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Zimmerberg J, Soubias O, Pastor RW. Special issue for Klaus Gawrisch. Biophys J 2023; 122:E1-E8. [PMID: 36921597 PMCID: PMC10111273 DOI: 10.1016/j.bpj.2023.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/17/2023] Open
Affiliation(s)
- Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Olivier Soubias
- Macromolecular NMR Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Das S, Meinel MK, Wu Z, Müller-Plathe F. The role of the envelope protein in the stability of a coronavirus model membrane against an ethanolic disinfectant. J Chem Phys 2021; 154:245101. [PMID: 34241335 DOI: 10.1063/5.0055331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ethanol is highly effective against various enveloped viruses and can disable the virus by disintegrating the protective envelope surrounding it. The interactions between the coronavirus envelope (E) protein and its membrane environment play key roles in the stability and function of the viral envelope. By using molecular dynamics simulation, we explore the underlying mechanism of ethanol-induced disruption of a model coronavirus membrane and, in detail, interactions of the E-protein and lipids. We model the membrane bilayer as N-palmitoyl-sphingomyelin and 1-palmitoyl-2-oleoylphosphatidylcholine lipids and the coronavirus E-protein. The study reveals that ethanol causes an increase in the lateral area of the bilayer along with thinning of the bilayer membrane and orientational disordering of lipid tails. Ethanol resides at the head-tail region of the membrane and enhances bilayer permeability. We found an envelope-protein-mediated increase in the ordering of lipid tails. Our simulations also provide important insights into the orientation of the envelope protein in a model membrane environment. At ∼25 mol. % of ethanol in the surrounding ethanol-water phase, we observe disintegration of the lipid bilayer and dislocation of the E-protein from the membrane environment.
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Affiliation(s)
- Shubhadip Das
- Technische Universität Darmstadt, Eduard-Zintl-Institute für Anorganische und Physikalische Chemie, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Melissa K Meinel
- Technische Universität Darmstadt, Eduard-Zintl-Institute für Anorganische und Physikalische Chemie, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Zhenghao Wu
- Technische Universität Darmstadt, Eduard-Zintl-Institute für Anorganische und Physikalische Chemie, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Technische Universität Darmstadt, Eduard-Zintl-Institute für Anorganische und Physikalische Chemie, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
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3
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Muñoz-Gacitúa D, Monroy-Cárdenas M, Araya-Maturana R, Weiss-López B. Characterization of an anionic membrane mimetic with natural phospholipid content and magnetic orienting capabilities. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Effects of gabergic phenols on the dynamic and structure of lipid bilayers: A molecular dynamic simulation approach. PLoS One 2019; 14:e0218042. [PMID: 31237897 PMCID: PMC6592534 DOI: 10.1371/journal.pone.0218042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/24/2019] [Indexed: 11/19/2022] Open
Abstract
γ-Aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the vertebrate and invertebrate nervous system. GABAA receptors are activated by GABA and their agonists, and modulated by a wide variety of recognized drugs, including barbiturates, anesthetics, and benzodiazepines. The phenols propofol, thymol, chlorothymol, carvacrol and eugenol act as positive allosteric modulators on GABAA-R receptor. These GABAergic phenols interact with the lipid membrane, therefore, their anesthetic activity could be the combined result of their specific activity (with receptor proteins) as well as nonspecific interactions (with surrounding lipid molecules) modulating the supramolecular organization of the receptor environment. Therefore, we aimed to contribute to a description of the molecular events that occur at the membrane level as part of the mechanism of general anesthesia, using a molecular dynamic simulation approach. Equilibrium molecular dynamics simulations indicate that the presence of GABAergic phenols in a DPPC bilayer orders lipid acyl chains for carbons near the interface and their effect is not significant at the bilayer center. Phenols interacts with the polar interface of phospholipid bilayer, particularly forming hydrogen bonds with the glycerol and phosphate group. Also, potential of mean force calculations using umbrella sampling show that propofol partition is mainly enthalpic driven at the polar region and entropic driven at the hydrocarbon chains. Finally, potential of mean force indicates that propofol partition into a gel DPPC phase is not favorable. Our in silico results were positively contrasted with previous experimental data.
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5
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Dürr UH, Soong R, Ramamoorthy A. When detergent meets bilayer: birth and coming of age of lipid bicelles. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 69:1-22. [PMID: 23465641 PMCID: PMC3741677 DOI: 10.1016/j.pnmrs.2013.01.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 08/30/2012] [Indexed: 05/12/2023]
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6
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Tian K, Li H, Ye S. Methanol Perturbing Modeling Cell Membranes Investigated using Linear and Nonlinear Vibrational Spectroscopy. CHINESE J CHEM PHYS 2013. [DOI: 10.1063/1674-0068/26/01/27-34] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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7
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Al-Abdul-Wahid MS, Evanics F, Prosser RS. Dioxygen transmembrane distributions and partitioning thermodynamics in lipid bilayers and micelles. Biochemistry 2011; 50:3975-83. [PMID: 21510612 DOI: 10.1021/bi200168n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cellular respiration, mediated by the passive diffusion of oxygen across lipid membranes, is key to many basic cellular processes. In this work, we report the detailed distribution of oxygen across lipid bilayers and examine the thermodynamics of oxygen partitioning via NMR studies of lipids in a small unilamellar vesicle (SUV) morphology. Dissolved oxygen gives rise to paramagnetic chemical shift perturbations and relaxation rate enhancements, both of which report on local oxygen concentration. From SUVs containing the phospholipid sn-2-perdeuterio-1-myristelaidoyl, 2-myristoyl-sn-glycero-3-phosphocholine (MLMPC), an analogue of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), we deduced the complete trans-bilayer oxygen distribution by measuring (13)C paramagnetic chemical shifts perturbations for 18 different sites on MLMPC arising from oxygen at a partial pressure of 30 bar. The overall oxygen solubility at 45 °C spans a factor of 7 between the bulk water (23.7 mM) and the bilayer center (170 mM) and is lowest in the vicinity of the phosphocholine headgroup, suggesting that oxygen diffusion across the glycerol backbone should be the rate-limiting step in diffusion-mediated passive transport of oxygen across the lipid bilayer. Lowering of the temperature from 45 to 25 °C gave rise to a slight decrease of the oxygen solubility within the hydrocarbon interior of the membrane. An analysis of the temperature dependence of the oxygen solubility profile, as measured by (1)H paramagnetic relaxation rate enhancements, reveals that oxygen partitioning into the bilayer is entropically favored (ΔS° = 54 ± 3 J K(-1) mol(-1)) and must overcome an enthalpic barrier (ΔH° = 12.0 ± 0.9 kJ mol(-1)).
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Affiliation(s)
- M Sameer Al-Abdul-Wahid
- Department of Chemistry, University of Toronto, UTM, North Mississauga, Ontario, Canada L5L 1C6
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8
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Schmidt P, Berger C, Scheidt HA, Berndt S, Bunge A, Beck-Sickinger AG, Huster D. A reconstitution protocol for the in vitro folded human G protein-coupled Y2 receptor into lipid environment. Biophys Chem 2010; 150:29-36. [PMID: 20421142 DOI: 10.1016/j.bpc.2010.02.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 02/10/2010] [Indexed: 10/19/2022]
Abstract
Although highly resolved crystal structures of G protein-coupled receptors have become available within the last decade, the need for studying these molecules in their natural membrane environment, where the molecules are rather dynamic, has been widely appreciated. Solid-state NMR spectroscopy is an excellent method to study structure and dynamics of membrane proteins in their native lipid environment. We developed a reconstitution protocol for the uniformly (15)N labeled Y(2) receptor into a bicelle-like lipid structure with high yields suitable for NMR studies. Milligram quantities of target protein were expressed in Escherichia coli using an optimized fermentation process in defined medium yielding in over 10mg/L medium of purified Y(2) receptor solubilized in SDS micelles. The structural integrity of the receptor molecules was strongly increased through refolding and subsequent reconstitution into phospholipid membranes. Specific ligand binding to the integrated receptor was determined using radioligand affinity assay. Further, by NMR measurement a dispersion of the (15)N signals comparable to native rhodopsin was shown. The efficiency of the reconstitution could also be inferred from the fact that reasonable (13)C NMR spectra at natural abundance could be acquired.
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Affiliation(s)
- Peter Schmidt
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany
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Ledbetter MP, Crawford CW, Pines A, Wemmer DE, Knappe S, Kitching J, Budker D. Optical detection of NMR J-spectra at zero magnetic field. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 199:25-29. [PMID: 19406678 DOI: 10.1016/j.jmr.2009.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 03/24/2009] [Accepted: 03/24/2009] [Indexed: 05/27/2023]
Abstract
Scalar couplings of the form JI(1) x I(2) between nuclei impart valuable information about molecular structure to nuclear magnetic-resonance spectra. Here we demonstrate direct detection of J-spectra due to both heteronuclear and homonuclear J-coupling in a zero-field environment where the Zeeman interaction is completely absent. We show that characteristic functional groups exhibit distinct spectra with straightforward interpretation for chemical identification. Detection is performed with a microfabricated optical atomic magnetometer, providing high sensitivity to samples of microliter volumes. We obtain 0.1 Hz linewidths and measure scalar-coupling parameters with 4-mHz statistical uncertainty. We anticipate that the technique described here will provide a new modality for high-precision "J spectroscopy" using small samples on microchip devices for multiplexed screening, assaying, and sample identification in chemistry and biomedicine.
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Affiliation(s)
- M P Ledbetter
- Department of Physics, University of California, Berkeley, CA 94720-7300, USA.
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The influence of 1-alkanols and external pressure on the lateral pressure profiles of lipid bilayers. Biophys J 2008; 95:5766-78. [PMID: 18849412 DOI: 10.1529/biophysj.108.142125] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The suggestion by Robert Cantor, that drug-induced pressure changes in lipid bilayers can change the conformational equilibrium between open and closed states of membrane proteins and thereby cause anesthesia, attracted much attention lately. Here, we studied the effect of both large external pressure and of 1-alkanols of different chain lengths--some of them anesthetics, others not--on the lateral pressure profiles across dimyristoylphosphatidylcholine (DMPC) bilayers by molecular dynamics simulations. For a pure DMPC bilayer, high pressure both reduced and broadened the tension at the interface hydrophobic/hydrophilic and diminished the repulsion between the phospholipid headgroups. Whereas the effect of ethanol on the lateral pressure profile was similar to the effect of a large external pressure on a DMPC bilayer, long-chain 1-alkanols significantly amplified local maxima and minima in the lateral pressure profile. For most 1-alkanols, external pressure had moderate effects and did not reverse the changes 1-alkanols exerted on the pressure profile. Nevertheless, assuming the bent helix model as a simple geometric model for the transmembrane region of a membrane protein, protein conformational equilibria were shifted in opposite directions by addition of 1-alkanols and additional application of external pressure.
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11
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Naumann C, Kuchel PW. Prochiral and Chiral Resolution in 2H NMR Spectra: Solutes in Stretched and Compressed Gelatin Gels. J Phys Chem A 2008; 112:8659-64. [DOI: 10.1021/jp802982t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Naumann
- School of Molecular and Microbial Biosciences, University of Sydney, New South Wales 2006, Australia
| | - Philip W. Kuchel
- School of Molecular and Microbial Biosciences, University of Sydney, New South Wales 2006, Australia
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12
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Efrat R, Shalev DE, Hoffman RE, Aserin A, Garti N. Effect of sodium diclofenac loads on mesophase components and structure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:7590-7595. [PMID: 18547072 DOI: 10.1021/la800603f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We studied the effect of a model electrolytic drug on intermolecular interactions, conformational changes, and phase transitions in structured discontinuous cubic QL lyotropic liquid crystals. These changes were due to competition with hydration of the lipid headgroups. Structural changes of the phase induced by solubilization loads of sodium diclofenac (Na-DFC) were investigated by directly observing the water, ethanol, and Na-DFC components of the resulting phases using 2H and 23Na NMR. Na-DFC interacted with the surfactant glycerol monoolein (GMO) at the interface while interfering with the mesophase curvature and also competed with hydration of the surfactant headgroups. Increasing quantities of solubilized Na-DFC promoted phase transitions from cubic phase (discontinuous (QL) and bicontinuous (Q)) into lamellar structures and subsequently into a disordered lamellar phase. Quadrupolar coupling of deuterated ethanol by 2H NMR showed that it is located near the headgroups of the lipid and apparently is hydrogen bonded to the GMO headgroups. A phase transition between two lamellar phases (L alpha to L alpha*) was seen by 23Na NMR of Na-DFC at a concentration where the characteristics of the drug change from kosmotropic to chaotropic. These findings show that loads of solubilized drug may affect the structure of its vehicle and, as a result, its transport across skin-blood barriers. The structural changes of the mesophase may also aid controlled drug delivery.
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Affiliation(s)
- Rivka Efrat
- Casali Institute of Applied Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
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Thaning J, Högberg CJ, Stevensson B, Lyubartsev AP, Maliniak A. Molecular Conformations in a Phospholipid Bilayer Extracted from Dipolar Couplings: A Computer Simulation Study. J Phys Chem B 2007; 111:13638-44. [DOI: 10.1021/jp075278t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johan Thaning
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Carl-Johan Högberg
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Baltzar Stevensson
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Alexander P. Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Arnold Maliniak
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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Griepernau B, Leis S, Schneider MF, Sikor M, Steppich D, Böckmann RA. 1-Alkanols and membranes: a story of attraction. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2899-913. [PMID: 17916322 DOI: 10.1016/j.bbamem.2007.08.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 06/22/2007] [Accepted: 08/03/2007] [Indexed: 10/22/2022]
Abstract
Although 1-alkanols have long been known to act as penetration enhancers and anesthetics, the mode of operation is not yet understood. In this study, long-time molecular dynamics simulations have been performed to investigate the effect of 1-alkanols of various carbon chain lengths onto the structure and dynamics of dimyristoylphosphatidylcholine bilayers. The simulations were complemented by microcalorimetry, continuous bleaching and film balance experiments. In the simulations, all investigated 1-alkanols assembled inside the lipid bilayer within tens of nanoseconds. Their hydroxyl groups bound preferentially to the lipid carbonyl group and the hydrocarbon chains stretched into the hydrophobic core of the bilayer. Both molecular dynamics simulations and experiments showed that all 1-alkanols drastically affected the bilayer properties. Insertion of long-chain 1-alkanols decreased the area per lipid while increasing the thickness of the bilayer and the order of the lipids. The bilayer elasticity was reduced and the diffusive motion of the lipids within the bilayer plane was suppressed. On the other hand, integration of ethanol into the bilayer enlarged the area per lipid. The bilayer became softer and lipid diffusion was enhanced.
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Affiliation(s)
- Beate Griepernau
- Theoretical and Computational Membrane Biology, Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
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Akitake B, Spelbrink REJ, Anishkin A, Killian JA, de Kruijff B, Sukharev S. 2,2,2-Trifluoroethanol changes the transition kinetics and subunit interactions in the small bacterial mechanosensitive channel MscS. Biophys J 2007; 92:2771-84. [PMID: 17277184 PMCID: PMC1831691 DOI: 10.1529/biophysj.106.098715] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
2,2,2-Trifluoroethanol (TFE), a low-dielectric solvent, has recently been used as a promising tool to probe the strength of intersubunit interactions in membrane proteins. An analysis of inner membrane proteins of Escherichia coli has identified several SDS-resistant protein complexes that separate into subunits upon exposure to TFE. One of these was the homo-heptameric stretch-activated mechanosensitive channel of small conductance (MscS), a ubiquitous component of the bacterial turgor-regulation system. Here we show that a substantial fraction of MscS retains its oligomeric state in cold lithium-dodecyl-sulfate gel electrophoresis. Exposure of MscS complexes to 10-15 vol % TFE in native membranes or nonionic detergent micelles before lithium-dodecyl-sulfate electrophoresis results in a complete dissociation into monomers, suggesting that at these concentrations TFE by itself disrupts or critically compromises intersubunit interactions. Patch-clamp analysis of giant E. coli spheroplasts expressing MscS shows that exposure to TFE in lower concentrations (0.5-5.0 vol %) causes leftward shifts of the dose-response curves when applied extracellularly, and rightward shifts when added from the cytoplasmic side. In the latter case, TFE increases the rate of tension-dependent inactivation and lengthens the process of recovery to the resting state. MscS responses to pressure ramps of different speeds indicate that in the presence of TFE most channels reside in the resting state and only at tensions near the activation threshold does TFE dramatically speed up inactivation. The effect of TFE is reversible as normal channel activity returns 15-30 min after a TFE washout. We interpret the observed midpoint shifts in terms of asymmetric partitioning of TFE into the membrane and distortion of the bilayer lateral pressure profile. We also relate the increased rate of inactivation and subunit separation with the capacity of TFE to perturb buried interhelical contacts in proteins and discuss these effects in the framework of the proposed gating mechanism of MscS.
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Affiliation(s)
- Bradley Akitake
- Department of Biology, University of Maryland, College Park, Maryland
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The Bacterial Mechanosensitive Channel MscS: Emerging Principles of Gating and Modulation. CURRENT TOPICS IN MEMBRANES 2007. [DOI: 10.1016/s1063-5823(06)58009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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17
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Residual Dipolar Couplings Report on the Active Conformation of Rhodopsin-Bound Protein Fragments. Top Curr Chem (Cham) 2006. [DOI: 10.1007/128_2006_088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Li X, Newberry C, Saha I, Nikolaou P, Whiting N, Goodson BM. Interactions between xenon and phospholipid bicelles studied by 2H/129Xe/131Xe NMR and optical pumping of nuclear spins. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2005.11.086] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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