1
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Nguyen MHL, Dziura D, DiPasquale M, Castillo SR, Kelley EG, Marquardt D. Investigating the cut-off effect of n-alcohols on lipid movement: a biophysical study. SOFT MATTER 2023. [PMID: 37357554 DOI: 10.1039/d2sm01583h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
Cellular membranes are responsible for absorbing the effects of external perturbants for the cell's survival. Such perturbants include small ubiquitous molecules like n-alcohols which were observed to exhibit anesthetic capabilities, with this effect tapering off at a cut-off alcohol chain length. To explain this cut-off effect and complement prior biochemical studies, we investigated a series of n-alcohols (with carbon lengths 2-18) and their impact on several bilayer properties, including lipid flip-flop, intervesicular exchange, diffusion, membrane bending rigidity and more. To this end, we employed an array of biophysical techniques such as time-resolved small angle neutron scattering (TR-SANS), small angle X-ray scattering (SAXS), all atomistic and coarse-grained molecular dynamics (MD) simulations, and calcein leakage assays. At an alcohol concentration of 30 mol% of the overall lipid content, TR-SANS showed 1-hexanol (C6OH) increased transverse lipid diffusion, i.e. flip-flop. As alcohol chain length increased from C6 to C10 and longer, lipid flip-flop slowed by factors of 5.6 to 32.2. Intervesicular lipid exchange contrasted these results with only a slight cut-off at alcohol concentrations of 30 mol% but not 10 mol%. SAXS, MD simulations, and leakage assays revealed changes to key bilayer properties, such as bilayer thickness and fluidity, that correlate well with the effects on lipid flip-flop rates. Finally, we tie our results to a defect-mediated pathway for alcohol-induced lipid flip-flop.
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Affiliation(s)
- Michael H L Nguyen
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Dominik Dziura
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Mitchell DiPasquale
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Stuart R Castillo
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Elizabeth G Kelley
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
- Department of Physics, University of Windsor, Windsor, Ontario, Canada.
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2
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Klacsová M, Bóta A, Westh P, de Souza Funari S, Uhríková D, Balgavý P. Thermodynamic and structural study of DMPC-alkanol systems. Phys Chem Chem Phys 2021; 23:8598-8606. [PMID: 33876021 DOI: 10.1039/d0cp04991c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The thermodynamic and structural behaviors of lamellar dimyristoylphosphatidylcholine-alkanol (abbreviation DMPC-CnOH, n = 8-18 is the even number of carbons in the alkyl chain) systems were studied by using DSC and SAXD/WAXD methods at a 0-0.8 CnOH : DMPC molar ratio range. Up to n≤ 10 a significant biphasic effect depending on the main transition temperature tm on the CnOH concentration was observed. Two breakpoints were revealed: turning point (TP), corresponding to the minimum, and threshold concentration (cT), corresponding to the end of the biphasic tendency. These breakpoints were also observed in the alkanol concentration dependent change in the enthalpy of the main transition ΔHm. In the case of CnOHs with n > 10 we propose a marked shift of TP and cT to very low concentrations; consequently, only increase of tm is observed. A partial phase diagram was constructed for a pseudo-binary DMPC-C12OH system. We suggest a fluid-fluid immiscibility of the DMPC-C12OH system above cT with a consequent formation of domains with different C12OH contents. At a constant CnOH concentration, the effects of CnOHs on ΔHm and bilayer repeat distance were found to depend predominantly on the mismatch between CnOH and lipid chain lengths. Observed effects are suggested to be underlined by a counterbalancing effect of interchain van der Waals interactions and headgroup repulsion.
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Affiliation(s)
- Mária Klacsová
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 832 32 Bratislava, Slovakia.
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3
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Maiti A, Daschakraborty S. Effect of TMAO on the Structure and Phase Transition of Lipid Membranes: Potential Role of TMAO in Stabilizing Cell Membranes under Osmotic Stress. J Phys Chem B 2021; 125:1167-1180. [PMID: 33481606 DOI: 10.1021/acs.jpcb.0c08335] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Extremophiles adopt strategies to deal with different environmental stresses, some of which are severely damaging to their cell membrane. To combat high osmotic stress, deep-sea organisms synthesize osmolytes, small polar organic molecules, like trimethylamine-N-oxide (TMAO), and incorporate them in the cell. TMAO is known to protect cells from high osmotic or hydrostatic pressure. Several experimental and simulation studies have revealed the roles of such osmolytes on stabilizing proteins. In contrast, the effect of osmolytes on the lipid membrane is poorly understood and broadly debated. A recent experiment has found strong evidence of the possible role of TMAO in stabilizing lipid membranes. Using the molecular dynamics (MD) simulation technique, we have demonstrated the effect of TMAO on two saturated fully hydrated lipid membranes in their fluid and gel phases. We have captured the impact of TMAO's concentration on the membrane's structural properties along with the fluid/gel phase transition temperatures. On increasing the concentration of TMAO, we see a substantial increase in the packing density of the membrane (estimated by area, thickness, and volume) and enhancement in the orientational order of lipid molecules. Having repulsive interaction with the lipid head group, the TMAO molecules are expelled away from the membrane surface, which induces dehydration of the lipid head groups, increasing the packing density. The addition of TMAO also increases the fluid/gel phase transition temperature of the membrane. All of these results are in close agreement with the experimental observations. This study, therefore, provides a molecular-level understanding of how TMAO can influence the cell membrane of deep-sea organisms and help in combating the osmotic stress condition.
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Affiliation(s)
- Archita Maiti
- Department of Chemistry, Indian Institute of Technology Patna, Patna, Bihar 801106, India
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4
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Ludwig J, Maibaum L. Effect of alcohol on the phase separation in model membranes. Chem Phys Lipids 2020; 233:104986. [PMID: 33080278 DOI: 10.1016/j.chemphyslip.2020.104986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/20/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022]
Abstract
The discovery of coexisting liquid-ordered and liquid-disordered phases in multicomponent lipid bilayers has received widespread attention due to its potential relevance for biological systems. One of the many open questions is how the presence of additional components affects the nature of the coexisting phases. Of particular interest is the addition of alcohols because their anesthetic properties may arise from modulating bilayer behavior. We use coarse-grained Molecular Dynamics simulations to gain insight into the partitioning preferences of linear n-alcohols into ordered and disordered bilayers alongside their effects on local membrane structure. We find that alcohols cause only small changes to membrane composition alongside a lack of significant effects on membrane thickness and lipid tail order. Cholesterol and n-alcohol trans-bilayer motion is measured and found to be near or within the range of previous atomistic results. The cholesterol flip-flop rates increase with both n-alcohol length and concentration for octanol, dodecanol, and hexadecanol, indicating a decrease in lipid order. Umbrella sampling simulations of removing cholesterol from tertiary membranes find no significant difference with or without n-alcohols at various concentrations. Simulations of a phase-separated bilayer show that octanol preferentially partitions into the liquid-disordered phase in a ratio of approximately 3:1 over the liquid-ordered phase. Furthermore, partition coefficients of alcohol in single-phase membranes show a preference for longer alcohols (dodecanol and hexadecanol) to partition preferentially into the liquid-ordered phase, while decreasing the length of the alcohol reverses this trend. Our work tests experimental results while also investigating the ability for coarse-grained MARTINI simulations to capture minute differences in model membrane spatial arrangements on the nanoscale level.
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Affiliation(s)
- James Ludwig
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States.
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5
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Martinotti C, Ruiz-Perez L, Deplazes E, Mancera RL. Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes. Chemphyschem 2020; 21:1486-1514. [PMID: 32452115 DOI: 10.1002/cphc.202000219] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/22/2020] [Indexed: 12/12/2022]
Abstract
Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.
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Affiliation(s)
- Carlo Martinotti
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Lanie Ruiz-Perez
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
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6
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Kučerka N, Gallová J, Uhríková D. The membrane structure and function affected by water. Chem Phys Lipids 2019; 221:140-144. [DOI: 10.1016/j.chemphyslip.2019.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 01/24/2023]
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7
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Subramaniam R, Lynch S, Cen Y, Balaz S. Polarity of Hydrated Phosphatidylcholine Headgroups. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8460-8471. [PMID: 31244216 PMCID: PMC6853183 DOI: 10.1021/acs.langmuir.8b03992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The headgroup (H) stratum (sometimes called the polar region) of membrane bilayers is a relevant yet poorly understood solvation phase for small molecules and macromolecules interacting with the membranes. Solvation of compounds in bilayer strata is characterized experimentally by wide- and small-angle X-ray scattering, neutron diffraction, and various NMR techniques. The quantification is tedious and only available for a limited set of small molecules. Our recently published model of liposome partitioning of small molecules shows that solvation of compounds in the H-stratum of fluid phosphatidylcholine (PC) bilayers correlates well with their solvation in hydrated diacetyl phosphatidylcholine (DAcPC), and solvation in the core (C) depends in a similar way on that in n-hexadecane. These two correlations became a basis for a model describing the location of compounds in the H- and C-strata and at the connecting interface as a nonlinear function of the fragment solvation characteristics of the compounds. In this study, refractivity of hydrated DAcPC phases with varying water contents was measured and polarity was determined using the steady-state fluorescence of indole and Nile Red. The results were compared with the published data obtained by other techniques for PC bilayers in liposomes or on solid supports. The demonstrated qualitative agreement, as well as the polarity and refractivity dependencies on the DAcPC concentration, supports the suitability of hydrated DAcPC as the H-stratum surrogate. Interestingly, depending on hydrations typical for the H-strata of fluid PC bilayers, the dielectric constant could decrease significantly from 31.0 to 7.3 for 16 and 8 water molecules per headgroup, respectively. Although additional experiments are needed for confirmation, this observation could help set proper dielectric constant magnitudes in continuum-based computational models of accumulation and crossing of the PC bilayers with varying hydration levels thanks to the temperature or the structure of fatty acid chains.
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Affiliation(s)
| | | | | | - Stefan Balaz
- Corresponding author: Stefan Balaz, Albany College of Pharmacy and Health Sciences, Vermont Campus, Department of Pharmaceutical Sciences, 261 Mountain View Road, Colchester, VT 05446, United States, phone 802-735-2615,
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8
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Nguyen MHL, DiPasquale M, Rickeard BW, Stanley CB, Kelley EG, Marquardt D. Methanol Accelerates DMPC Flip-Flop and Transfer: A SANS Study on Lipid Dynamics. Biophys J 2019; 116:755-759. [PMID: 30777306 DOI: 10.1016/j.bpj.2019.01.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/17/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022] Open
Abstract
Methanol is a common solubilizing agent used to study transmembrane proteins/peptides in biological and synthetic membranes. Using small angle neutron scattering and a strategic contrast-matching scheme, we show that methanol has a major impact on lipid dynamics. Under increasing methanol concentrations, isotopically distinct 1,2-dimyristoyl-sn-glycero-3-phosphocholine large unilamellar vesicle populations exhibit increased mixing. Specifically, 1,2-dimyristoyl-sn-glycero-3-phosphocholine transfer and flip-flop kinetics display linear and exponential rate enhancements, respectively. Ultimately, methanol is capable of influencing the structure-function relationship associated with bilayer composition (e.g., lipid asymmetry). The use of methanol as a carrier solvent, despite better simulating some biological conditions (e.g., antimicrobial attack), can help misconstrue lipid scrambling as the action of proteins or peptides, when in actuality it is a combination of solvent and biological agent. As bilayer compositional stability is crucial to cell survival and protein reconstitution, these results highlight the importance of methanol, and solvents in general, in biomembrane and proteolipid studies.
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Affiliation(s)
- Michael H L Nguyen
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Mitchell DiPasquale
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Brett W Rickeard
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | | | - Elizabeth G Kelley
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada.
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9
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Luna MA, Gutierrez JA, Cobo Solis AK, Molina PG, Correa NM. Vehiculization of noscapine in large unilamellar vesicles. Study of its protective role against lipid peroxidation by electrochemical techniques. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2018.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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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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11
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Kondela T, Gallová J, Hauß T, Ivankov O, Kučerka N, Balgavý P. Effect of alkan-1-ols on the structure of dopc model membrane. EUROPEAN PHARMACEUTICAL JOURNAL 2017. [DOI: 10.1515/afpuc-2017-0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
The effect of general anaesthetics alkan-1-ols (CnOH, where n = 10, 12, 14, 16 and 18 is the number of carbon atoms in the molecule) on the structure of dioleoylphosphatidylcholine (DOPC) model membrane was studied by small-angle neutron scattering (SANS) and small-angle neutron diffraction (SAND). Fluid bilayers were prepared at CnOH:DOPC = 0.3 molar ratio. The results of both the experiments show that bilayer thickness - a thickness parameter dg in the case of SANS and lamellar repeat distance D in the case of SAND - increases with increasing n. A coexistence of two lamellar phases with different D was detected by measuring the C18OH+DOPC oriented sample.
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Affiliation(s)
- T. Kondela
- Comenius University in Bratislava, Faculty of Pharmacy, Department of Physical Chemistry, Bratislava , Slovak Republic
| | - J. Gallová
- Comenius University in Bratislava, Faculty of Pharmacy, Department of Physical Chemistry, Bratislava , Slovakia
| | - T. Hauß
- Helmholtz Zentrum Berlin für Materialen und Energie, Berlin , Germany
| | - O. Ivankov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna , Russian Federation
- Moscow Institute of Physics and Technology, MIPT, Dolgoprudny , Russian Federation
- Institute for Safety Problems of Nuclear Power Plants, NAS Ukraine, Kiev , Ukraine
| | - N. Kučerka
- Comenius University in Bratislava, Faculty of Pharmacy, Department of Physical Chemistry, Bratislava , Slovak Republic
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna , Russian Federation
| | - P. Balgavý
- Comenius University in Bratislava, Faculty of Pharmacy, Department of Physical Chemistry, Bratislava , Slovakia
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12
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Kondela T, Gallová J, Hauß T, Barnoud J, Marrink SJ, Kučerka N. Alcohol Interactions with Lipid Bilayers. Molecules 2017; 22:E2078. [PMID: 29182554 PMCID: PMC6149720 DOI: 10.3390/molecules22122078] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 11/17/2022] Open
Abstract
We investigate the structural changes to lipid membrane that ensue from the addition of aliphatic alcohols with various alkyl tail lengths. Small angle neutron diffraction from flat lipid bilayers that are hydrated through water vapor has been employed to eliminate possible artefacts of the membrane curvature and the alcohol's membrane-water partitioning. We have observed clear changes to membrane structure in both transversal and lateral directions. Most importantly, our results suggest the alteration of the membrane-water interface. The water encroachment has shifted in the way that alcohol loaded bilayers absorbed more water molecules when compared to the neat lipid bilayers. The experimental results have been corroborated by molecular dynamics simulations to reveal further details. Namely, the order parameter profiles have been fruitful in correlating the mechanical model of structural changes to the effect of anesthesia.
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Affiliation(s)
- Tomáš Kondela
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, 832 32 Bratislava, Slovakia.
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russian.
| | - Jana Gallová
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, 832 32 Bratislava, Slovakia.
| | - Thomas Hauß
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, D-14109 Berlin, Germany.
| | - Jonathan Barnoud
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.
| | - Siewert-J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.
| | - Norbert Kučerka
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, 832 32 Bratislava, Slovakia.
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russian.
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13
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Usma CL, Pacios IE, Renamayor CS. Lyotropic Lamellar Structures of a Long-Chain Imidazolium and Their Application as Nanoreactors for X-ray-Initiated Polymerization. J Phys Chem B 2017; 121:2502-2510. [PMID: 28240884 DOI: 10.1021/acs.jpcb.6b12101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The lyotropic behavior of the ternary system formed by 1-tetradecyl-3-methylimidazolium chloride, 1-decanol, and water is investigated. A lamellar mesophase is formed for a wide range of compositions and is characterized by polarized optical microscopy, low-temperature scanning electron microscopy, small- and wide-angle X-ray scattering with synchrotron radiation, and differential scanning calorimetry. This phase presents onionlike structures. Two lamellar structures are formed: an Lα mesophase between 25 and 50 °C, with an isobaric thermal expansivity of the bilayer thickness of -3.2 × 10-3 K-1, and a lamellar gel phase, when the temperature decreases below 25 °C. This new medium is employed to perform in situ X-ray-initiated polymerization of N-isopropylacrylamide. When the monomer is incorporated in the lamellar structure, it is distributed between the water layer and bilayer interface and its polymerization can be followed by variations in the diffractograms with time.
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Affiliation(s)
- Cesar L Usma
- Departamento de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, UNED , Paseo Senda del Rey, 9, 28040 Madrid, Spain
| | - Isabel E Pacios
- Departamento de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, UNED , Paseo Senda del Rey, 9, 28040 Madrid, Spain
| | - Carmen S Renamayor
- Departamento de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, UNED , Paseo Senda del Rey, 9, 28040 Madrid, Spain
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14
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Melo M, Arnarez C, Sikkema H, Kumar N, Walko M, Berendsen HJC, Kocer A, Marrink SJ, Ingólfsson HI. High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. J Am Chem Soc 2017; 139:2664-2671. [PMID: 28122455 PMCID: PMC5343553 DOI: 10.1021/jacs.6b11091] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Indexed: 12/18/2022]
Abstract
The mechanosensitive channels of large conductance (MscL) are bacterial membrane proteins that serve as last resort emergency release valves in case of severe osmotic downshock. Sensing bilayer tension, MscL channels are sensitive to changes in the bilayer environment and are, therefore, an ideal test case for exploring membrane protein coupling. Here, we use high-throughput coarse-grained molecular dynamics simulations to characterize MscL gating kinetics in different bilayer environments under the influence of alcohols. We performed over five hundred simulations to obtain sufficient statistics to reveal the subtle effects of changes in the membrane environment on MscL gating. MscL opening times were found to increase with the addition of the straight-chain alcohols ethanol, octanol, and to some extent dodecanol but not with hexadecanol. Increasing concentration of octanol increased the impeding effect, but only up to 10-20 mol %. Our in silico predictions were experimentally confirmed using reconstituted MscL in a liposomal fluorescent efflux assay. Our combined data reveal that the effect of alcohols on MscL gating arises not through specific binding sites but through a combination of the alcohol-induced changes to a number of bilayer properties and their alteration of the MscL-bilayer interface. Our work provides a key example of how extensive molecular simulations can be used to predict the functional modification of membrane proteins by subtle changes in their bilayer environment.
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Affiliation(s)
- Manuel
N. Melo
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
| | - Clément Arnarez
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
| | - Hendrik Sikkema
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
| | - Neeraj Kumar
- Groningen
Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Martin Walko
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Herman J. C. Berendsen
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
| | - Armagan Kocer
- Department
of Neuroscience, University Medical Center
Groningen, University of Groningen, Antonius Deusinglaan 1, 99713 AV, Groningen, The
Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
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15
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Assessing gastric toxicity of xanthone derivatives of anti-inflammatory activity using simulation and experimental approaches. Biophys Chem 2016; 220:20-33. [PMID: 27846425 DOI: 10.1016/j.bpc.2016.10.007] [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: 07/17/2016] [Revised: 10/12/2016] [Accepted: 10/26/2016] [Indexed: 01/21/2023]
Abstract
Xanthones are tricyclic compounds of natural or synthetic origin exhibiting a broad spectrum of therapeutic activities. Three synthetic xanthone derivatives (KS1, KS2, and KS3) with properties typical for nonsteroidal anti-inflammatory drugs (NSAID) were objects of the presented model study. NSAIDs are in common use however; several of them exhibit gastric toxicity predominantly resulting from their direct interactions with the outermost lipid layer of the gastric mucosa that impair its hydrophobic barrier property. Among the studied xanthones, gastric toxicity of only KS2 has been determined in previous pharmacological studies, and it is low. In this study, carried out using X-ray diffraction and computer simulation, a palmitoyloleoylphosphatidylcholine-cholesterol bilayer (POPC-Chol) was used as a model of a hydrophobic layer of lipids protecting gastric mucosa as POPC and Chol are the main lipids in human mucus. X-ray diffraction data were used to validate the computer model. The aim of the study was to assess potential gastric toxicity of the xanthones by analysing their atomic level interactions with lipids, ions, and water in the lipid bilayer and their effect on the bilayer physicochemical properties. The results show that xanthones have small effect on the bilayer properties except for its rigidity whereas their interactions with water, ions, and lipids depend on their protonation state and for a given state, are similar for all the xanthones. As gastric toxicity of KS2 is low, based on MD simulations one can predict that toxicity of KS1 and KS3 is also low.
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Méndez-Bermúdez JG, Dominguez H. Structural changes of a sodium dodecyl sulfate (SDS) micelle induced by alcohol molecules. J Mol Model 2016; 22:33. [PMID: 26768159 DOI: 10.1007/s00894-015-2904-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/28/2015] [Indexed: 11/28/2022]
Abstract
Coarse-grained dynamical simulations have been performed to investigate the behavior of a surfactant micelle in the presence of six different alcohols: hexanol, octanol, decanol, dodecanol, tetradecanol, and hexadecanol. The self-assembly of sodium dodecyl sulfate (SDS) is modified by the alcohol molecules into cylindrical and bilayer micelles as a function of the alcohol/SDS mass ratio. Therefore, in order to understand, from a molecular point of view, how SDS and alcohol molecules self-organize to form the new micelles, different studies were carried out. Analysis of micelle structures, density profiles, and parameters of order were conducted to characterize the shape and size of those micelles. The density profiles revealed that the alcohol molecules were located at the water-micelle interface next to the SDS molecules at low alcohol/SDS mass ratio. At high alcohol/SDS mass ratios, alcohol molecules moved to the middle of the micelle by increasing their size and by producing a structural change. Moreover, micelle structures and sizes were influenced not only by the alcohol/SDS mass ratio but also by the order of the SDS and alcohol tails. Finally, the size of the micelles and enthalpy calculations were used as order parameters to determine a structural phase diagram of alcohol/SDS mixtures in water. Graphical Abstract Structural transition of SDS/alcohol mixtures.
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Affiliation(s)
- Jose G Méndez-Bermúdez
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, México, D.F., 04510, México
| | - Hector Dominguez
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, V6T1Z4, Canada.
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Eremin RA, Kholmurodov KT, Petrenko VI, Rosta L, Grigoryeva NA, Avdeev MV. On the microstructure of organic solutions of mono-carboxylic acids: Combined study by infrared spectroscopy, small-angle neutron scattering and molecular dynamics simulations. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.08.017] [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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18
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Belička M, Gerelli Y, Kučerka N, Fragneto G. The component group structure of DPPC bilayers obtained by specular neutron reflectometry. SOFT MATTER 2015; 11:6275-6283. [PMID: 26160133 DOI: 10.1039/c5sm00274e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Specular neutron reflectometry was measured on a floating bilayer system consisting of 1,2-dipalmitoyl-d62-sn-glycero-3-phosphocholine deposited over a 1,2-dibehenoyl-sn-glycero-3-phosphocholine bilayer at 25 and 55 °C. The internal structure of lipid bilayers was described by a one-dimensional neutron scattering length density profile model, originally developed for the evaluation of small-angle scattering data. The reflectivity data from the supported bilayer were evaluated separately and used further as constraints in modeling the floating bilayer reflectivity curves. The model reflectivity curves successfully describe the experimental reflectivities of the supported bilayer in the gel phase and the floating bilayer system in the liquid-crystalline phase. The results yield an internal structure of a deposited bilayer and a floating bilayer on the level of component groups of lipid molecules. The obtained structure of the floating d62-diC16:0PC bilayer displays high resemblance of the bilayer structure in the form of unilamellar vesicles. At the same time, however, the results show differences in comparison to unilamellar vesicle bilayers, most likely due to the undulations of supported bilayers.
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Affiliation(s)
- Michal Belička
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
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de Ghellinck A, Fragneto G, Laux V, Haertlein M, Jouhet J, Sferrazza M, Wacklin H. Lipid polyunsaturation determines the extent of membrane structural changes induced by Amphotericin B in Pichia pastoris yeast. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2317-25. [PMID: 26055896 DOI: 10.1016/j.bbamem.2015.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/20/2015] [Accepted: 06/04/2015] [Indexed: 12/18/2022]
Abstract
The activity of the potent but highly toxic antifungal drug Amphotericin B (AmB), used intravenously to treat systemic fungal and parasitic infections, is widely accepted to result from its specific interaction with the fungal sterol ergosterol. While the effect of sterols on AmB activity has been intensely investigated, the role of membrane phospholipid composition has largely been ignored, and structural studies of native membranes have been hampered by their complex and disordered nature. We show for the first time that the structure of fungal membranes derived from Pichia pastoris yeast depends on the degree of lipid polyunsaturation, which has an impact on the structural consequences of AmB activity. AmB inserts in yeast membranes even in the absence of ergosterol, and forms an extra-membraneous layer whose thickness is resolved to be 4-5 nm. In ergosterol-containing membranes, AmB insertion is accompanied by ergosterol extraction into this layer. The AmB-sponge mediated depletion of ergosterol from P. pastoris membranes gives rise to a significant membrane thinning effect that depends on the degree of lipid polyunsaturation. The resulting hydrophobic mismatch is likely to interfere with a much broader range of membrane protein functions than those directly involving ergosterol, and suggests that polyunsaturated lipids could boost the efficiency of AmB. Furthermore, a low degree of lipid polyunsaturation leads to least AmB insertion and may protect host cells against the toxic effects of AmB. These results provide a new framework based on lipid composition and membrane structure through which we can understand its antifungal action and develop better treatments.
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Affiliation(s)
- Alexis de Ghellinck
- Institut Laue-Langevin, 71 av des Martyrs, P.O. Box 156, 38000 Grenoble, France; Departement de Physique, Faculté des Sciences, Université Libre de Bruxelles, Bd du Triomphe CP223, 1050 Bruxelles, Belgium
| | - Giovanna Fragneto
- Institut Laue-Langevin, 71 av des Martyrs, P.O. Box 156, 38000 Grenoble, France
| | - Valerie Laux
- Institut Laue-Langevin, 71 av des Martyrs, P.O. Box 156, 38000 Grenoble, France
| | - Michael Haertlein
- Institut Laue-Langevin, 71 av des Martyrs, P.O. Box 156, 38000 Grenoble, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS/CEA/Univ. Grenoble Alpes/INRA, 38000 Grenoble, France
| | - Michele Sferrazza
- Departement de Physique, Faculté des Sciences, Université Libre de Bruxelles, Bd du Triomphe CP223, 1050 Bruxelles, Belgium
| | - Hanna Wacklin
- European Spallation Source ESS AB, P.O. Box 176, 22100 Lund, Sweden; Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.
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Natesan S, Lukacova V, Peng M, Subramaniam R, Lynch S, Wang Z, Tandlich R, Balaz S. Structure-based prediction of drug distribution across the headgroup and core strata of a phospholipid bilayer using surrogate phases. Mol Pharm 2014; 11:3577-95. [PMID: 25179490 PMCID: PMC4186683 DOI: 10.1021/mp5003366] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Solvation of drugs in the core (C)
and headgroup (H) strata of
phospholipid bilayers affects their physiological transport rates
and accumulation. These characteristics, especially a complete drug
distribution profile across the bilayer strata, are tedious to obtain
experimentally, to the point that even simplified preferred locations
are only available for a few dozen compounds. Recently, we showed
that the partition coefficient (P) values in the
system of hydrated diacetyl phosphatidylcholine (DAcPC) and n-hexadecane (C16), as surrogates of the H- and C-strata
of the bilayer composed of the most abundant mammalian phospholipid,
PC, agree well with the preferred bilayer location of compounds. High P values are typical for lipophiles accumulating in the
core, and low P values are characteristic of cephalophiles
preferring the headgroups. This simple pattern does not hold for most
compounds, which usually have more even distribution and may also
accumulate at the H/C interface. To model complete distribution, the
correlates of solvation energies are needed for each drug state in
the bilayer: (1) for the H-stratum it is the DAcPC/W P value, calculated as the ratio of the C16/W and C16/DAcPC (W for
water) P values; (2) for the C-stratum, the C16/W P value; (3) for the H/C interface, the P values for all plausible molecular poses are characterized using
the fragment DAcPC/W and C16/W solvation parameters for the parts
of the molecule embedded in the H- and C-strata, respectively. The
correlates, each scaled by two Collander coefficients, were used in
a nonlinear, mass-balance based model of intrabilayer distribution,
which was applied to the easily measurable overall P values of compounds in the DMPC (M = myristoyl) bilayers and monolayers
as the dependent variables. The calibrated model for 107 neutral compounds
explains 94% of experimental variance, achieves similar cross-validation
levels, and agrees well with the nontrivial, experimentally determined
bilayer locations for 27 compounds. The resulting structure-based
prediction system for intrabilayer distribution will facilitate more
realistic modeling of passive transport and drug interactions with
those integral membrane proteins, which have the binding sites located
in the bilayer, such as some enzymes, influx and efflux transporters,
and receptors. If only overall bilayer accumulation is of interest,
the 1-octanol/W P values suffice to model the studied
set.
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Affiliation(s)
- Senthil Natesan
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences , Vermont Campus, Colchester, Vermont 05446, United States
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Peters GH, Werge M, Elf-Lind MN, Madsen JJ, Velardez GF, Westh P. Interaction of neurotransmitters with a phospholipid bilayer: a molecular dynamics study. Chem Phys Lipids 2014; 184:7-17. [PMID: 25159594 DOI: 10.1016/j.chemphyslip.2014.08.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/14/2014] [Accepted: 08/22/2014] [Indexed: 11/15/2022]
Abstract
We have performed a series of molecular dynamics simulations to study the interactions between the neurotransmitters (NTs) γ-aminobutyrate (GABA), glycine (GLY), acetylcholine (ACH) and glutamate (GLU) as well as the amidated/acetylated γ-aminobutyrate (GABA(neu)) and the osmolyte molecule glycerol (GOL) with a dipalmitoylphosphatidylcholine (DPPC) bilayer. In agreement with previously published experimental data, we found the lowest membrane affinity for the charged molecules and a moderate affinity for zwitterionic and polar molecules. The affinity can be ranked as follows: ACH-GLU<<GABA<GLY<<GABA(neu)<<GOL. The latter three penetrated the bilayer at most with the deepest location being close to the glycerol backbone of the phospholipids. Even at that position, these solutes were noticeably hydrated and carried ∼30-80% of the bulk water along. The mobility of hydration water at the solute is also affected by the penetration into the bilayer. Two time scales of exchanging water molecules could be determined. In the bulk phase, the hydration layer contains ∼20% slow exchanging water molecules which increases 2-3 times as the solutes entered the bilayer. Our results indicate that there is no intermediate exchange of slow moving water molecules from the solutes to the lipid atoms and vice versa. Instead, the exchange relies on the reservoir of unbounded ("free") water molecules in the interfacial bilayer region. Results from the equilibrium simulations are in good agreement with the results from umbrella sampling simulations, which were conducted for the four naturally occurring NTs. Free energy profiles for ACH and GLU show a minimum of ∼2-3 kJ/mol close to the bilayer interface, while for GABA and GLY, a minimum of respectively ∼2 kJ/mol and ∼5 kJ/mol is observed when these NTs are located in the vicinity of the lipid glycerol backbone. The most important interaction of NTs with the bilayer is the charged amino group of NTs with the lipid phosphate group.
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Affiliation(s)
- Günther H Peters
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby 2800, Denmark.
| | - Mikkel Werge
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | | | - Jesper J Madsen
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Gustavo F Velardez
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Peter Westh
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Roskilde 4000, Denmark.
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Klacsová M, Karlovská J, Uhríková D, Funari SS, Balgavý P. Phase behavior of the DOPE + DOPC + alkanol system. SOFT MATTER 2014; 10:5842-5848. [PMID: 24980804 DOI: 10.1039/c4sm00530a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Small- and wide-angle X-ray diffraction was used to study the effect of 1-alkanols, as simple models of general anesthetics, (abbreviation CnOH, n = 8-18 is the even number of carbons in the aliphatic chain) on the lamellar to hexagonal Lα→ H(II) phase transition in the dioleoylphosphatidylethanolamine-dioleoylphosphatidylcholine = 3 : 1 mol/mol (DOPE + DOPC) system. All studied CnOHs were found to decrease the phase transition temperature of the DOPE + DOPC system in a CnOH chain length and concentration dependent manner and thus promote the formation of the HII phase. Anesthetically active C8OH and C10OH were found to decrease the lattice parameter d of the Lα phase, however longer non-anesthetic CnOHs increased the parameter d; this effect being more pronounced with increasing CnOH concentration. The lattice parameter of the HII phase was decreased in the presence of all CnOHs, even at the lowest concentrations studied. In the scope of the indirect mechanism of general anesthesia observed changes in the lattice parameter d (reflecting changes in the bilayer thickness) due to the intercalation of C8OH and C10OH might induce changes in the activity of integral membrane proteins engaged in neuronal pathways.
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Affiliation(s)
- Mária Klacsová
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
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Belička M, Kučerka N, Uhríková D, Islamov AK, Kuklin AI, Devínsky F, Balgavý P. Effects of N,N-dimethyl-N-alkylamine-N-oxides on DOPC bilayers in unilamellar vesicles: small-angle neutron scattering study. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:179-89. [DOI: 10.1007/s00249-014-0954-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 02/27/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
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25
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Bulacu M, Périole X, Marrink SJ. In Silico Design of Robust Bolalipid Membranes. Biomacromolecules 2011; 13:196-205. [DOI: 10.1021/bm201454j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Monica Bulacu
- Groningen
Biomolecular Sciences and Biotechnology Institute
and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Xavier Périole
- Groningen
Biomolecular Sciences and Biotechnology Institute
and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute
and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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