1
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Muñoz-Gacitúa D, Monroy-Cárdenas M, Araya-Maturana R, Weiss-López B. Characterization of an anionic membrane mimetic with natural phospholipid content and magnetic orienting capabilities. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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2
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Frigini EN, López Cascales JJ, Porasso RD. Influence of Lipid Composition on the Insertion Process of Glyphosate into Membranes: A Thermodynamic Study. J Phys Chem B 2021; 125:184-192. [PMID: 33375787 DOI: 10.1021/acs.jpcb.0c09561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, molecular dynamics simulations were applied to investigate the influence of lipid composition of the model membrane on the insertion of glyphosate (in its charged state, GLYP2-). The profiles of free energy, entropy and enthalpy were obtained through umbrella sampling calculations, for lipid bilayers composed by only 1,2-dipalmitoyl-sn-glycerol-3-phosphocholine (DPPC), only 1,2-dipalmitoyl-sn-glycerol-3-phosphoserine (DPPS) or a symmetric binary mixture of DPPC and DPPS. In general, the location, the values of minima and maxima of the free energy, and the trend of free energy profiles are influenced by the lipid composition of the lipid bilayer. The driving force in the glyphosate insertion process depends on the lipid composition of the membrane model. If the lipid bilayer is composed solely of DPPS or DPPC, GLYP2- insertion is driven by a favorable enthalpic change. However, if the membrane is composed of a mixture of both lipids, this process is driven by a favorable entropic change. In the lipid bilayer containing DPPS, the glyphosate was found to penetrate hydrated and coordinated with Na+ ions, in contrast to the pure zwitterionic lipid bilayer which penetrated only hydrated. This effect is independent of the concentration of sodium ions present in the bulk solution.
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Affiliation(s)
- Ezequiel N Frigini
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Avenue Ejército de los Andes 950, 5700 San Luis, Argentina
| | - J J López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoléculas (BioMac), Área de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Física Matemáticas y Naturales, Universidad Nacional de San Luis, Avenue Ejército de los Andes 950, 5700 San Luis, Argentina
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3
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Zenak S, Sabeur S, López-Cascales J. Study of the insertion of a small symmetric star polymer into different phospholipid bilayers. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Fuster MG, Montalbán MG, Carissimi G, Lima B, Feresin GE, Cano M, Giner-Casares JJ, López-Cascales JJ, Enriz RD, Víllora G. Antibacterial Effect of Chitosan-Gold Nanoparticles and Computational Modeling of the Interaction between Chitosan and a Lipid Bilayer Model. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2340. [PMID: 33255714 PMCID: PMC7761461 DOI: 10.3390/nano10122340] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/08/2020] [Accepted: 11/23/2020] [Indexed: 01/14/2023]
Abstract
Pathogenic bacteria have the ability to develop antibiotic resistance mechanisms. Their action consists mainly in the production of bacterial enzymes that inactivate antibiotics or the appearance of modifications that prevent the arrival of the drug at the target point or the alteration of the target point itself, becoming a growing problem for health systems. Chitosan-gold nanoparticles (Cs-AuNPs) have been shown as effective bactericidal materials avoiding damage to human cells. In this work, Cs-AuNPs were synthesized using chitosan as the reducing agent, and a systematic analysis of the influence of the synthesis parameters on the size and zeta potential of the Cs-AuNPs and their UV-vis spectra was carried out. We used a simulation model to characterize the interaction of chitosan with bacterial membranes, using a symmetric charged bilayer and two different chitosan models with different degrees of the chitosan amine protonation as a function of pH, with the aim to elucidate the antibacterial mechanism involving the cell wall disruption. The Cs-AuNP antibacterial activity was evaluated to check the simulation model.
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Grants
- CTQ2017-87708-R Ministerio de Economía, Industria y Competitividad, Gobierno de España
- CTQ2017-83961-R Ministerio de Economía, Industria y Competitividad, Gobierno de España
- CTQ2017-92264-EXP Ministerio de Economía, Industria y Competitividad, Gobierno de España
- RyC-2014-14956 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- PRE2018-086441 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- 20977/PI/18 Fundación Séneca
- CONICET-SECITI N°022 Consejo Nacional de Investigaciones Científicas y Técnicas
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Affiliation(s)
- M. G. Fuster
- Chemical Engineering Department, Faculty of Chemistry, University of Murcia, 30100 Murcia, Spain; (M.G.F.); (G.C.); (G.V.)
| | - M. G. Montalbán
- Chemical Engineering Department, Faculty of Chemistry, University of Murcia, 30100 Murcia, Spain; (M.G.F.); (G.C.); (G.V.)
| | - G. Carissimi
- Chemical Engineering Department, Faculty of Chemistry, University of Murcia, 30100 Murcia, Spain; (M.G.F.); (G.C.); (G.V.)
| | - B. Lima
- Instituto de Biotecnología, Universidad Nacional de San Juan, Av. Libertador General San Martín 1109 (O), San Juan CP 5400, Argentina; (B.L.); (G.E.F.)
- CONICET (Consejo Nacional de Ciencia y Tecnología), CABA, Buenos Aires C1405DJR, Argentina
| | - G. E. Feresin
- Instituto de Biotecnología, Universidad Nacional de San Juan, Av. Libertador General San Martín 1109 (O), San Juan CP 5400, Argentina; (B.L.); (G.E.F.)
- CONICET (Consejo Nacional de Ciencia y Tecnología), CABA, Buenos Aires C1405DJR, Argentina
| | - M. Cano
- Departamento de Química Física y Termodinámica Aplicada, Instituto Universitario de Nanoquímica (IUNAN), Facultad de Ciencias, Universidad de Córdoba, Campus de Rabanales, Ed. Marie Curie, E-14071 Córdoba, Spain; (M.C.); (J.J.G.-C.)
| | - J. J. Giner-Casares
- Departamento de Química Física y Termodinámica Aplicada, Instituto Universitario de Nanoquímica (IUNAN), Facultad de Ciencias, Universidad de Córdoba, Campus de Rabanales, Ed. Marie Curie, E-14071 Córdoba, Spain; (M.C.); (J.J.G.-C.)
| | - J. J. López-Cascales
- Departamento Ingeniería Química y Ambiental, Campus Alfonso XIII, Universidad Politécnica de Cartagena, Aulario C, Cartagena, 30203 Murcia, Spain;
| | - R. D. Enriz
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), CONICET, Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina;
| | - G. Víllora
- Chemical Engineering Department, Faculty of Chemistry, University of Murcia, 30100 Murcia, Spain; (M.G.F.); (G.C.); (G.V.)
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5
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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: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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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6
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Oakes V, Domene C. Capturing the Molecular Mechanism of Anesthetic Action by Simulation Methods. Chem Rev 2018; 119:5998-6014. [DOI: 10.1021/acs.chemrev.8b00366] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Victoria Oakes
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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7
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Frigini EN, López Cascales JJ, Porasso RD. Molecular dynamics simulations of glyphosate in a DPPC lipid bilayer. Chem Phys Lipids 2018; 213:111-117. [PMID: 29684323 DOI: 10.1016/j.chemphyslip.2018.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 11/26/2022]
Abstract
Extensive molecular dynamics simulations have been performed to study the effect of glyphosate (in their neutral and charged forms, GLYP and GLYP2-, respectively) on fully hydrated DiPalmitoylPhosphatidylCholine (DPPC) lipid bilayer. First, we calculated the free energy profile (using the Umbrella Sampling technique) for both states of charge of glyphosate. The minimum value for the free energy for GLYP is ∼-60 kJ mol-1 located at z = ±1.7 nm (from the lipid bilayer center), and there is almost no maximum at the center of the lipid bilayer. By contrast, the minimum for GLYP2- is ∼-35 kJ mol-1 located at z = ± 1.4 nm (from the lipid bilayer center), and the maximum reaches ∼35 kJ mol-1 at the center of the lipid bilayer. Then, different lipid bilayer properties were analyzed for different glyphosate:lipid (G:L) ratios. The mean area per lipid was slightly affected, increasing only 5% (in the presence of glyphosate at high concentrations), which is in agreement with the slight decrease in deuterium order parameters. As for the thickness of the bilayer, it is observed that the state of charge produces opposite effects. On one hand, the neutral state produces an increase in the thickness of the lipid bilayer; on the other, the charged form produces a decrease in the thickness, which not depend linearly on the G:L ratios, either. The orientation of the DPPC head groups is practically unaffected throughout the range of the G:L ratios studied. Finally, the mobility of the lipids of the bilayer is strongly affected by the presence of glyphosate, considerably increasing its lateral diffusion coefficient noteworthy (one order of magnitude), with increasing G:L ratio.
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Affiliation(s)
- Ezequiel N Frigini
- Instituto de Matemática Aplicada San Luis, IMASL, Universidad Nacional de San Luis and CONICET, Ejército de los Andes 950, D5700HHW San Luis, Argentina
| | - J J López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoléculas (BioMac), Área de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Rodolfo D Porasso
- Instituto de Matemática Aplicada San Luis, IMASL, Universidad Nacional de San Luis and CONICET, Ejército de los Andes 950, D5700HHW San Luis, Argentina.
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8
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Buyan A, Sun D, Corry B. Protonation state of inhibitors determines interaction sites within voltage-gated sodium channels. Proc Natl Acad Sci U S A 2018; 115:E3135-E3144. [PMID: 29467289 PMCID: PMC5889629 DOI: 10.1073/pnas.1714131115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Voltage-gated sodium channels are essential for carrying electrical signals throughout the body, and mutations in these proteins are responsible for a variety of disorders, including epilepsy and pain syndromes. As such, they are the target of a number of drugs used for reducing pain or combatting arrhythmias and seizures. However, these drugs affect all sodium channel subtypes found in the body. Designing compounds to target select sodium channel subtypes will provide a new therapeutic pathway and would maximize treatment efficacy while minimizing side effects. Here, we examine the binding preferences of nine compounds known to be sodium channel pore blockers in molecular dynamics simulations. We use the approach of replica exchange solute tempering (REST) to gain a more complete understanding of the inhibitors' behavior inside the pore of NavMs, a bacterial sodium channel, and NavPas, a eukaryotic sodium channel. Using these simulations, we are able to show that both charged and neutral compounds partition into the bilayer, but neutral forms more readily cross it. We show that there are two possible binding sites for the compounds: (i) a site on helix 6, which has been previously determined by many experimental and computational studies, and (ii) an additional site, occupied by protonated compounds in which the positively charged part of the drug is attracted into the selectivity filter. Distinguishing distinct binding poses for neutral and charged compounds is essential for understanding the nature of pore block and will aid the design of subtype-selective sodium channel inhibitors.
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Affiliation(s)
- Amanda Buyan
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Delin Sun
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Ben Corry
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
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9
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10
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Lopes D, Jakobtorweihen S, Nunes C, Sarmento B, Reis S. Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations. Prog Lipid Res 2017; 65:24-44. [DOI: 10.1016/j.plipres.2016.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/30/2016] [Accepted: 12/03/2016] [Indexed: 12/20/2022]
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11
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Bunker A, Magarkar A, Viitala T. Rational design of liposomal drug delivery systems, a review: Combined experimental and computational studies of lipid membranes, liposomes and their PEGylation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2334-2352. [DOI: 10.1016/j.bbamem.2016.02.025] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/09/2016] [Accepted: 02/10/2016] [Indexed: 01/22/2023]
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12
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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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13
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Pöyry S, Vattulainen I. Role of charged lipids in membrane structures - Insight given by simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2322-2333. [PMID: 27003126 DOI: 10.1016/j.bbamem.2016.03.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/09/2016] [Accepted: 03/11/2016] [Indexed: 01/28/2023]
Abstract
Lipids and proteins are the main components of cell membranes. It is becoming increasingly clear that lipids, in addition to providing an environment for proteins to work in, are in many cases also able to modulate the structure and function of those proteins. Particularly charged lipids such as phosphatidylinositols and phosphatidylserines are involved in several examples of such effects. Molecular dynamics simulations have proved an invaluable tool in exploring these aspects. This so-called computational microscope can provide both complementing explanations for the experimental results and guide experiments to fruitful directions. In this paper, we review studies that have utilized molecular dynamics simulations to unravel the roles of charged lipids in membrane structures. We focus on lipids as active constituents of the membranes, affecting both general membrane properties as well as non-lipid membrane components, mainly proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sanja Pöyry
- Department of Physics, Tampere University of Technology, POB 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, POB 692, FI-33101 Tampere, Finland; MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark; Department of Physics, University of Helsinki, POB 64, FI-00014 Helsinki, Finland.
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14
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Ruiz-Fernández AR, López-Cascales JJ, Giner-Casares JJ, Araya-Maturana R, Díaz-Baños FG, Weiss-López BE. Composition effect on the aggregate/solution interface of a nematic lyotropic liquid crystal. RSC Adv 2016. [DOI: 10.1039/c6ra13597h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We study how the concentration of phospholipids, decanol and NaCl affects the bilayer and the liquid crystal/solution interface structures of lyotropic nematic liquid crystals.
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Affiliation(s)
| | - J. J. López-Cascales
- Universidad Politécnica de Cartagena
- Grupo de Bioinformática y Macromoléculas (BioMac)
- 30203 Cartagena
- Spain
| | - J. J. Giner-Casares
- CIC biomaGUNE
- Biofunctional Nanomaterials – Laboratory 6 Parque tecnológico de San Sebastián
- 20009 Donostia – San Sebastián
- Spain
| | - R. Araya-Maturana
- Universidad de Talca
- Instituto de Química de Recursos Naturales
- Talca
- Chile
| | - F. G. Díaz-Baños
- Uni. de Murcia
- Fac. de Química
- Dep. de Química Física
- 30100 Espinardo
- Spain
| | - B. E. Weiss-López
- Universidad de Chile
- Facultad de Ciencias
- Departamento de Química
- Santiago
- Chile
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15
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Casalegno M, Raos G, Sello G. From dioxin to dioxin congeners: understanding the differences in hydrophobic aggregation in water and absorption into lipid membranes by means of atomistic simulations. Phys Chem Chem Phys 2016; 18:17731-9. [DOI: 10.1039/c6cp01728b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular dynamics simulations indicate that dioxin likely accumulates in cell membranes more than its congeners (anthracene, tetrahydrodioxin, 3,3′,5,5′-tetrachlorobiphenyl, and 1,2-dihydroxytetrahydrodibenzo-p-dioxin).
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Affiliation(s)
- Mosé Casalegno
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “G. Natta”
- Politecnico di Milano
- 20131 Milano
- Italy
| | - Guido Raos
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “G. Natta”
- Politecnico di Milano
- 20131 Milano
- Italy
| | - Guido Sello
- Dipartimento di Chimica
- Università degli Studi di Milano
- I-20133 Milano
- Italy
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16
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Casalegno M, Raos G, Sello G. Hydrophobic aggregation and collective absorption of dioxin into lipid membranes: insights from atomistic simulations. Phys Chem Chem Phys 2014; 17:2344-8. [PMID: 25503360 DOI: 10.1039/c4cp05466k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dioxins are a highly toxic class of chlorinated aromatic chemicals. They have been extensively studied, but several molecular-level details of their action are still missing. Here we present molecular dynamics simulations of their absorption and diffusion through cell membranes. We show that, due to their hydrophobic character, dioxins can quickly penetrate into a lipid membrane, both as single molecules and as aggregates. We find clear evidence for their ability to accumulate in cell membranes. Our free energy calculations indicate that subsequent transport into the cell is unlikely to be a simple diffusive process.
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Affiliation(s)
- M Casalegno
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy
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17
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Herold KF, Sanford RL, Lee W, Schultz MF, Ingólfsson HI, Andersen OS, Hemmings HC. Volatile anesthetics inhibit sodium channels without altering bulk lipid bilayer properties. J Gen Physiol 2014; 144:545-60. [PMID: 25385786 PMCID: PMC4242807 DOI: 10.1085/jgp.201411172] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 10/08/2014] [Indexed: 01/05/2023] Open
Abstract
Although general anesthetics are clinically important and widely used, their molecular mechanisms of action remain poorly understood. Volatile anesthetics such as isoflurane (ISO) are thought to alter neuronal function by depressing excitatory and facilitating inhibitory neurotransmission through direct interactions with specific protein targets, including voltage-gated sodium channels (Na(v)). Many anesthetics alter lipid bilayer properties, suggesting that ion channel function might also be altered indirectly through effects on the lipid bilayer. We compared the effects of ISO and of a series of fluorobenzene (FB) model volatile anesthetics on Na(v) function and lipid bilayer properties. We examined the effects of these agents on Na(v) in neuronal cells using whole-cell electrophysiology, and on lipid bilayer properties using a gramicidin-based fluorescence assay, which is a functional assay for detecting changes in lipid bilayer properties sensed by a bilayer-spanning ion channel. At clinically relevant concentrations (defined by the minimum alveolar concentration), both the FBs and ISO produced prepulse-dependent inhibition of Na(v) and shifted the voltage dependence of inactivation toward more hyperpolarized potentials without affecting lipid bilayer properties, as sensed by gramicidin channels. Only at supra-anesthetic (toxic) concentrations did ISO alter lipid bilayer properties. These results suggest that clinically relevant concentrations of volatile anesthetics alter Na(v) function through direct interactions with the channel protein with little, if any, contribution from changes in bulk lipid bilayer properties. Our findings further suggest that changes in lipid bilayer properties are not involved in clinical anesthesia.
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Affiliation(s)
- Karl F Herold
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - R Lea Sanford
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - William Lee
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Margaret F Schultz
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Helgi I Ingólfsson
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Olaf S Andersen
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Hugh C Hemmings
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065 Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
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Jakobtorweihen S, Zuniga AC, Ingram T, Gerlach T, Keil FJ, Smirnova I. Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic. J Chem Phys 2014; 141:045102. [DOI: 10.1063/1.4890877] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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19
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Bahamonde-Padilla VE, López-Cascales JJ, Araya-Maturana R, Martínez-Cifuentes M, Weiss López BE. Thermodynamics and2H NMR Study on the Insertion of Small Quinones into a Discotic Nematic Lyotropic Liquid Crystal. Chemphyschem 2014; 15:1422-31. [DOI: 10.1002/cphc.201301146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/07/2014] [Indexed: 01/28/2023]
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20
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Martin LJ, Chao R, Corry B. Molecular dynamics simulation of the partitioning of benzocaine and phenytoin into a lipid bilayer. Biophys Chem 2013; 185:98-107. [PMID: 24406394 DOI: 10.1016/j.bpc.2013.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/04/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
Abstract
Molecular dynamics simulations were used to examine the partitioning behaviour of the local anaesthetic benzocaine and the anti-epileptic phenytoin into lipid bilayers, a factor that is critical to their mode of action. Free energy methods are used to quantify the thermodynamics of drug movement between water and octanol as well as for permeation across a POPC membrane. Both drugs are shown to favourably partition into the lipid bilayer from water and are likely to accumulate just inside the lipid headgroups where they may alter bilayer properties or interact with target proteins. Phenytoin experiences a large barrier to cross the centre of the bilayer due to less favourable energetic interactions in this less dense region of the bilayer. Remarkably, in our simulations both drugs are able to pull water into the bilayer, creating water chains that extend back to bulk, and which may modify the local bilayer properties. We find that the choice of atomic partial charges can have a significant impact on the quantitative results, meaning that careful validation of parameters for new drugs, such as performed here, should be performed prior to their use in biomolecular simulations.
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Affiliation(s)
- Lewis J Martin
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - Rebecca Chao
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - Ben Corry
- Research School of Biology, Australian National University, Canberra 0200, Australia.
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21
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Rabinovich AL, Lyubartsev AP. Computer simulation of lipid membranes: Methodology and achievements. POLYMER SCIENCE SERIES C 2013. [DOI: 10.1134/s1811238213070060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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22
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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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23
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López Cascales J, Oliveira Costa S. Effect of the interfacial tension and ionic strength on the thermodynamic barrier associated to the benzocaine insertion into a cell membrane. Biophys Chem 2013; 172:1-7. [DOI: 10.1016/j.bpc.2012.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 12/04/2012] [Accepted: 12/05/2012] [Indexed: 11/29/2022]
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