Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Yi Wang
- Shenzhen Research Institute , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China.,Department of Physics , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
| | - Christophe Chipot
- Laboratoire International Associé Centre, National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7019 , Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex , France.,Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , 405 North Mathews Avenue , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
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14
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Structural design of intrinsically fluorescent oxysterols. Chem Phys Lipids 2018; 212:26-34. [DOI: 10.1016/j.chemphyslip.2017.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/22/2017] [Accepted: 12/25/2017] [Indexed: 12/14/2022]
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15
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Mizuguchi T, Matubayasi N. Free-Energy Analysis of Peptide Binding in Lipid Membrane Using All-Atom Molecular Dynamics Simulation Combined with Theory of Solutions. J Phys Chem B 2018; 122:3219-3229. [DOI: 10.1021/acs.jpcb.7b08241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tomoko Mizuguchi
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- Institute for the Promotion of University Strategy, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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16
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Czuba E, Steliga A, Lietzau G, Kowiański P. Cholesterol as a modifying agent of the neurovascular unit structure and function under physiological and pathological conditions. Metab Brain Dis 2017; 32:935-948. [PMID: 28432486 PMCID: PMC5504126 DOI: 10.1007/s11011-017-0015-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/17/2017] [Indexed: 02/08/2023]
Abstract
The brain, demanding constant level of cholesterol, precisely controls its synthesis and homeostasis. The brain cholesterol pool is almost completely separated from the rest of the body by the functional blood-brain barrier (BBB). Only a part of cholesterol pool can be exchanged with the blood circulation in the form of the oxysterol metabolites such, as 27-hydroxycholesterol (27-OHC) and 24S-hydroxycholesterol (24S-OHC). Not only neurons but also blood vessels and neuroglia, constituting neurovascular unit (NVU), are crucial for the brain cholesterol metabolism and undergo precise regulation by numerous modulators, metabolites and signal molecules. In physiological conditions maintaining the optimal cholesterol concentration is important for the energetic metabolism, composition of cell membranes and myelination. However, a growing body of evidence indicates the consequences of the cholesterol homeostasis dysregulation in several pathophysiological processes. There is a causal relationship between hypercholesterolemia and 1) development of type 2 diabetes due to long-term high-fat diet consumption, 2) significance of the oxidative stress consequences for cerebral amyloid angiopathy and neurodegenerative diseases, 3) insulin resistance on progression of the neurodegenerative brain diseases. In this review, we summarize the current state of knowledge concerning the cholesterol influence upon functioning of the NVU under physiological and pathological conditions.
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Affiliation(s)
- Ewelina Czuba
- Department of Anatomy and Neurobiology, Medical University of Gdańsk, 1 Dębinki Str, 80-211, Gdańsk, Poland.
| | - Aleksandra Steliga
- Department of Health Sciences, Pomeranian University of Słupsk, 64 Bohaterów Westerplatte Str, 76-200, Słupsk, Poland
| | - Grażyna Lietzau
- Department of Anatomy and Neurobiology, Medical University of Gdańsk, 1 Dębinki Str, 80-211, Gdańsk, Poland
| | - Przemysław Kowiański
- Department of Anatomy and Neurobiology, Medical University of Gdańsk, 1 Dębinki Str, 80-211, Gdańsk, Poland
- Department of Health Sciences, Pomeranian University of Słupsk, 64 Bohaterów Westerplatte Str, 76-200, Słupsk, Poland
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17
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Kulig W, Cwiklik L, Jurkiewicz P, Rog T, Vattulainen I. Cholesterol oxidation products and their biological importance. Chem Phys Lipids 2016; 199:144-160. [DOI: 10.1016/j.chemphyslip.2016.03.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/14/2022]
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18
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Hanson SM, Newstead S, Swartz KJ, Sansom MSP. Capsaicin interaction with TRPV1 channels in a lipid bilayer: molecular dynamics simulation. Biophys J 2016; 108:1425-1434. [PMID: 25809255 PMCID: PMC4375533 DOI: 10.1016/j.bpj.2015.02.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 01/29/2015] [Accepted: 02/03/2015] [Indexed: 12/18/2022] Open
Abstract
Transient receptor potential vanilloid subtype 1 (TRPV1) is a heat-sensitive ion channel also involved in pain sensation, and is the receptor for capsaicin, the active ingredient of hot chili peppers. The recent structures of TRPV1 revealed putative ligand density within the S1 to S4 voltage-sensor-like domain of the protein. However, questions remain regarding the dynamic role of the lipid bilayer in ligand binding to TRPV1. Molecular dynamics simulations were used to explore behavior of capsaicin in a 1-palmitoyl-2-oleoyl phosphatidylcholine bilayer and with the target S1–S4 transmembrane helices of TRPV1. Equilibrium simulations reveal a preferred interfacial localization for capsaicin. We also observed a capsaicin molecule flipping from the extracellular to the intracellular leaflet, and subsequently able to access the intracellular TRPV1 binding site. Calculation of the potential of mean force (i.e., free energy profile) of capsaicin along the bilayer normal confirms that it prefers an interfacial localization. The free energy profile indicates that there is a nontrivial but surmountable barrier to the flipping of capsaicin between opposing leaflets of the bilayer. Molecular dynamics of the S1–S4 transmembrane helices of the TRPV1 in a lipid bilayer confirm that Y511, known to be crucial to capsaicin binding, has a distribution along the bilayer normal similar to that of the aromatic group of capsaicin. Simulations were conducted of the TRPV1 S1–S4 transmembrane helices in the presence of capsaicin placed in the aqueous phase, in the lipid, or docked to the protein. No stable interaction between ligand and protein was seen for simulations initiated with capsaicin in the bilayer. However, interactions were seen between TRPV1 and capsaicin starting from the cytosolic aqueous phase, and capsaicin remained stable in the majority of simulations from the docked pose. We discuss the significance of capsaicin flipping from the extracellular to the intracellular leaflet and mechanisms of binding site access by capsaicin.
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Affiliation(s)
- Sonya M Hanson
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York; Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Kenton J Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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19
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Zhang L, Bennett WFD, Zheng T, Ouyang PK, Ouyang X, Qiu X, Luo A, Karttunen M, Chen P. Effect of Cholesterol on Cellular Uptake of Cancer Drugs Pirarubicin and Ellipticine. J Phys Chem B 2016; 120:3148-56. [PMID: 26937690 DOI: 10.1021/acs.jpcb.5b12337] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Lei Zhang
- Biological
and Pharmaceutical Engineering, Nanjing Technology University, 30 Puzhu Road South, Nanjing, Jiangsu, China, 211816
- Department
of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada, N2L 3G1
| | - W. F. Drew Bennett
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Tao Zheng
- Biological
and Pharmaceutical Engineering, Nanjing Technology University, 30 Puzhu Road South, Nanjing, Jiangsu, China, 211816
| | - Ping-Kai Ouyang
- Biological
and Pharmaceutical Engineering, Nanjing Technology University, 30 Puzhu Road South, Nanjing, Jiangsu, China, 211816
| | - Xinping Ouyang
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, P.R. China, 510640
| | - Xueqing Qiu
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, P.R. China, 510640
| | - Anqi Luo
- Department
of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada, N2L 3G1
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, MetaForum, 5600 MB Eindhoven, The Netherlands
| | - P. Chen
- Biological
and Pharmaceutical Engineering, Nanjing Technology University, 30 Puzhu Road South, Nanjing, Jiangsu, China, 211816
- Department
of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada, N2L 3G1
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20
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Abstract
Work done by Bennett et al. [ Nature 2002 , 420 , 398 - 401 ] demonstrated that Ca(2+) ions can be actively transported through a lipid bilayer membrane by an artificial photosynthetic machine. However, details of the pump process, such as the oxidation state of the shuttle molecule and stoichiometry of the shuttle-ion complex, are not fully understood, which hinders the development of ion pumps of this type with higher efficiency. In this study, we combine all atom molecular dynamics simulations and quantum mechanics calculations to estimate the time scale of the shuttle-ion complex diffusion process and charge transfer step. We find that the process of shuttle-ion complex diffusion across the lipid bilayer membrane is the rate-limiting step, with a time scale of seconds to minutes. Other processes such as charge transfer between the redox reaction center and the shuttle molecule have picoseconds time scales. We also show that a shuttle-ion complex with 2:1 stoichiometry ratio has a lower energy barrier across the lipid membrane than other choices of complexes. The calculations show that the Ca(2+) ion is likely to be shuttled by a semiquinone type of shuttle molecule as this has the lowest free energy barrier across the lipid bilayer membrane, the fewest electrons transferred in the redox cycle, and it does not generate (or require) proton flow. Estimates of ion flow rates are consistent with measured values.
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Affiliation(s)
- Cheng-Tsung Lai
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Yu Zhang
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Center for Bioinspired Energy Science, Northwestern University , Chicago, Illinois 60611, United States
| | - George C Schatz
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Center for Bioinspired Energy Science, Northwestern University , Chicago, Illinois 60611, United States
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21
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Nåbo LJ, List NH, Witzke S, Wüstner D, Khandelia H, Kongsted J. Design of new fluorescent cholesterol and ergosterol analogs: Insights from theory. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2188-99. [DOI: 10.1016/j.bbamem.2015.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/24/2015] [Accepted: 04/29/2015] [Indexed: 12/23/2022]
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22
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Wüstner D, Solanko K. How cholesterol interacts with proteins and lipids during its intracellular transport. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1908-26. [DOI: 10.1016/j.bbamem.2015.05.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 04/14/2015] [Accepted: 05/13/2015] [Indexed: 12/13/2022]
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23
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Zhu D, Bungart BL, Yang X, Zhumadilov Z, Lee JCM, Askarova S. Role of membrane biophysics in Alzheimer's-related cell pathways. Front Neurosci 2015; 9:186. [PMID: 26074758 PMCID: PMC4444756 DOI: 10.3389/fnins.2015.00186] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/11/2015] [Indexed: 01/04/2023] Open
Abstract
Cellular membrane alterations are commonly observed in many diseases, including Alzheimer's disease (AD). Membrane biophysical properties, such as membrane molecular order, membrane fluidity, organization of lipid rafts, and adhesion between membrane and cytoskeleton, play an important role in various cellular activities and functions. While membrane biophysics impacts a broad range of cellular pathways, this review addresses the role of membrane biophysics in amyloid-β peptide aggregation, Aβ-induced oxidative pathways, amyloid precursor protein processing, and cerebral endothelial functions in AD. Understanding the mechanism(s) underlying the effects of cell membrane properties on cellular processes should shed light on the development of new preventive and therapeutic strategies for this devastating disease.
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Affiliation(s)
- Donghui Zhu
- Department of Chemical, Biological and Bioengineering, North Carolina A&T State UniversityGreensboro, NC, USA
| | - Brittani L. Bungart
- Indiana University School of Medicine Medical Scientist Training Program, Indiana University School of MedicineIndianapolis, IN, USA
| | - Xiaoguang Yang
- Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of GothenburgGothenburg, Sweden
- The Hope Center for Neurological Disorders and Department of Neurology, Washington University School of MedicineSt. Louis, MO, USA
| | - Zhaxybay Zhumadilov
- Department of Bioengineering and Regenerative Medicine, Center for Life Sciences, Nazarbayev UniversityAstana, Kazakhstan
| | - James C-M. Lee
- Department of Bioengineering, University of Illinois at ChicagoChicago, IL, USA
| | - Sholpan Askarova
- Department of Bioengineering and Regenerative Medicine, Center for Life Sciences, Nazarbayev UniversityAstana, Kazakhstan
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24
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Mendanha SA, Alonso A. Effects of terpenes on fluidity and lipid extraction in phospholipid membranes. Biophys Chem 2015; 198:45-54. [PMID: 25687600 DOI: 10.1016/j.bpc.2015.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 12/16/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy was used in a detailed study of the interactions of several terpenes with DPPC membranes. EPR spectra of a spin-label lipid allowed the identification of two well-resolved spectral components at temperatures below and above the main phase transition of the lipid bilayer. Terpenes caused only slight mobility increases in each of these spectral components; however, they substantially increased the population of the more mobile component. In addition, the terpenes reduced the temperature of the main phase transition by more than 8 °C and caused the extraction of the spin-labeled lipid. Nerolidol, which had the highest octanol-water partition coefficient, generated the highest amount of spin label extraction. Acting as spacers, terpenes should cause major reorganization in cell membranes, leading to an increase in the overall molecular dynamics of the membrane. At higher concentrations, terpenes may cause lipid extraction and thus leakage of the cytoplasmic content.
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Affiliation(s)
| | - Antonio Alonso
- Instituto de Física, Universidade Federal de Goiás, Goiânia, GO, Brazil.
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25
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Róg T, Vattulainen I. Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes? Chem Phys Lipids 2014; 184:82-104. [PMID: 25444976 DOI: 10.1016/j.chemphyslip.2014.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
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26
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Wei C, Pohorille A. Flip-flop of oleic acid in a phospholipid membrane: rate and mechanism. J Phys Chem B 2014; 118:12919-26. [PMID: 25319959 DOI: 10.1021/jp508163e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Flip-flop of protonated oleic acid molecules dissolved at two different concentrations in membranes made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine is studied with the aid of molecular dynamics simulations at a time scale of several microseconds. Direct, single-molecule flip-flop events are observed at this time scale, and the flip-flop rate is estimated at 0.2-0.3 μs(-1). As oleic acid molecules move toward the center of the bilayer during flip-flop, they undergo gradual, correlated translational, and rotational motion. Rare, double-flipping events of two hydrogen-bonded oleic acid molecules are also observed. A two-dimensional free energy surface is obtained for the translational and rotational degree of freedom of the oleic acid molecule, and the minimum energy path on this surface is determined. A barrier to flip-flop of ~4.2 kcal/mol is found at the center of the bilayer. A two-dimensional diffusion model is found to provide a good description of the flip-flop process. The fast flip-flop rate lends support to the proposal that fatty acids permeate membranes without assistance of transport proteins. It also suggests that desorption rather than flip-flop is the rate-limiting step in fatty acid transport through membranes. The relation of flip-flop rates to the evolution of ancestral cellular systems is discussed.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center , Mail Stop 229-1, Moffett Field, California 94035, United States
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27
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Arai N, Akimoto T, Yamamoto E, Yasui M, Yasuoka K. Poisson property of the occurrence of flip-flops in a model membrane. J Chem Phys 2014; 140:064901. [PMID: 24527934 DOI: 10.1063/1.4863330] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
How do lipid molecules in membranes perform a flip-flop? The flip-flops of lipid molecules play a crucial role in the formation and flexibility of membranes. However, little has been determined about the behavior of flip-flops, either experimentally, or in molecular dynamics simulations. Here, we provide numerical results of the flip-flops of model lipid molecules in a model membrane and investigate the statistical properties, using millisecond-order coarse-grained molecular simulations (dissipative particle dynamics). We find that there are three different ways of flip-flops, which can be clearly characterized by their paths on the free energy surface. Furthermore, we found that the probability of the number of the flip-flops is well fitted by the Poisson distribution, and the probability density function for the inter-occurrence times of flip-flops coincides with that of the forward recurrence times. These results indicate that the occurrence of flip-flops is a Poisson process, which will play an important role in the flexibilities of membranes.
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Affiliation(s)
- Noriyoshi Arai
- Department of Mechanical Engineering and Intelligent Systems, University of Electro-Communications, Tokyo 182-8585, Japan
| | - Takuma Akimoto
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
| | - Eiji Yamamoto
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
| | - Masato Yasui
- Department of Pharmacology, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
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28
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Benesch MG, Lewis RN, Mannock DA, McElhaney RN. A DSC and FTIR spectroscopic study of the effects of the epimeric 4,6-cholestadien-3-ols and 4,6-cholestadien-3-one on the thermotropic phase behaviour and organization of dipalmitoylphosphatidylcholine bilayer membranes. Chem Phys Lipids 2014; 183:142-58. [DOI: 10.1016/j.chemphyslip.2014.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/27/2014] [Accepted: 06/10/2014] [Indexed: 10/25/2022]
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29
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Neuvonen M, Manna M, Mokkila S, Javanainen M, Rog T, Liu Z, Bittman R, Vattulainen I, Ikonen E. Enzymatic oxidation of cholesterol: properties and functional effects of cholestenone in cell membranes. PLoS One 2014; 9:e103743. [PMID: 25157633 PMCID: PMC4144813 DOI: 10.1371/journal.pone.0103743] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/01/2014] [Indexed: 11/19/2022] Open
Abstract
Bacterial cholesterol oxidase is commonly used as an experimental tool to reduce cellular cholesterol content. That the treatment also generates the poorly degradable metabolite 4-cholesten-3-one (cholestenone) has received less attention. Here, we investigated the membrane partitioning of cholestenone using simulations and cell biological experiments and assessed the functional effects of cholestenone in human cells. Atomistic simulations predicted that cholestenone reduces membrane order, undergoes faster flip-flop and desorbs more readily from membranes than cholesterol. In primary human fibroblasts, cholestenone was released from membranes to physiological extracellular acceptors more avidly than cholesterol, but without acceptors it remained in cells over a day. To address the functional effects of cholestenone, we studied fibroblast migration during wound healing. When cells were either cholesterol oxidase treated or part of cellular cholesterol was exchanged for cholestenone with cyclodextrin, cell migration during 22 h was markedly inhibited. Instead, when a similar fraction of cholesterol was removed using cyclodextrin, cells replenished their cholesterol content in 3 h and migrated similarly to control cells. Thus, cholesterol oxidation produces long-term functional effects in cells and these are in part due to the generated membrane active cholestenone.
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Affiliation(s)
- Maarit Neuvonen
- Institute of Biomedicine, Anatomy, University of Helsinki, Helsinki, Finland
| | - Moutusi Manna
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Sini Mokkila
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Matti Javanainen
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Tomasz Rog
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Zheng Liu
- Department of Chemistry and Biochemistry, Queens College, The City University of New York, Flushing, NY, United States of America
| | - Robert Bittman
- Department of Chemistry and Biochemistry, Queens College, The City University of New York, Flushing, NY, United States of America
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland
- MEMPHYS – Center of Biomembrane Physics, University of Southern Denmark, Odense, Denmark
| | - Elina Ikonen
- Institute of Biomedicine, Anatomy, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
- * E-mail:
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30
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Pourmousa M, Róg T, Mikkeli R, Vattulainen L, Solanko LM, Wüstner D, List NH, Kongsted J, Karttunen M. Dehydroergosterol as an Analogue for Cholesterol: Why It Mimics Cholesterol So Well—or Does It? J Phys Chem B 2014; 118:7345-57. [DOI: 10.1021/jp406883k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Mohsen Pourmousa
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 3, 33720 Tampere, Finland
| | - Tomasz Róg
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 3, 33720 Tampere, Finland
| | - Risto Mikkeli
- Department
of Applied Physics, Aalto University, P.O. Box 11100, FI-00076 Aalto, Finland
| | - llpo Vattulainen
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 3, 33720 Tampere, Finland
- MEMPHYS−Center
of Biomembrane Physics, Physics Department, University of Southern Denmark, Odense, Denmark
| | | | | | | | | | - Mikko Karttunen
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
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31
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Cellular membrane fluidity in amyloid precursor protein processing. Mol Neurobiol 2014; 50:119-29. [PMID: 24553856 DOI: 10.1007/s12035-014-8652-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/23/2014] [Indexed: 12/20/2022]
Abstract
The senile plaque is a pathologic hallmark of Alzheimer's disease (AD). Amyloid-β peptide (Aβ), the main constituent of senile plaques, is neurotoxic especially in its oligomeric form. Aβ is derived from the sequential cleavage of amyloid precursor protein (APP) by β- and γ-secretases in the amyloidogenic pathway. Alternatively, APP can be cleaved by α-secretases within the Aβ domain to produce neurotrophic and neuroprotective α-secretase-cleaved soluble APP (sAPPα) in the nonamyloidogenic pathway. Since APP and α-, β-, and γ-secretases are membrane proteins, APP processing should be highly dependent on the membrane composition and the biophysical properties of cellular membrane. In this review, we discuss the role of the biophysical properties of cellular membrane in APP processing, especially the effects of phospholipases A(2) (PLA(2)s), fatty acids, cholesterol, and Aβ on membrane fluidity in relation to their effects on APP processing.
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32
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Choi Y, Attwood SJ, Hoopes MI, Drolle E, Karttunen M, Leonenko Z. Melatonin directly interacts with cholesterol and alleviates cholesterol effects in dipalmitoylphosphatidylcholine monolayers. SOFT MATTER 2014; 10:206-213. [PMID: 24651707 DOI: 10.1039/c3sm52064a] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Melatonin is a pineal hormone that has been shown to have protective effects in several diseases that are associated with cholesterol dysregulation, including cardiovascular disease, Alzheimer's disease, and certain types of cancers. Cholesterol is a major membrane constituent with both a structural and functional influence. It is also known that melatonin readily partitions into cellular membranes. We investigated the effects of melatonin and cholesterol on the structure and physical properties of a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) monolayer as a simple membrane model using the Langmuir-Blodgett (L-B) monolayer technique and molecular dynamics (MD) simulations. We report that melatonin increases the area per lipid and elastic compressibility of the DPPC monolayer in a concentration dependent manner, while cholesterol has the opposite effect. When both melatonin and cholesterol were present in the monolayer, the compression isotherms showed normalization of the area per molecule towards that of the pure DPPC monolayer, thus indicating that melatonin counteracts and alleviates cholesterol's effects. Atomistic MD simulations of melatonin enriched DPPC systems correlate with our experimental findings and illustrate the structural effects of both cholesterol and melatonin. Our results suggest that melatonin is able to lessen the influence of cholesterol through two different mechanisms. Firstly, we have shown that melatonin has a fluidizing effect on monolayers comprising only lipid molecules. Secondly, we also observe that melatonin interacts directly with cholesterol. Our findings suggest a direct nonspecific interaction of melatonin may be a mechanism involved in reducing cholesterol associated membrane effects, thus suggesting the existence of a new mechanism of melatonin's action. This may have important biological relevance in addition to the well-known anti-oxidative and receptor binding effects.
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Affiliation(s)
- Youngjik Choi
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, CanadaN2L 3G1.
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33
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A DSC and FTIR spectroscopic study of the effects of the epimeric 4-cholesten-3-ols and 4-cholesten-3-one on the thermotropic phase behaviour and organization of dipalmitoylphosphatidylcholine bilayer membranes: Comparison with their 5-cholesten analogues. Chem Phys Lipids 2014; 177:71-90. [DOI: 10.1016/j.chemphyslip.2013.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/20/2013] [Accepted: 11/21/2013] [Indexed: 01/08/2023]
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34
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Robalo JR, Ramalho JPP, Loura LMS. NBD-Labeled Cholesterol Analogues in Phospholipid Bilayers: Insights from Molecular Dynamics. J Phys Chem B 2013; 117:13731-42. [DOI: 10.1021/jp406135a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- João R. Robalo
- Departamento
de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
- Centro
de Química de Évora, Universidade de Évora, Rua
Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - J. P. Prates Ramalho
- Departamento
de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
- Centro
de Química de Évora, Universidade de Évora, Rua
Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - Luís M. S. Loura
- Faculdade
de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Centro
de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
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35
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Kopeć W, Telenius J, Khandelia H. Molecular dynamics simulations of the interactions of medicinal plant extracts and drugs with lipid bilayer membranes. FEBS J 2013; 280:2785-805. [DOI: 10.1111/febs.12286] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/10/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Wojciech Kopeć
- MEMPHYS - Center for Biomembrane Physics; University of Southern Denmark; Odense; Denmark
| | - Jelena Telenius
- MEMPHYS - Center for Biomembrane Physics; University of Southern Denmark; Odense; Denmark
| | - Himanshu Khandelia
- MEMPHYS - Center for Biomembrane Physics; University of Southern Denmark; Odense; Denmark
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36
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Hughes ZE, Malajczuk CJ, Mancera RL. The Effects of Cryosolvents on DOPC−β-Sitosterol Bilayers Determined from Molecular Dynamics Simulations. J Phys Chem B 2013; 117:3362-75. [DOI: 10.1021/jp400975y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Zak E. Hughes
- Western Australian Biomedical
Research Institute, Curtin
Health Innovation Research Institute, School of Biomedical Sciences, Curtin University, P.O. Box U1987, Perth WA, 6845,
Australia
| | - Chris J. Malajczuk
- Western Australian Biomedical
Research Institute, Curtin
Health Innovation Research Institute, School of Biomedical Sciences, Curtin University, P.O. Box U1987, Perth WA, 6845,
Australia
| | - Ricardo L. Mancera
- Western Australian Biomedical
Research Institute, Curtin
Health Innovation Research Institute, School of Biomedical Sciences, Curtin University, P.O. Box U1987, Perth WA, 6845,
Australia
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37
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Polley A, Vemparala S. Partitioning of ethanol in multi-component membranes: Effects on membrane structure. Chem Phys Lipids 2013; 166:1-11. [DOI: 10.1016/j.chemphyslip.2012.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 11/23/2012] [Accepted: 11/24/2012] [Indexed: 12/12/2022]
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38
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Dindia L, Murray J, Faught E, Davis TL, Leonenko Z, Vijayan MM. Novel nongenomic signaling by glucocorticoid may involve changes to liver membrane order in rainbow trout. PLoS One 2012; 7:e46859. [PMID: 23056491 PMCID: PMC3466178 DOI: 10.1371/journal.pone.0046859] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/06/2012] [Indexed: 11/21/2022] Open
Abstract
Stress-induced glucocorticoid elevation is a highly conserved response among vertebrates. This facilitates stress adaptation and the mode of action involves activation of the intracellular glucocorticoid receptor leading to the modulation of target gene expression. However, this genomic effect is slow acting and, therefore, a role for glucocorticoid in the rapid response to stress is unclear. Here we show that stress levels of cortisol, the primary glucocorticoid in teleosts, rapidly fluidizes rainbow trout (Oncorhynchus mykiss) liver plasma membranes in vitro. This involved incorporation of the steroid into the lipid domains, as cortisol coupled to a membrane impermeable peptide moiety, did not affect membrane order. Studies confirmed that cortisol, but not sex steroids, increases liver plasma membrane fluidity. Atomic force microscopy revealed cortisol-mediated changes to membrane surface topography and viscoelasticity confirming changes to membrane order. Treating trout hepatocytes with stress levels of cortisol led to the modulation of cell signaling pathways, including the phosphorylation status of putative PKA, PKC and AKT substrate proteins within 10 minutes. The phosphorylation by protein kinases in the presence of cortisol was consistent with that seen with benzyl alcohol, a known membrane fluidizer. Our results suggest that biophysical changes to plasma membrane properties, triggered by stressor-induced glucocorticoid elevation, act as a nonspecific stress response and may rapidly modulate acute stress-signaling pathways.
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Affiliation(s)
- Laura Dindia
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Josh Murray
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Erin Faught
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Tracy L. Davis
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Zoya Leonenko
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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39
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Parisio G, Sperotto MM, Ferrarini A. Flip-Flop of Steroids in Phospholipid Bilayers: Effects of the Chemical Structure on Transbilayer Diffusion. J Am Chem Soc 2012; 134:12198-208. [DOI: 10.1021/ja304007t] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Giulia Parisio
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova,
Italy
| | - Maria Maddalena Sperotto
- Center for Biological
Sequence
Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kgs. Lyngby,
Denmark
| | - Alberta Ferrarini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova,
Italy
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40
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41
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Hąc-Wydro K, Flasiński M, Broniatowski M, Dynarowicz-Łątka P, Majewski J. Properties of β-sitostanol/DPPC monolayers studied with Grazing Incidence X-ray Diffraction (GIXD) and Brewster Angle Microscopy. J Colloid Interface Sci 2011; 364:133-9. [PMID: 21903220 DOI: 10.1016/j.jcis.2011.08.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 08/11/2011] [Accepted: 08/12/2011] [Indexed: 10/17/2022]
Abstract
Although the influence of structurally modified sterols on artificial membranes has been intensively investigated, studies on the properties of stanols, which are saturated analogs of sterols, are very rare. Therefore, we have performed Grazing Incidence X-ray Diffraction (GIXD) experiments aimed at studying in-plane organization of a plant stanol-β-sitostanol monolayer and its mixtures with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine - DPPC at the air/water interface. The collected GIXD data, resulting in-plane parameters and BAM images provide information on molecular organization and in-plane ordering of the investigated films. It was found that the lateral organization of β-sitostanol/DPPC monolayers depends on their composition. The oblique structure of the in-plane lattice of tilted hydrophobic region of molecules, found for DPPC film, is maintained at 10 mol% of stanol in the system. However, at 30 and 90 mol% of stanol in the mixture, the arrangement of molecules is hexagonal and they are oriented perpendicularly to the interface. With the addition of stanol the extend of the in-plane order of the monolayers decreases. Moreover, in mixtures the ordered domains consist of both monolayer's components. Additionally, β-sitostanol film is of similar in-plane organization as the corresponding sterol monolayer (β-sitosterol) and stanol induces condensing effect on DPPC.
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Affiliation(s)
- Katarzyna Hąc-Wydro
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland.
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42
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The influence of plant stanol on phospholipids monolayers – The effect of phospholipid structure. J Colloid Interface Sci 2011; 360:681-9. [DOI: 10.1016/j.jcis.2011.04.089] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Revised: 04/20/2011] [Accepted: 04/21/2011] [Indexed: 11/18/2022]
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43
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Askarova S, Yang X, Lee JCM. Impacts of membrane biophysics in Alzheimer's disease: from amyloid precursor protein processing to aβ Peptide-induced membrane changes. Int J Alzheimers Dis 2011; 2011:134971. [PMID: 21547213 PMCID: PMC3087431 DOI: 10.4061/2011/134971] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/30/2010] [Accepted: 01/21/2011] [Indexed: 12/11/2022] Open
Abstract
An increasing amount of evidence supports the notion that cytotoxic effects of amyloid-β peptide (Aβ), the main constituent of senile plaques in Alzheimer's disease (AD), are strongly associated with its ability to interact with membranes of neurons and other cerebral cells. Aβ is derived from amyloidogenic cleavage of amyloid precursor protein (AβPP) by β- and γ-secretase. In the nonamyloidogenic pathway, AβPP is cleaved by α-secretases. These two pathways compete with each other, and enhancing the non-amyloidogenic pathway has been suggested as a potential pharmacological approach for the treatment of AD. Since AβPP, α-, β-, and γ-secretases are membrane-associated proteins, AβPP processing and Aβ production can be affected by the membrane composition and properties. There is evidence that membrane composition and properties, in turn, play a critical role in Aβ cytotoxicity associated with its conformational changes and aggregation into oligomers and fibrils. Understanding the mechanisms leading to changes in a membrane's biophysical properties and how they affect AβPP processing and Aβ toxicity should prove to provide new therapeutic strategies for prevention and treatment of AD.
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Affiliation(s)
- Sholpan Askarova
- Department of Biological Engineering, University of Missouri, Columbia, MO 65211, USA
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44
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Eriksson ESE, Eriksson LA. The Influence of Cholesterol on the Properties and Permeability of Hypericin Derivatives in Lipid Membranes. J Chem Theory Comput 2011; 7:560-74. [DOI: 10.1021/ct100528u] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - Leif A. Eriksson
- School of Chemistry, National University of Ireland—Galway, Galway, Ireland
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45
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Mannock DA, Lewis RN, McMullen TP, McElhaney RN. The effect of variations in phospholipid and sterol structure on the nature of lipid–sterol interactions in lipid bilayer model membranes. Chem Phys Lipids 2010; 163:403-48. [DOI: 10.1016/j.chemphyslip.2010.03.011] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 03/13/2010] [Accepted: 03/27/2010] [Indexed: 01/30/2023]
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46
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Dai J, Alwarawrah M, Huang J. Instability of cholesterol clusters in lipid bilayers and the cholesterol's Umbrella effect. J Phys Chem B 2010; 114:840-8. [PMID: 20041657 DOI: 10.1021/jp909061h] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The instability of cholesterol clusters and the Umbrella effect of cholesterol in dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC) lipid bilayers were investigated via atomistic molecular dynamics (MD) simulation. Cholesterol clusters in phosphatidylcholine (PC) bilayers are found to be very unstable and to readily disperse into cholesterol monomers. This instability results from the difficulty of the bilayer system in preventing water exposure to cholesterol's bulky hydrophobic bodies in a cluster. The system responds to artificially arranged cholesterol clusters in several interesting manners: (i) cholesterol clusters quickly form a "frustum" shape to reduce water penetration between cholesterol headgroups; (ii) many clusters bury themselves deeper into the bilayer interior, causing bilayer deformation; and (iii) cholesterol fluctuates rapidly, both laterally and vertically, to escape clusters. These fluctuations result in the disintegration of clusters and, in one incidence, a highly unusual flip-flop event of cholesterol across the DOPC bilayer. Our results show that cholesterols have a strong tendency to avoid forming clusters in lipid bilayers and that the fundamental cholesterol-cholesterol interaction is unfavorable. Furthermore, the radial distribution functions of cholesterol hydroxyl oxygen to various headgroup atoms of PC reveal that the PC headgroups surrounding cholesterol have a clear tendency to reorient and to extend toward cholesterol. This reorientation has a layered structure that extends 2-3 nm from the cholesterol molecule. This study demonstrates that the Umbrella hypothesis is valid in both saturated and unsaturated lipid bilayers.
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Affiliation(s)
- Jian Dai
- Department of Physics, Texas Tech University, Lubbock, Texas 79409, USA
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47
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Liu JP, Tang Y, Zhou S, Toh BH, McLean C, Li H. Cholesterol involvement in the pathogenesis of neurodegenerative diseases. Mol Cell Neurosci 2010; 43:33-42. [DOI: 10.1016/j.mcn.2009.07.013] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 07/29/2009] [Accepted: 07/29/2009] [Indexed: 11/27/2022] Open
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48
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Perlmutter JD, Sachs JN. Inhibiting Lateral Domain Formation in Lipid Bilayers: Simulations of Alternative Steroid Headgroup Chemistries. J Am Chem Soc 2009; 131:16362-3. [DOI: 10.1021/ja9079258] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jason D. Perlmutter
- Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jonathan N. Sachs
- Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455
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49
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Petruk AA, Marti MA, Álvarez RMS. Thyroid Hormone Interactions with DMPC Bilayers. A Molecular Dynamics Study. J Phys Chem B 2009; 113:13357-64. [DOI: 10.1021/jp9055522] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ariel A. Petruk
- Instituto Superior de investigaciones Biológicas (CONICET-UNT), Chacabuco 461, San Miguel de Tucumán, Tucumán, T4000CAN, Argentina, Departamento de Química Biológica y Departamento de Química Inorgánica, Analítica y Química Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, and Instituto de Química Física, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San
| | - Marcelo A. Marti
- Instituto Superior de investigaciones Biológicas (CONICET-UNT), Chacabuco 461, San Miguel de Tucumán, Tucumán, T4000CAN, Argentina, Departamento de Química Biológica y Departamento de Química Inorgánica, Analítica y Química Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, and Instituto de Química Física, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San
| | - Rosa María S. Álvarez
- Instituto Superior de investigaciones Biológicas (CONICET-UNT), Chacabuco 461, San Miguel de Tucumán, Tucumán, T4000CAN, Argentina, Departamento de Química Biológica y Departamento de Química Inorgánica, Analítica y Química Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, and Instituto de Química Física, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San
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50
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Bennett WFD, MacCallum JL, Hinner MJ, Marrink SJ, Tieleman DP. Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments. J Am Chem Soc 2009; 131:12714-20. [DOI: 10.1021/ja903529f] [Citation(s) in RCA: 228] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- W. F. Drew Bennett
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada, Institute of Chemical Sciences and Engineering, Laboratory of Protein Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Justin L. MacCallum
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada, Institute of Chemical Sciences and Engineering, Laboratory of Protein Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marlon J. Hinner
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada, Institute of Chemical Sciences and Engineering, Laboratory of Protein Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Siewert J. Marrink
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada, Institute of Chemical Sciences and Engineering, Laboratory of Protein Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada, Institute of Chemical Sciences and Engineering, Laboratory of Protein Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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