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Rózsa ZB, Hantal G, Szőri M, Fábián B, Jedlovszky P. Understanding the Molecular Mechanism of Anesthesia: Effect of General Anesthetics and Structurally Similar Non-Anesthetics on the Properties of Lipid Membranes. J Phys Chem B 2023. [PMID: 37368412 DOI: 10.1021/acs.jpcb.3c02976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
General anesthesia can be caused by various, chemically very different molecules, while several other molecules, many of which are structurally rather similar to them, do not exhibit anesthetic effects at all. To understand the origin of this difference and shed some light on the molecular mechanism of general anesthesia, we report here molecular dynamics simulations of the neat dipalmitoylphosphatidylcholine (DPPC) membrane as well as DPPC membranes containing the anesthetics diethyl ether and chloroform and the structurally similar non-anesthetics n-pentane and carbon tetrachloride, respectively. To also account for the pressure reversal of anesthesia, these simulations are performed both at 1 bar and at 600 bar. Our results indicate that all solutes considered prefer to stay both in the middle of the membrane and close to the boundary of the hydrocarbon domain, at the vicinity of the crowded region of the polar headgroups. However, this latter preference is considerably stronger for the (weakly polar) anesthetics than for the (apolar) non-anesthetics. Anesthetics staying in this outer preferred position increase the lateral separation between the lipid molecules, giving rise to a decrease of the lateral density. The lower lateral density leads to an increased mobility of the DPPC molecules, a decreased order of their tails, an increase of the free volume around this outer preferred position, and a decrease of the lateral pressure at the hydrocarbon side of the apolar/polar interface, a change that might well be in a causal relation with the occurrence of the anesthetic effect. All these changes are clearly reverted by the increase of pressure. Furthermore, non-anesthetics occur in this outer preferred position in a considerably smaller concentration and hence either induce such changes in a much weaker form or do not induce them at all.
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Affiliation(s)
- Zsófia B Rózsa
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - György Hantal
- Institute of Physics and Materials Science, University of Natural Resources and Life Sciences, Peter Jordan Straße 82, A-1190 Vienna, Austria
| | - Milán Szőri
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - Balázs Fábián
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly Catholic University, Leányka utca 6, H-3300 Eger, Hungary
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2
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Exploring 129Xe NMR parameters for structural investigation of biomolecules: relativistic, solvent, and thermal effects. J Mol Model 2022; 28:372. [DOI: 10.1007/s00894-022-05365-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022]
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3
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Zizzi EA, Cavaglià M, Tuszynski JA, Deriu MA. Alteration of lipid bilayer mechanics by volatile anesthetics: Insights from μs-long molecular dynamics simulations. iScience 2022; 25:103946. [PMID: 35265816 PMCID: PMC8898909 DOI: 10.1016/j.isci.2022.103946] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 11/24/2022] Open
Abstract
Very few drugs in clinical practice feature the chemical diversity, narrow therapeutic window, unique route of administration, and reversible cognitive effects of volatile anesthetics. The correlation between their hydrophobicity and their potency and the increasing amount of evidence suggesting that anesthetics exert their action on transmembrane proteins, justifies the investigation of their effects on phospholipid bilayers at the molecular level, given the strong functional and structural link between transmembrane proteins and the surrounding lipid matrix. Molecular dynamics simulations of a model lipid bilayer in the presence of ethylene, desflurane, methoxyflurane, and the nonimmobilizer 1,2-dichlorohexafluorocyclobutane (also called F6 or 2N) at different concentrations highlight the structural consequences of VA partitioning in the lipid phase, with a decrease of lipid order and bilayer thickness, an increase in overall lipid lateral mobility and area-per-lipid, and a marked reduction in the mechanical stiffness of the membrane, that strongly correlates with the compounds' hydrophobicity. Molecular simulations of lipid bilayer interaction with volatile anesthetics Comparison of volatile anesthetics' and nonimmobilizers' effects on lipid bilayers Ligand-dependent partitioning of the compounds in the lipid phase Effects on bilayer thickness, stiffness, and lipid order upon ligand partitioning
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Shi P, Luo H, Tan X, Lu Y, Zhang H, Yang X. Molecular dynamics simulation study of adsorption of anionic–nonionic surfactants at oil/water interfaces. RSC Adv 2022; 12:27330-27343. [PMID: 36276041 PMCID: PMC9514088 DOI: 10.1039/d2ra04772a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/10/2022] [Indexed: 11/21/2022] Open
Abstract
Four anionic–nonionic surfactants with the same headgroups and different units of oxygen ethyl (EO) and oxygen propyl (PO) were adopted to investigate the influence on oil/water interfacial tensions in this article. Molecular dynamics (MD) simulations were conducted to study the interfacial property of the four surfactants. Four parameters were proposed to reveal the effecting mechanism of molecular structure on interfacial tension, which included the interfacial thickness, order parameter of the hydrophobic chain, radial distribution function, and the solvent accessible surface area. In addition, the electrostatic potential of the four surfactants was calculated. The research results indicated that the interface facial mask formed by the surfactants, which contained three EO or three PO units was more stable, and it was easier for the surfactants of six EO or six PO units to form a microemulsion at higher concentrations. The adsorption mechanism of the anionic–nonionic surfactant systems at the oil/water interfaces was supplemented at a molecular level, which provided fundamental guidance for an in-depth understanding of the optimal selection of the surfactants in enhancing oil recovery. Four anionic–nonionic surfactants with the same headgroups and different units of oxygen ethyl (EO) and oxygen propyl (PO) were adopted to investigate the influence on oil/water interfacial tensions in this article.![]()
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Affiliation(s)
- Peng Shi
- College of Materials and Chemical Engineering, Heilongjiang Institute of Technology, Harbin 150026, People's Republic of China
- College of Chemical Engineering, Harbin Institute of Petroleum, Harbin 150028, People's Republic of China
| | - Haibin Luo
- College of Chemical Engineering, Harbin Institute of Petroleum, Harbin 150028, People's Republic of China
| | - Xuefei Tan
- College of Materials and Chemical Engineering, Heilongjiang Institute of Technology, Harbin 150026, People's Republic of China
| | - Yang Lu
- College of Materials and Chemical Engineering, Heilongjiang Institute of Technology, Harbin 150026, People's Republic of China
| | - Hui Zhang
- College of Science, Harbin University of Science and Technology, Harbin 150080, People's Republic of China
| | - Xin Yang
- College of Chemical Engineering, Harbin Institute of Petroleum, Harbin 150028, People's Republic of China
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5
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Hantal G, Fábián B, Sega M, Jójárt B, Jedlovszky P. Effect of general anesthetics on the properties of lipid membranes of various compositions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:594-609. [PMID: 30571949 DOI: 10.1016/j.bbamem.2018.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 10/27/2022]
Abstract
Computer simulations of four lipid membranes of different compositions, namely neat DPPC and PSM, and equimolar DPPC-cholesterol and PSM-cholesterol mixtures, are performed in the presence and absence of the general anesthetics diethylether and sevoflurane both at 1 and 600 bar. The results are analyzed in order to identify membrane properties that are potentially related to the molecular mechanism of anesthesia, namely that change in the same way in any membrane with any anesthetics, and change oppositely with increasing pressure. We find that the lateral lipid density satisfies both criteria: it is decreased by anesthetics and increased by pressure. This anesthetic-induced swelling is attributed to only those anesthetic molecules that are located close to the boundary of the apolar phase. This lateral expansion is found to lead to increased lateral mobility of the lipids, an effect often thought to be related to general anesthesia; to an increased fraction of the free volume around the outer preferred position of anesthetics; and to the decrease of the lateral pressure in the nearby range of the ester and amide groups, a region into which anesthetic molecules already cannot penetrate. All these changes are reverted by the increase of pressure. Another important finding of this study is that cholesterol has an opposite effect on the membrane properties than anesthetics, and, correspondingly, these changes are less marked in the presence of cholesterol. Therefore, changes in the membrane that can lead to general anesthesia are expected to occur in the membrane domains of low cholesterol content.
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Affiliation(s)
- György Hantal
- Faculty of Physics, University of Vienna, Sensengasse 8/9, A-1090 Vienna, Austria
| | - Balázs Fábián
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, H-1111 Budapest, Hungary; Institut UTINAM (CNRS UMR 6213), Université Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon, France
| | - Marcello Sega
- Faculty of Physics, University of Vienna, Sensengasse 8/9, A-1090 Vienna, Austria
| | - Balázs Jójárt
- Institute of Food Engineering, University of Szeged, Moszkvai krt 5-7, H-6725 Szeged, Hungary
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly University, Leányka utca 6, H-3300 Eger, Hungary.
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6
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Arvayo-Zatarain JA, Favela-Rosales F, Contreras-Aburto C, Urrutia-Bañuelos E, Maldonado A. Molecular dynamics simulation study of the effect of halothane on mixed DPPC/DPPE phospholipid membranes. J Mol Model 2018; 25:4. [PMID: 30554281 DOI: 10.1007/s00894-018-3890-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 12/03/2018] [Indexed: 11/26/2022]
Abstract
We report results of a molecular dynamics simulation study of the effect of one general anesthetic, halothane, on some properties of mixed DPPC/DPPE phospholipid membranes. This is a suitable model for the study of simple, two-phospholipid membrane systems. From the simulation runs, we determined several membrane properties for five different molecular proportions of DPPC/DPPE. The effect of halothane on the studied membrane properties (area per lipid molecule, density of membrane, order parameter, etc.) was rather small. The distribution of halothane is not uniform through the bilayer thickness. Instead, there is a maximum of anesthetic concentration around 1.2 nm from the center of the membrane. The anesthetic molecule is located close to the phospholipid headgroups. The position of the halothane density maximum depends slightly on the DPPC/DPPE molar proportion. Snapshots taken over the plane of the membrane, as well as calculated two-dimensional radial distribution functions show that the anesthetic has no preference for either phospholipid (DPPC or DPPE). Our results indicate that this anesthetic molecule has only small effects on DPPC/DPPE mixed membranes. In addition, halothane displays no preferential location around DPPC or DPPE. This is probably due to the hydrophobic nature of halothane and to the fact that the chosen phospholipids have the same hydrophobic tails.
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Affiliation(s)
| | - Fernando Favela-Rosales
- Departamento de Investigación, Instituto Tecnológico Superior Zacatecas Occidente, Ave. Tecnológico 2000, 99102, Sombrerete, Zacatecas, Mexico
| | - Claudio Contreras-Aburto
- Facultad de Ciencias en Física y Matemáticas, Universidad Autónoma de Chiapas, Carretera Emiliano Zapata km 8, 29050, Tuxtla Gutiérrez, Chiapas, Mexico
| | - Efrain Urrutia-Bañuelos
- Departamento de Investigación en Física, Universidad de Sonora, Rosales y Luis Encinas s/n, 83000, Hermosillo, Sonora, Mexico
| | - Amir Maldonado
- Departamento de Física, Universidad de Sonora, Rosales y Luis Encinas s/n, 83000, Hermosillo, Sonora, Mexico.
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7
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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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8
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Matsuki H, Kato K, Okamoto H, Yoshida S, Goto M, Tamai N, Kaneshina S. Ligand partitioning into lipid bilayer membranes under high pressure: Implication of variation in phase-transition temperatures. Chem Phys Lipids 2017; 209:9-18. [PMID: 29042237 DOI: 10.1016/j.chemphyslip.2017.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/07/2017] [Accepted: 10/08/2017] [Indexed: 11/30/2022]
Abstract
The variation in phase-transition temperatures of dipalmitoylphosphatidylcholine (DPPC) bilayer membrane by adding two membrane-active ligands, a long-chain fatty acid (palmitic acid (PA)) and an inhalation anesthetic (halothane (HAL)), was investigated by light-transmittance measurements and fluorometry. By assuming the thermodynamic colligative property for the bilayer membrane at low ligand concentrations, the partitioning behavior of these ligands into the DPPC bilayer membrane was considered. It was proved from the differential partition coefficients between two phases that PA has strong affinity with the gel (lamellar gel) phase in a micro-molal concentration range and makes the bilayer membrane more ordered, while HAL has strong affinity with the liquid crystalline phase in a milli-molal concentration range and does the bilayer membrane more disordered. The transfer volumes of both ligands from the aqueous solution to each phase of the DPPC bilayer membrane showed that the preferential partitioning of the PA molecule into the gel (lamellar gel) produces about 20% decrease in transfer volume as compared with the liquid crystalline phase, whereas that of the HAL molecule into the liquid crystalline phase does about twice increase in transfer volume as compared with the gel (ripple gel) phase. Furthermore, changes in thermotropic and barotropic phase behavior of the DPPC bilayer membrane by adding the ligand was discussed from the viewpoint of the ligand partitioning. Reflecting the contrastive partitioning of PA and HAL into the pressure-induced interdigitated gel phase among the gel phases, it was revealed that PA suppresses the formation of the interdigitated gel phase under high pressure while HAL promotes it. These results clearly indicate that each phase of the DPPC bilayer membrane has a potential to recognize various ligand molecules.
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Affiliation(s)
- Hitoshi Matsuki
- Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, 770-8513, Japan.
| | - Kentaro Kato
- Department of Biological Science and Technology, Faculty of Engineering, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, 770-8506, Japan
| | - Hirotsugu Okamoto
- Department of Biological Science and Technology, Faculty of Engineering, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, 770-8506, Japan
| | - Shuntaro Yoshida
- Department of Biological Science and Technology, Faculty of Engineering, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, 770-8506, Japan
| | - Masaki Goto
- Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, 770-8513, Japan
| | - Nobutake Tamai
- Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, 770-8513, Japan
| | - Shoji Kaneshina
- Department of Biological Science and Technology, Faculty of Engineering, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, 770-8506, Japan
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9
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Theodorakis PE, Müller EA, Craster RV, Matar OK. Physical insights into the blood-brain barrier translocation mechanisms. Phys Biol 2017; 14:041001. [PMID: 28586313 DOI: 10.1088/1478-3975/aa708a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The number of individuals suffering from diseases of the central nervous system (CNS) is growing with an aging population. While candidate drugs for many of these diseases are available, most of these pharmaceutical agents cannot reach the brain rendering most of the drug therapies that target the CNS inefficient. The reason is the blood-brain barrier (BBB), a complex and dynamic interface that controls the influx and efflux of substances through a number of different translocation mechanisms. Here, we present these mechanisms providing, also, the necessary background related to the morphology and various characteristics of the BBB. Moreover, we discuss various numerical and simulation approaches used to study the BBB, and possible future directions based on multi-scale methods. We anticipate that this review will motivate multi-disciplinary research on the BBB aiming at the design of effective drug therapies.
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10
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Fábián B, Sega M, Voloshin VP, Medvedev NN, Jedlovszky P. Lateral Pressure Profile and Free Volume Properties in Phospholipid Membranes Containing Anesthetics. J Phys Chem B 2017; 121:2814-2824. [DOI: 10.1021/acs.jpcb.7b00990] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Balázs Fábián
- Department of Inorganic
and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary
- Institut UTINAM (CNRS UMR 6213), Université Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon, France
| | - Marcello Sega
- Faculty of
Physics, University of Vienna, Sensengasse 8/9, A-1090 Vienna, Austria
| | - Vladimir P. Voloshin
- Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Nikolai N. Medvedev
- Novosibirsk State University, Novosibirsk 630090, Russia
- Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly University, Leányka utca 6, H-3300 Eger, Hungary
- MTA-BME Research Group of Technical Analytical Chemistry, Szent Gellért tér
4, H-1111 Budapest, Hungary
- Laboratory of Interfaces and Nanosize Systems,
Institute of Chemistry, Eötvös Loránd University, Pázmány Peter Stny 1/A, H-1117 Budapest, Hungary
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11
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Vrbanović Mijatović V, Šerman L, Gamulin O. Analysis of pulmonary surfactant by Fourier transform infrared spectroscopy after exposure to sevoflurane and isoflurane. Bosn J Basic Med Sci 2017; 17:38-46. [PMID: 28027455 DOI: 10.17305/bjbms.2016.1680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 11/16/2022] Open
Abstract
Pulmonary surfactant, consisting primarily of phospholipids and four surfactant-specific proteins, is among the first structures that is exposed to inhalation anesthetics. Consequently, changes of pulmonary surfactant due to this exposure could cause respiratory complications after long anesthetic procedures. Fourier transform infrared (FTIR) spectroscopy was used to explore the effects of two inhalation anesthetics, sevoflurane and isoflurane, on a commercially available pulmonary surfactant. The research was primarily focused on the effect of anesthetics on the lipid component of the surfactant. Four different concentrations of anesthetics were added, and the doses were higher from the low clinical doses typically used. Recorded spectra were analyzed using principal component analysis, and the Student's t-test was performed to confirm the results. The exposure to both anesthetics induced similar changes, consistent with the increase of the anesthetic concentration. The most pronounced effect was on the hydrophilic head group of phospholipids, which is in agreement with the disruption of the hydrogen bond, caused by the anesthetics. A change in the band intensities of CH2 stretching vibrations, indicative of a disordering effect of anesthetics on the hydrophobic tails of phospholipids, was also observed. Changes induced by isoflurane appear to be more pronounced than those induced by sevoflurane. Furthermore, our results suggest that FTIR spectroscopy is a promising tool in studying anesthetic effects on pulmonary surfactant.
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Affiliation(s)
- Vilena Vrbanović Mijatović
- Department of Anesthesiology, Resuscitation and Intensive Care, University Hospital Center Zagreb, Zagreb, Croatia.
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12
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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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13
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Mayne CG, Arcario MJ, Mahinthichaichan P, Baylon JL, Vermaas JV, Navidpour L, Wen PC, Thangapandian S, Tajkhorshid E. The cellular membrane as a mediator for small molecule interaction with membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:2290-2304. [PMID: 27163493 PMCID: PMC4983535 DOI: 10.1016/j.bbamem.2016.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 01/05/2023]
Abstract
The cellular membrane constitutes the first element that encounters a wide variety of molecular species to which a cell might be exposed. Hosting a large number of structurally and functionally diverse proteins associated with this key metabolic compartment, the membrane not only directly controls the traffic of various molecules in and out of the cell, it also participates in such diverse and important processes as signal transduction and chemical processing of incoming molecular species. In this article, we present a number of cases where details of interaction of small molecular species such as drugs with the membrane, which are often experimentally inaccessible, have been studied using advanced molecular simulation techniques. We have selected systems in which partitioning of the small molecule with the membrane constitutes a key step for its final biological function, often binding to and interacting with a protein associated with the membrane. These examples demonstrate that membrane partitioning is not only important for the overall distribution of drugs and other small molecules into different compartments of the body, it may also play a key role in determining the efficiency and the mode of interaction of the drug with its target protein. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Christopher G Mayne
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Mark J Arcario
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
| | - Paween Mahinthichaichan
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Javier L Baylon
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Josh V Vermaas
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Latifeh Navidpour
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Po-Chao Wen
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Sundarapandian Thangapandian
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
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14
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Jalili S, Saeedi M. Study of procaine and tetracaine in the lipid bilayer using molecular dynamics simulation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:265-282. [PMID: 27557558 DOI: 10.1007/s00249-016-1164-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 07/18/2016] [Accepted: 08/12/2016] [Indexed: 11/29/2022]
Abstract
Despite available experimental results, the molecular mechanism of action of local anesthetics upon the nervous system and contribution of the cell membrane to the process are still controversial. In this work, molecular dynamics simulations were performed to investigate the effect of two clinically used local anesthetics, procaine and tetracaine, on the structure and dynamics of a fully hydrated dimyristoylphosphatidylcholine lipid bilayer. We focused on comparing the main effects of uncharged and charged drugs on various properties of the lipid membrane: mass density distribution, diffusion coefficient, order parameter, radial distribution function, hydrogen bonding, electrostatic potential, headgroup angle, and water dipole orientation. To compare the diffusive nature of anesthetic through the lipid membrane quantitatively, we investigated the hexadecane/water partition coefficient using expanded ensemble simulation. We predicted the permeability coefficient of anesthetics in the following order: uncharged tetracaine > uncharged procaine > charged tetracaine > charged procaine. We also shown that the charged forms of drugs are more potent in hydrogen bonding, disturbing the lipid headgroups, changing the orientation of water dipoles, and increasing the headgroup electrostatic potential more than uncharged drugs, while the uncharged drugs make the lipid diffusion faster and increase the tail order parameter. The results of these simulation studies suggest that the different forms of anesthetics induce different structural modifications in the lipid bilayer, which provides new insights into their molecular mechanism.
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Affiliation(s)
- Seifollah Jalili
- Department of Chemistry, K. N. Toosi University of Technology, Tehran, P.O. Box 15875-4416, Iran. .,Computational Physical Sciences Research Laboratory, School of Nano-Science, Institute for Research in Fundamental Sciences (IPM), Tehran, P.O. Box 19395-5531, Iran. .,Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Marzieh Saeedi
- Department of Chemistry, K. N. Toosi University of Technology, Tehran, P.O. Box 15875-4416, Iran
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15
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Wood I, Pickholz M. Naratriptan aggregation in lipid bilayers: perspectives from molecular dynamics simulations. J Mol Model 2016; 22:221. [PMID: 27558798 DOI: 10.1007/s00894-016-3096-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/08/2016] [Indexed: 11/27/2022]
Abstract
In order to understand the interaction between naratriptan and a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC), we carried out molecular dynamics simulations. The simulations were performed considering neutral and protonated ionization states, starting from different initial conditions. At physiological pH, the protonated state of naratriptan is predominant. It is expected that neutral compounds could have larger membrane partition than charged compounds. However, for the specific case of triptans, it is difficult to study neutral species in membranes experimentally, making computer simulations an interesting tool. When the naratriptan molecules were originally placed in water, they partitioned between the bilayer/water interface and water phase, as has been described for similar compounds. From this condition, the drugs displayed low access to the hydrophobic environment, with no significant effects on bilayer organization. The molecules anchored in the interface, due mainly to the barrier function of the polar and oriented lipid heads. On the other hand, when placed inside the bilayer, both neutral and protonated naratriptan showed self-aggregation in the lipid tail environment. In particular, the protonated species exhibited a pore-like structure, dragging water through this environment. Graphical Abstract Different behaviour of Naratriptan and Sumatriptan, when the drugs were originally placed in the lipid core.
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Affiliation(s)
- Irene Wood
- Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, CONICET, Junin 956 CP 1113, Buenos Aires, Argentina.,National Science Research Council (CONICET), Buenos Aires, Argentina
| | - Mónica Pickholz
- Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, CONICET, Junin 956 CP 1113, Buenos Aires, Argentina. .,National Science Research Council (CONICET), Buenos Aires, Argentina.
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16
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Fábián B, Darvas M, Picaud S, Sega M, Jedlovszky P. The effect of anaesthetics on the properties of a lipid membrane in the biologically relevant phase: a computer simulation study. Phys Chem Chem Phys 2015; 17:14750-60. [DOI: 10.1039/c5cp00851d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phospholipid membranes containing four different general anaesthetic molecules are simulated in the biologically relevant Lα phase at atmospheric and high pressures.
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Affiliation(s)
- Balázs Fábián
- Laboratory of Interfaces and Nanosize Systems
- Institute of Chemistry
- Eötvös Loránd University
- H-1117 Budapest
- Hungary
| | - Mária Darvas
- SISSA
- Sector of Molecular and Statistical Biophysics
- 34136 Trieste
- Italy
| | - Sylvain Picaud
- Institut UTINAM (CNRS UMR 6213)
- Université de Franche-Comté
- F-25030 Besançon
- France
| | - Marcello Sega
- Institut für Computergestützte Biologische Chemie
- University of Vienna
- A-1090 Vienna
- Austria
| | - Pál Jedlovszky
- Laboratory of Interfaces and Nanosize Systems
- Institute of Chemistry
- Eötvös Loránd University
- H-1117 Budapest
- Hungary
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17
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Hoyo J, Guaus E, Oncins G, Torrent-Burgués J, Sanz F. Incorporation of ubiquinone in supported lipid bilayers on ITO. J Phys Chem B 2013; 117:7498-506. [PMID: 23725098 DOI: 10.1021/jp4004517] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Ubiquinone (UQ) is one of the main electron and proton shuttle molecules in biological systems, and dipalmitoylphosphatidylcholine (DPPC) is one of the most used model lipids. Supported planar bilayers (SPBs) are extensively accepted as biological model membranes. In this study, SPBs have been deposited on ITO, which is a semiconductor with good electrical and optical features. Specifically, topographic atomic force microscopy (AFM) images and force curves have been performed on SPBs with several DPPC:UQ ratios to study the location and the interaction of UQ in the SPB. Additionally, cyclic voltammetry has been used to understand the electrochemical behavior of DPPC:UQ SPBs. Obtained results show that, in our case, UQ is placed in two main different positions in SPBs. First, between the DPPC hydrophobic chains, fact that originates a decrease in the breakthrough force of the bilayer, and the second between the two leaflets that form the SPBs. This second position occurs when increasing the UQ content, fact that eventually forms UQ aggregates at high concentrations. The formation of aggregates produces an expansion of the SPB average height and a bimodal distribution of the breakthrough force. The voltammetric response of UQ depends on its position on the bilayer.
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Affiliation(s)
- Javier Hoyo
- Universitat Politècnica de Catalunya, Dpt. Enginyeria Química, 08222 Terrassa (Barcelona), Spain
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18
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Jämbeck JPM, Lyubartsev AP. Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers. J Phys Chem Lett 2013; 4:1781-1787. [PMID: 26283109 DOI: 10.1021/jz4007993] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Free energy calculations are vital for our understanding of biological processes on an atomistic scale and can offer insight to various mechanisms. However, in some cases, degrees of freedom (DOFs) orthogonal to the reaction coordinate have high energy barriers and/or long equilibration times, which prohibit proper sampling. Here we identify these orthogonal DOFs when studying the transfer of a solute from water to a model membrane. Important DOFs are identified in bulk liquids of different dielectric nature with metadynamics simulations and are used as reaction coordinates for the translocation process, resulting in two- and three-dimensional space of reaction coordinates. The results are in good agreement with experiments and elucidate the pitfalls of using one-dimensional reaction coordinates. The calculations performed here offer the most detailed free energy landscape of solutes embedded in lipid bilayers to date and show that free energy calculations can be used to study complex membrane translocation phenomena.
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Affiliation(s)
- Joakim P M Jämbeck
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
| | - Alexander P Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
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19
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Booker RD, Sum AK. Biophysical changes induced by xenon on phospholipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1347-56. [PMID: 23376329 DOI: 10.1016/j.bbamem.2013.01.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 12/28/2012] [Accepted: 01/22/2013] [Indexed: 12/20/2022]
Abstract
Structural and dynamic changes in cell membrane properties induced by xenon, a volatile anesthetic molecule, may affect the function of membrane-mediated proteins, providing a hypothesis for the mechanism of general anesthetic action. Here, we use molecular dynamics simulation and differential scanning calorimetry to examine the biophysical and thermodynamic effects of xenon on model lipid membranes. Our results indicate that xenon atoms preferentially localize in the hydrophobic core of the lipid bilayer, inducing substantial increases in the area per lipid and bilayer thickness. Xenon depresses the membrane gel-liquid crystalline phase transition temperature, increasing membrane fluidity and lipid head group spacing, while inducing net local ordering effects in a small region of the lipid carbon tails and modulating the bilayer lateral pressure profile. Our results are consistent with a role for nonspecific, lipid bilayer-mediated mechanisms in producing xenon's general anesthetic action.
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Affiliation(s)
- Ryan D Booker
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO 80401, USA
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20
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Jämbeck JPM, Lyubartsev AP. Implicit inclusion of atomic polarization in modeling of partitioning between water and lipid bilayers. Phys Chem Chem Phys 2013; 15:4677-86. [DOI: 10.1039/c3cp44472d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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21
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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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22
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Tu K, Matubayasi N, Liang K, Todorov I, Chan S, Chau PL. A possible molecular mechanism for the pressure reversal of general anaesthetics: Aggregation of halothane in POPC bilayers at high pressure. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.06.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Yamamoto E, Akimoto T, Shimizu H, Hirano Y, Yasui M, Yasuoka K. Diffusive nature of xenon anesthetic changes properties of a lipid bilayer: molecular dynamics simulations. J Phys Chem B 2012; 116:8989-95. [PMID: 22715916 DOI: 10.1021/jp303330c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Effects of general anesthesia can be controllable by the ambient pressure. We perform molecular dynamics simulations for a 1-palmitoyl-2-oleoyl phosphatidylethanolamine lipid bilayer with or without xenon molecules by changing the pressure to elucidate the mechanism of the pressure reversal of general anesthesia. According to the diffusive nature of xenon molecules in the lipid bilayer, a decrease in the orientational order of the lipid tails, an increase in the area and volume per lipid molecule, and an increase in the diffusivity of lipid molecules are observed. We show that the properties of the lipid bilayer with xenon molecules at high pressure come close to those without xenon molecules at 0.1 MPa. Furthermore, we find that xenon molecules are concentrated in the middle of the lipid bilayer at high pressures by the pushing effect and that the diffusivity of xenon molecules is suppressed. These results suggest that the pressure reversal originates from a jamming and suppression of the diffusivity of xenon molecules in lipid bilayers.
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Affiliation(s)
- Eiji Yamamoto
- Department of Mechanical Engineering, Keio University, 3-4-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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24
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Ghaemi Z, Minozzi M, Carloni P, Laio A. A novel approach to the investigation of passive molecular permeation through lipid bilayers from atomistic simulations. J Phys Chem B 2012; 116:8714-21. [PMID: 22540377 DOI: 10.1021/jp301083h] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Predicting the permeability coefficient (P) of drugs permeating through the cell membrane is of paramount importance in drug discovery. We here propose an approach for calculating P based on bias-exchange metadynamics. The approach allows constructing from atomistic simulations a model of permeation taking explicitly into account not only the "trivial" reaction coordinate, the position of the drug along the direction normal to the lipid membrane plane, but also other degrees of freedom, for example, the torsional angles of the permeating molecule, or variables describing its solvation/desolvation. This allows deriving an accurate picture of the permeation process, and constructing a detailed molecular model of the transition state, making a rational control of permeation properties possible. We benchmarked this approach on the permeation of ethanol molecules through a POPC membrane, showing that the value of P calculated with our model agrees with the one calculated by a long unbiased molecular dynamics of the same system.
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Affiliation(s)
- Zhaleh Ghaemi
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
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25
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Nelson SC, Neeley SK, Melonakos ED, Bell JD, Busath DD. Fluorescence anisotropy of diphenylhexatriene and its cationic Trimethylamino derivative in liquid dipalmitoylphosphatidylcholine liposomes: opposing responses to isoflurane. BMC BIOPHYSICS 2012; 5:5. [PMID: 22444827 PMCID: PMC3359235 DOI: 10.1186/2046-1682-5-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 03/24/2012] [Indexed: 12/02/2022]
Abstract
Background The mechanism of action of volatile general anesthetics has not yet been resolved. In order to identify the effects of isoflurane on the membrane, we measured the steady-state anisotropy of two fluorescent probes that reside at different depths. Incorporation of anesthetic was confirmed by shifting of the main phase transition temperature. Results In liquid crystalline dipalmitoylphosphatidylcholine liposomes, isoflurane (7-25 mM in the bath) increases trimethylammonium-diphenylhexatriene fluorescence anisotropy by ~0.02 units and decreases diphenylhexatriene anisotropy by the same amount. Conclusions The anisotropy data suggest that isoflurane decreases non-axial dye mobility in the headgroup region, while increasing it in the tail region. We propose that these results reflect changes in the lateral pressure profile of the membrane.
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Affiliation(s)
- Steven C Nelson
- WIDB 574, Dept, of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA.
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26
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Vorobyov I, Bennett WFD, Tieleman DP, Allen TW, Noskov S. The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers. J Chem Theory Comput 2012; 8:618-28. [PMID: 26596610 DOI: 10.1021/ct200417p] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In spite of extensive research and use in medical practice, the precise molecular mechanism of volatile anesthetic action remains unknown. The distribution of anesthetics within lipid bilayers and potential targeting to membrane proteins is thought to be central to therapeutic function. Therefore, obtaining a molecular level understanding of volatile anesthetic partitioning into lipid bilayers is of vital importance to modern pharmacology. In this study we investigate the partitioning of the prototypical anesthetic, chloroform, into lipid bilayers and different organic solvents using molecular dynamics simulations with potential models ranging from simplified coarse-grained MARTINI to additive and polarizable CHARMM all-atom force fields. Many volatile anesthetics display significant inducible dipole moments, which correlate with their potency, yet the exact role of molecular polarizability in their stabilization within lipid bilayers remains unknown. We observe that explicit treatment of atomic polarizability makes it possible to accurately reproduce solvation free energies in solvents with different polarities, allowing for quantitative studies in heterogeneous molecular distributions, such as lipid bilayers. We calculate the free energy profiles for chloroform crossing lipid bilayers to reveal a role of polarizability in modulating chloroform partitioning thermodynamics via the chloroform-induced dipole moment and highlight competitive binding to the membrane core and toward the glycerol backbone that may have significant implications for understanding anesthetic action.
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Affiliation(s)
- Igor Vorobyov
- Department of Chemistry, University of California , Davis, One Shields Avenue, Davis, California 95616, United States
| | - W F Drew Bennett
- Department of Biological Sciences, University of Calgary , 2500 University Drive, Calgary, Canada, T2N 2N4
| | - D Peter Tieleman
- Department of Biological Sciences, University of Calgary , 2500 University Drive, Calgary, Canada, T2N 2N4
| | - Toby W Allen
- Department of Chemistry, University of California , Davis, One Shields Avenue, Davis, California 95616, United States
| | - Sergei Noskov
- Department of Biological Sciences, University of Calgary , 2500 University Drive, Calgary, Canada, T2N 2N4
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27
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Darvas M, Hoang PNM, Picaud S, Sega M, Jedlovszky P. Anesthetic molecules embedded in a lipid membrane: a computer simulation study. Phys Chem Chem Phys 2012; 14:12956-69. [DOI: 10.1039/c2cp41581j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Yi Z, Nagao M, Bossev DP. Effect of charged lidocaine on static and dynamic properties of model bio-membranes. Biophys Chem 2012; 160:20-7. [DOI: 10.1016/j.bpc.2011.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 08/28/2011] [Accepted: 08/30/2011] [Indexed: 11/28/2022]
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29
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Nishimoto M, Komatsu U, Tamai N, Yamanaka M, Kaneshina S, Ogli K, Matsuki H. Intrinsic interaction mode of an inhalation anesthetic with globular proteins: a comparative study on ligand recognition. Colloid Polym Sci 2011. [DOI: 10.1007/s00396-011-2491-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Tsai MR, Chen SY, Shieh DB, Lou PJ, Sun CK. In vivo optical virtual biopsy of human oral mucosa with harmonic generation microscopy. BIOMEDICAL OPTICS EXPRESS 2011; 2:2317-28. [PMID: 21833368 PMCID: PMC3149529 DOI: 10.1364/boe.2.002317] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 07/16/2011] [Accepted: 07/20/2011] [Indexed: 05/20/2023]
Abstract
Recent clinical studies on human skin indicated that in vivo multi-harmonic generation microscopy (HGM) can achieve sub-micron resolution for histopathological analysis with a high penetration depth and leave no energy or photodamages in the interacted tissues. It is thus highly desired to apply HGM for in vivo mucosa histopathological diagnosis. In this paper, the first in vivo optical virtual biopsy of human oral mucosa by using epi-HGM is demonstrated. We modified an upright microscope to rotate the angle of objective for in vivo observation. Our clinical study reveals the capability of HGM to in vivo image cell distributions in human oral mucosa, including epithelium and lamina propria with a high penetration depth greater than 280 μm and a high spatial resolution better than 500 nm. We also found that the third-harmonic-generation (THG) contrast on nucleus depends strongly on its thicknesses, in agreement with a numerical simulation. Besides, 4% acetic acid was found to be able to enhance the THG contrast of nucleus in oral mucosa, while such enhancement was found to decay due to the metabolic clearance of the contrast enhancer by the oral mucosa. Our clinical study indicated that, the combined epi-THG and epi-second-harmonic-generation (SHG) microscopy is a promising imaging tool for in vivo noninvasive optical virtual biopsy and disease diagnosis in human mucosa.
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Affiliation(s)
- Ming-Rung Tsai
- Graduate Inst. of Photonics and Optoelectronics and Department of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Szu-Yu Chen
- Graduate Inst. of Photonics and Optoelectronics and Department of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Dar-Bin Shieh
- Institute of Oral Medical and Department of Stomatology, Cheng Kung University Medical College and Hospital, Tainan 70101, Taiwan, and Advanced Optoelectronic Technology Center, Center for Micro/Nano Science and Technology, and Innovation Center for Advanced Medical Device Technology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Pei-Jen Lou
- Department of Otolaryngology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, 100, Taiwan
| | - Chi-Kuang Sun
- Graduate Inst. of Photonics and Optoelectronics and Department of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan
- Institute of Physics and Research Center for Applied Sciences, Academia Sinica, Taipei, 115, Taiwan
- Molecular Imaging Center and Graduate Inst. of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
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31
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Mondal Roy S, Sarkar M. Membrane fusion induced by small molecules and ions. J Lipids 2011; 2011:528784. [PMID: 21660306 PMCID: PMC3108104 DOI: 10.1155/2011/528784] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 01/28/2011] [Accepted: 02/25/2011] [Indexed: 01/11/2023] Open
Abstract
Membrane fusion is a key event in many biological processes. These processes are controlled by various fusogenic agents of which proteins and peptides from the principal group. The fusion process is characterized by three major steps, namely, inter membrane contact, lipid mixing forming the intermediate step, pore opening and finally mixing of inner contents of the cells/vesicles. These steps are governed by energy barriers, which need to be overcome to complete fusion. Structural reorganization of big molecules like proteins/peptides, supplies the required driving force to overcome the energy barrier of the different intermediate steps. Small molecules/ions do not share this advantage. Hence fusion induced by small molecules/ions is expected to be different from that induced by proteins/peptides. Although several reviews exist on membrane fusion, no recent review is devoted solely to small moleculs/ions induced membrane fusion. Here we intend to present, how a variety of small molecules/ions act as independent fusogens. The detailed mechanism of some are well understood but for many it is still an unanswered question. Clearer understanding of how a particular small molecule can control fusion will open up a vista to use these moleucles instead of proteins/peptides to induce fusion both in vivo and in vitro fusion processes.
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Affiliation(s)
- Sutapa Mondal Roy
- Chemical Sciences Division, Saha Institute of Nuclear Physics, Sector 1, Block AF, Bidhannagar, Kolkata 700064, India
| | - Munna Sarkar
- Chemical Sciences Division, Saha Institute of Nuclear Physics, Sector 1, Block AF, Bidhannagar, Kolkata 700064, India
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32
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Reigada R. Influence of Chloroform in Liquid-Ordered and Liquid-Disordered Phases in Lipid Membranes. J Phys Chem B 2011; 115:2527-35. [DOI: 10.1021/jp110699h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ramon Reigada
- Department of Physical Chemistry, Universitat de Barcelona, Barcelona, Spain, and Institut de Química Teòrica i Computacional (IQTCUB), Barcelona, Spain
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33
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Kyrychenko A, Sevriukov IY, Syzova ZA, Ladokhin AS, Doroshenko AO. Partitioning of 2,6-Bis(1H-Benzimidazol-2-yl)pyridine fluorophore into a phospholipid bilayer: complementary use of fluorescence quenching studies and molecular dynamics simulations. Biophys Chem 2011; 154:8-17. [PMID: 21211898 PMCID: PMC4167733 DOI: 10.1016/j.bpc.2010.12.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 12/04/2010] [Accepted: 12/05/2010] [Indexed: 10/18/2022]
Abstract
Successful use of fluorescence sensing in elucidating the biophysical properties of lipid membranes requires knowledge of the distribution and location of an emitting molecule in the bilayer. We report here that 2,6-bis(1H-benzimidazol-2-yl)pyridine (BBP), which is almost non-fluorescent in aqueous solutions, reveals a strong emission enhancement in a hydrophobic environment of a phospholipid bilayer, making it interesting for fluorescence probing of water content in a lipid membrane. Comparing the fluorescence behavior of BBP in a wide variety of solvents with those in phospholipid vesicles, we suggest that the hydrogen bonding interactions between a BBP fluorophore and water molecules play a crucial role in the observed "light switch effect". Therefore, the loss of water-induced fluorescence quenching inside a membrane are thought to be due to deep penetration of BBP into the hydrophobic, water-free region of a bilayer. Characterized by strong quenching by transition metal ions in solution, BBP also demonstrated significant shielding from the action of the quencher in the presence of phospholipid vesicles. We used the increase in fluorescence intensity, measured upon titration of probe molecules with lipid vesicles, to estimate the partition constant and the Gibbs free energy (ΔG) of transfer of BBP from aqueous buffer into a membrane. Partitioning BBP revealed strongly favorable ΔG, which depends only slightly on the lipid composition of a bilayer, varying in a range from -6.5 to -7.0kcal/mol. To elucidate the binding interactions of the probe with a membrane on the molecular level, a distribution and favorable location of BBP in a POPC bilayer were modeled via atomistic molecular dynamics (MD) simulations using two different approaches: (i) free, diffusion-driven partitioning of the probe molecules into a bilayer and (ii) constrained umbrella sampling of a penetration profile of the dye molecule across a bilayer. Both of these MD approaches agreed with regard to the preferred location of a BBP fluorophore within the interfacial region of a bilayer, located between the hydrocarbon acyl tails and the initial portion of the lipid headgroups. MD simulations also revealed restricted permeability of water molecules into this region of a POPC bilayer, determining the strong fluorescence enhancement observed experimentally for the membrane-partitioned form of BBP.
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Affiliation(s)
- Alexander Kyrychenko
- Institute for Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61077, Ukraine
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160-7421, United States
- Ukrainian-American Laboratory of Computational Chemistry, Kharkiv, Ukraine and Jackson, Mississippi, United States
| | - Igor Yu. Sevriukov
- Institute for Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61077, Ukraine
| | - Zoya A. Syzova
- Institute for Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61077, Ukraine
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160-7421, United States
| | - Andrey O. Doroshenko
- Institute for Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61077, Ukraine
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34
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Kyrychenko A, Wu F, Thummel RP, Waluk J, Ladokhin AS. Partitioning and localization of environment-sensitive 2-(2'-pyridyl)- and 2-(2'-pyrimidyl)-indoles in lipid membranes: a joint refinement using fluorescence measurements and molecular dynamics simulations. J Phys Chem B 2010; 114:13574-84. [PMID: 20925327 PMCID: PMC4470561 DOI: 10.1021/jp106981c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence of environment-sensitive dyes is widely applied to monitor local structure and solvation dynamics of biomolecules. It has been shown that, in comparison with a parent indole fluorophore, fluorescence of 2-(2'-pyridyl)-5-methylindole (5M-PyIn-0) and 2-[2'-(4',6'-dimethylpyrimidyl)]-indole (DMPmIn-0) is remarkably sensitive to hydrogen bonding with protic partners. Strong fluorescence, observed for these compounds in nonpolar and polar aprotic solvents, is efficiently quenched in aqueous solution. This study demonstrates that 5M-PyIn-0 and DMPmIn-0, which are almost nonemitting in aqueous solution, become highly fluorescent upon titrating with phospholipid vesicles. The fluorescence enhancement is accompanied by a significant blue shift of emission maximum. The Gibbs free energy of membrane partitioning, measured by the increase in the steady-state fluorescence intensities during transfer from an aqueous environment to a lipid bilayer, is very favorable for both compounds, being in a range from -7.1 to -8.0 kcal/mol and depending only slightly on lipid composition of the membrane. The fluorescence enhancement upon membrane partitioning is indicative of the loss of the specific hydrogen-bonding interactions between the excited fluorophore and water molecules, causing efficient fluorescence quenching in bulk water. This conclusion is supported by atomistic molecular dynamics (MD) simulations, demonstrating that both 5M-PyIn-0 and DMPmIn-0 bind rapidly and partition deeply into a lipid bilayer. MD simulations also show a rapid, nanosecond-scale decrease in the probability of solute-solvent hydrogen bonding during passive diffusion of the probe molecules from bulk water into a lipid bilayer. At equilibrium conditions, both 5M-PyIn-0 and DMPmIn-0 prefer deep localization within the hydrophobic, water-free region of the bilayer. A free energy profile of penetration across a bilayer estimated using MD umbrella sampling shows that both indole derivatives favor residence in a rather wide potential energy well located 10-15 Å from the bilayer center.
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Affiliation(s)
- Alexander Kyrychenko
- Corresponding authors. (A.K.) Phone: (+38)-057-707-5335. . (J.W.) Fax: (+48)-22-343-3333. . (A.S.L.) Fax: (+1)-913-588-7440.
| | | | | | - Jacek Waluk
- Corresponding authors. (A.K.) Phone: (+38)-057-707-5335. . (J.W.) Fax: (+48)-22-343-3333. . (A.S.L.) Fax: (+1)-913-588-7440.
| | - Alexey S. Ladokhin
- Corresponding authors. (A.K.) Phone: (+38)-057-707-5335. . (J.W.) Fax: (+48)-22-343-3333. . (A.S.L.) Fax: (+1)-913-588-7440.
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Pinnick ER, Erramilli S, Wang F. The potential of mean force of nitrous oxide in a 1,2-dimyristoylphosphatidylcholine lipid bilayer. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.02.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Hénin J, Brannigan G, Dailey WP, Eckenhoff R, Klein ML. An atomistic model for simulations of the general anesthetic isoflurane. J Phys Chem B 2010; 114:604-12. [PMID: 19924847 DOI: 10.1021/jp9088035] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An atomistic model of isoflurane is constructed and calibrated to describe its conformational preferences and intermolecular interactions. The model, which is compatible with the CHARMM force field for biomolecules, is based on target quantities including bulk liquid properties, molecular conformations, and local interactions with isolated water molecules. Reference data is obtained from tabulated thermodynamic properties and high-resolution structural information from gas-phase electron diffraction, as well as DFT calculations at the B3LYP level. The model is tested against experimentally known solvation properties in water and oil, and shows quantitative agreement. In particular, isoflurane is faithfully described as lipophilic, yet nonhydrophobic, a combination of properties critical to its pharmacological activity. Intermolecular interactions of the model are further probed through simulations of the binding of isoflurane to a binding site in horse spleen apoferritin (HSAF). The observed binding mode compares well with crystallographic data, and the calculated binding affinities are compatible with experimental results, although both computational and experimental measurements are challenging and provide results with limited precision. The model is expected to be useful for detailed simulations of the elementary molecular processes associated with anesthesia. Full parameters are provided as Supporting Information.
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Affiliation(s)
- Jérôme Hénin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS, Marseille, France.
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Vemparala S, Domene C, Klein ML. Computational studies on the interactions of inhalational anesthetics with proteins. Acc Chem Res 2010; 43:103-10. [PMID: 19788306 DOI: 10.1021/ar900149j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite the widespread clinical use of anesthetics since the 19th century, a clear understanding of the mechanism of anesthetic action has yet to emerge. On the basis of early experiments by Meyer, Overton, and subsequent researchers, the cell's lipid membrane was generally concluded to be the primary site of action of anesthetics. However, later experiments with lipid-free globular proteins, such as luciferase and apoferritin, shifted the focus of anesthetic action to proteins. Recent experimental studies, such as photoaffinity labeling and mutagenesis on membrane proteins, have suggested specific binding sites for anesthetic molecules, further strengthening the proteocentric view of anesthetic mechanism. With the increased availability of high-resolution crystal structures of ion channels and other integral membrane proteins, as well as the availability of powerful computers, the structure-function relationship of anesthetic-protein interactions can now be investigated in atomic detail. In this Account, we review recent experiments and related computer simulation studies involving interactions of inhalational anesthetics and proteins, with a particular focus on membrane proteins. Globular proteins have long been used as models for understanding the role of protein-anesthetic interactions and are accordingly examined in this Account. Using selected examples of membrane proteins, such as nicotinic acetyl choline receptor (nAChR) and potassium channels, we address the issues of anesthetic binding pockets in proteins, the role of conformation in anesthetic effects, and the modulation of local as well as global dynamics of proteins by inhaled anesthetics. In the case of nicotinic receptors, inhalational anesthetic halothane binds to the hydrophobic cavity close to the M2-M3 loop. This binding modulates the dynamics of the M2-M3 loop, which is implicated in allosterically transmitting the effects to the channel gate, thus altering the function of the protein. In potassium channels, anesthetic molecules preferentially potentiate the open conformation by quenching the motion of the aromatic residues implicated in the gating of the channel. These simulations suggest that low-affinity drugs (such as inhalational anesthetics) modulate the protein function by influencing local as well as global dynamics of proteins. Because of intrinsic experimental limitations, computational approaches represent an important avenue for exploring the mode of action of anesthetics. Molecular dynamics simulations-a computational technique frequently used in the general study of proteins-offer particular insight in the study of the interaction of inhalational anesthetics with membrane proteins.
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Affiliation(s)
- Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T Campus, Taramani, Chennai 600 113, India
| | - Carmen Domene
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ U.K
| | - Michael L. Klein
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323
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Anaesthetic mechanisms: update on the challenge of unravelling the mystery of anaesthesia. Eur J Anaesthesiol 2009; 26:807-20. [PMID: 19494779 DOI: 10.1097/eja.0b013e32832d6b0f] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
General anaesthesia is administered each day to thousands of patients worldwide. Although more than 160 years have passed since the first successful public demonstration of anaesthesia, a detailed understanding of the anaesthetic mechanism of action of these drugs is still lacking. An important early observation was the Meyer-Overton correlation, which associated the potency of an anaesthetic with its lipid solubility. This work focuses attention on the lipid membrane as a likely location for anaesthetic action. With the advent of cellular electrophysiology and molecular biology techniques, tools to dissect the components of the lipid membrane have led, in recent years, to the widespread acceptance of proteins, namely receptors and ion channels, as more likely targets for the anaesthetic effect. Yet these accumulated data have not produced a comprehensive explanation for how these drugs produce central nervous system depression. In this review, we follow the story of anaesthesia mechanisms research from its historical roots to the intensely neurophysiological research regarding it today. We will also describe recent findings that identify specific neuroanatomical locations mediating the actions of some anaesthetic agents.
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Effects of Halothane on Dimyristoylphosphatidylcholine Lipid Bilayer Structure: A Molecular Dynamics Simulation Study. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.9.2087] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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A comparative study on specific and nonspecific interactions in bovine serum albumin: thermal and volume effects of halothane and palmitic acid. Colloid Polym Sci 2009. [DOI: 10.1007/s00396-009-2054-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Affiliation(s)
- Stefan Balaz
- Department of Pharmaceutical Sciences, College of Pharmacy, North Dakota State University, Fargo, North Dakota 58105, USA.
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Weng Y, Hsu TT, Zhao J, Nishimura S, Fuller GG, Sonner JM. Isovaleric, methylmalonic, and propionic acid decrease anesthetic EC50 in tadpoles, modulate glycine receptor function, and interact with the lipid 1,2-dipalmitoyl-Sn-glycero-3-phosphocholine. Anesth Analg 2009; 108:1538-45. [PMID: 19372333 DOI: 10.1213/ane.0b013e31819cd964] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Elevated concentrations of isovaleric (IVA), methylmalonic (MMA), and propionic acid are associated with impaired consciousness in genetic diseases (organic acidemias). We conjectured that part of the central nervous system depression observed in these disorders was due to anesthetic effects of these metabolites. We tested three hypotheses. First, that these metabolites would have anesthetic-sparing effects, possibly being anesthetics by themselves. Second, that these compounds would modulate glycine and gamma-aminobutyric acid (GABA(A)) receptor function, increasing chloride currents through these channels as potent clinical inhaled anesthetics do. Third, that these compounds would affect physical properties of lipids. METHODS Anesthetic EC(50)s were measured in Xenopus laevis tadpoles. Glycine and GABA(A) receptors were expressed in Xenopus laevis oocytes and studied using two-electrode voltage clamping. Pressure-area isotherms of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) monolayers were measured with and without added organic acids. RESULTS IVA acid was an anesthetic in tadpoles, whereas MMA and propionic acid decreased isoflurane's EC(50) by half. All three organic acids concentration-dependently increased current through alpha(1) glycine receptors. There were minimal effects on alpha(1)beta(2)gamma(2s) GABA(A) receptors. The organic acids increased total lateral pressure (surface pressure) of DPPC monolayers, including at mean molecular areas typical of bilayers. CONCLUSION IVA, MMA, and propionic acid have anesthetic effects in tadpoles, positively modulate glycine receptor function and affect physical properties of DPPC monolayers.
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Affiliation(s)
- Yun Weng
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94143-0464, USA
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Nishimoto M, Hata T, Goto M, Tamai N, Kaneshina S, Matsuki H, Ueda I. Interaction modes of long-chain fatty acids in dipalmitoylphosphatidylcholine bilayer membrane: contrast to mode of inhalation anesthetics. Chem Phys Lipids 2009; 158:71-80. [DOI: 10.1016/j.chemphyslip.2009.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 12/22/2008] [Accepted: 02/06/2009] [Indexed: 10/21/2022]
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Jedlovszky P, Sega M, Vallauri R. GM1 Ganglioside Embedded in a Hydrated DOPC Membrane: A Molecular Dynamics Simulation Study. J Phys Chem B 2009; 113:4876-86. [DOI: 10.1021/jp808199p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pál Jedlovszky
- Laboratory of Interfaces and Nanosize Systems, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/a, H-1117 Budapest, Hungary, and HAS Research Group of Technical Analytical Chemistry, Szt. Gellért tér 4, H-1111 Budapest, Hungary
| | - Marcello Sega
- Department of Physics, University of Trento, via Sommarive 14, I-38050 Povo, Trento, Italy, and Frankfurt Institute for Advanced Studies, J. W. Goethe University, Ruth-Moufang Str. 1, D-60438 Frankfurt, Germany
| | - Renzo Vallauri
- Department of Physics, University of Trento, via Sommarive 14, I-38050 Povo, Trento, Italy
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Sonner JM. A hypothesis on the origin and evolution of the response to inhaled anesthetics. Anesth Analg 2008; 107:849-54. [PMID: 18713893 DOI: 10.1213/ane.0b013e31817ee684] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this article, I present an evolutionary explanation for why organisms respond to inhaled anesthetics. It is conjectured that organisms today respond to inhaled anesthetics owing to the sensitivity of ion channels to inhaled anesthetics, which in turn has arisen by common descent from ancestral, anesthetic-sensitive ion channels in one-celled organisms (i.e., that the response to anesthetics did not arise as an adaptation of the nervous system, but rather of ion channels that preceded the origin of multicellularity). This sensitivity may have been refined by continuing selection at synapses in multicellular organisms. In particular, it is hypothesized that 1) the beneficial trait that was selected for in one-celled organisms was the coordinated response of ion channels to compounds that were present in the environment, which influenced the conformational equilibrium of ion channels; 2) this coordinated response prevented the deleterious consequences of entry of positive charges into the cell, thereby increasing the fitness of the organism; and 3) these compounds (which may have included organic anions, cations, and zwitterions as well as uncharged compounds) mimicked inhaled anesthetics in that they were interfacially active, and modulated ion channel function by altering bilayer properties coupled to channel function. The proposed hypothesis is consistent with known properties of inhaled anesthetics. In addition, it leads to testable experimental predictions of nonvolatile compounds having anesthetic-like modulatory effects on ion channels and in animals, including endogenous compounds that may modulate ion channel function in health and disease. The latter included metabolites that are increased in some types of end-stage organ failure, and genetic metabolic diseases. Several of these predictions have been tested and proved to be correct.
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Affiliation(s)
- James M Sonner
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94143-0464, USA.
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Chau PL, Tu KM, Liang K, Chan S, Matubayasi N. Free-energy change of inserting halothane into different depths of a hydrated DMPC bilayer. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.07.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Kyrychenko A, Waluk J. Distribution and favorable binding sites of pyrroloquinoline and its analogues in a lipid bilayer studied by molecular dynamics simulations. Biophys Chem 2008; 136:128-35. [PMID: 18556112 DOI: 10.1016/j.bpc.2008.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2008] [Revised: 05/22/2008] [Accepted: 05/22/2008] [Indexed: 11/17/2022]
Abstract
The distribution of 1H-pyrrolo[3,2-h]quinoline (PQ), 11H-dipyrido[2,3-a]carbazole (PC) and 7-azaindole (7AI) at a water/membrane interface has been investigated by molecular dynamics (MD) simulations. The MD study focused on favorable binding sites of the azaaromatic probes across a dipalmitoylphosphatidylcholine (DPPC) bilayer. Our simulations show that PQ and PC are preferably accommodated at the hydrocarbon core of the bilayer below the glycerol moiety. In addition, it is found that the hydrophobic aromatic parts of the probes are located inside a more ordered region of DPPC, consisting of hydrophobic lipid chains. In contrast to PQ and PC, 7AI is characterized by a broad distribution between a DPPC interface and water, so that the three preferable binding sites are found across a water/membrane interface. It is found that in the sequence 7AI-PQ-PC, due to the increase of the number of aromatic rings and, hence, the hydrophobic character of the probes, the depth of the probe localization is gradually shifted deeper inside the hydrocarbon core of the bilayer. We found that the probe-lipid hydrogen-bonding contributes weakly to the favorable localizations of the azaaromatic probes inside the DPPC bilayer, so that the probe localization is mainly driven by electrostatic dipole-dipole and van der Waals interactions.
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Affiliation(s)
- Alexander Kyrychenko
- Institute for Chemistry, V.N. Karazin Kharkov National University, 4 Svobody Sq., 61077, Kharkov, Ukraine.
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Pereira CS, Hünenberger PH. The influence of polyhydroxylated compounds on a hydrated phospholipid bilayer: a molecular dynamics study. MOLECULAR SIMULATION 2008. [DOI: 10.1080/08927020701784762] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Matubayasi N, Shinoda W, Nakahara M. Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation. J Chem Phys 2008; 128:195107. [DOI: 10.1063/1.2919117] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Interaction of anesthetics with open and closed conformations of a potassium channel studied via molecular dynamics and normal mode analysis. Biophys J 2008; 94:4260-9. [PMID: 18310250 DOI: 10.1529/biophysj.107.119958] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A variety of experiments suggest that membrane proteins are important targets of anesthetic molecules, and that ion channels interact differently with anesthetics in their open and closed conformations. The availability of an open and a closed structural model for the KirBac1.1 potassium channel has made it possible to perform a comparative analysis of the interactions of anesthetics with the same channel in its open and closed states. To this end, all-atom molecular dynamics simulations supplemented by normal mode analysis have been employed to probe the interactions of the inhalational anesthetic halothane with both an open and closed conformer of KirBac1.1 embedded in a lipid bilayer. Normal mode analysis on the closed and open channel, in the presence and absence of halothane, reveals that the anesthetic modulates the global as well as the local dynamics of both conformations differently. In the case of the open channel, the observed reduction of flexibility of residues in the inner helices suggests a functional modification action of anesthetics on ion channels. In this context, preferential quenching of the aromatic residue motion and modulation of global dynamics by halothane may be seen as steps toward potentiating or favoring open state conformations. These molecular dynamics simulations provide the first insights into possible specific interactions between anesthetic molecules and ion channels in different conformations.
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