1
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Matsuki Y, Takashima M, Ueki M, Iwamoto M, Oiki S. Probing membrane deformation energy by KcsA potassium channel gating under varied membrane thickness and tension. FEBS Lett 2024. [PMID: 38880762 DOI: 10.1002/1873-3468.14956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024]
Abstract
This study investigated how membrane thickness and tension modify the gating of KcsA potassium channels when simultaneously varied. The KcsA channel undergoes global conformational changes upon gating: expansion of the cross-sectional area and longitudinal shortening upon opening. Thus, membranes impose differential effects on the open and closed conformations, such as hydrophobic mismatches. Here, the single-channel open probability was recorded in the contact bubble bilayer, by which variable thickness membranes under a defined tension were applied. A fully open channel in thin membranes turned to sporadic openings in thick membranes, where the channel responded moderately to tension increase. Quantitative gating analysis prompted the hypothesis that tension augmented the membrane deformation energy when hydrophobic mismatch was enhanced in thick membranes.
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Affiliation(s)
- Yuka Matsuki
- Department of Anesthesiology and Reanimatology, Faculty of Medical Sciences, University of Fukui, Yoshida-gun, Japan
- Life Science Innovation Center, University of Fukui, Yoshida-gun, Japan
| | - Masako Takashima
- Department of Molecular Neuroscience, Faculty of Medical Sciences, University of Fukui, Yoshida-gun, Japan
| | - Misuzu Ueki
- Life Science Innovation Center, University of Fukui, Yoshida-gun, Japan
- Department of Molecular Neuroscience, Faculty of Medical Sciences, University of Fukui, Yoshida-gun, Japan
| | - Masayuki Iwamoto
- Life Science Innovation Center, University of Fukui, Yoshida-gun, Japan
- Department of Molecular Neuroscience, Faculty of Medical Sciences, University of Fukui, Yoshida-gun, Japan
| | - Shigetoshi Oiki
- Biomedical Imaging Research Center, University of Fukui, Yoshida-gun, Japan
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2
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Kondrashov OV, Akimov SA. Gramicidin A as a mechanical sensor for mixed nonideal lipid membranes. Phys Rev E 2024; 109:064404. [PMID: 39020903 DOI: 10.1103/physreve.109.064404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/22/2024] [Indexed: 07/20/2024]
Abstract
Gramicidin A (gA) is a short hydrophobic β-helical peptide that forms cation-selective channels in lipid membranes in the course of transbilayer dimerization. The length of the gA helix is smaller than the thickness of a typical lipid monolayer. Consequently, elastic deformations of the membrane arise in the configurations of gA monomers, conducting dimer, and the intermediate state of coaxial pair, where gA monomers from opposing membrane monolayers are located one on top of the other. The gA channel is characterized by the average lifetime of the conducting state. The elastic properties of the membrane influence the average lifetime, thus making gA a convenient sensor of membrane elasticity. However, the utilization of gA to investigate the elastic properties of mixed membranes comprising two or more components frequently relies on the assumption of ideality, namely that the elastic parameters of mixed-lipid bilayers depend linearly on the concentrations of the components. Here, we developed a general approach that does not rely on the aforementioned assumption. Instead, we explicitly accounted for the possibility of inhomogeneous lateral distribution of all lipid components, as well as for membrane-mediated lateral interactions of gA monomers, dimer, coaxial pair, and minor lipid components. This approach enabled us to derive unknown elastic parameters of lipid monolayer from experimentally determined lifetimes of gA channel in mixed-lipid bilayers. A general algorithm was formulated that allows the unknown elastic parameters of a lipid monolayer to be obtained using gA as a mechanical sensor.
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3
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Ashrafuzzaman M, Koeppe RE, Andersen OS. Intrinsic Lipid Curvature and Bilayer Elasticity as Regulators of Channel Function: A Comparative Single-Molecule Study. Int J Mol Sci 2024; 25:2758. [PMID: 38474005 PMCID: PMC10931550 DOI: 10.3390/ijms25052758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Perturbations in bilayer material properties (thickness, lipid intrinsic curvature and elastic moduli) modulate the free energy difference between different membrane protein conformations, thereby leading to changes in the conformational preferences of bilayer-spanning proteins. To further explore the relative importance of curvature and elasticity in determining the changes in bilayer properties that underlie the modulation of channel function, we investigated how the micelle-forming amphiphiles Triton X-100, reduced Triton X-100 and the HII lipid phase promoter capsaicin modulate the function of alamethicin and gramicidin channels. Whether the amphiphile-induced changes in intrinsic curvature were negative or positive, amphiphile addition increased gramicidin channel appearance rates and lifetimes and stabilized the higher conductance states in alamethicin channels. When the intrinsic curvature was modulated by altering phospholipid head group interactions, however, maneuvers that promote a negative-going curvature stabilized the higher conductance states in alamethicin channels but destabilized gramicidin channels. Using gramicidin channels of different lengths to probe for changes in bilayer elasticity, we found that amphiphile adsorption increases bilayer elasticity, whereas altering head group interactions does not. We draw the following conclusions: first, confirming previous studies, both alamethicin and gramicidin channels are modulated by changes in lipid bilayer material properties, the changes occurring in parallel yet differing dependent on the property that is being changed; second, isolated, negative-going changes in curvature stabilize the higher current levels in alamethicin channels and destabilize gramicidin channels; third, increases in bilayer elasticity stabilize the higher current levels in alamethicin channels and stabilize gramicidin channels; and fourth, the energetic consequences of changes in elasticity tend to dominate over changes in curvature.
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Affiliation(s)
- Mohammad Ashrafuzzaman
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA;
| | - Roger E. Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA;
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4
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Rostovtseva TK, Weinrich M, Jacobs D, Rosencrans WM, Bezrukov SM. Dimeric Tubulin Modifies Mechanical Properties of Lipid Bilayer, as Probed Using Gramicidin A Channel. Int J Mol Sci 2024; 25:2204. [PMID: 38396879 PMCID: PMC10889239 DOI: 10.3390/ijms25042204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Using the gramicidin A channel as a molecular probe, we show that tubulin binding to planar lipid membranes changes the channel kinetics-seen as an increase in the lifetime of the channel dimer-and thus points towards modification of the membrane's mechanical properties. The effect is more pronounced in the presence of non-lamellar lipids in the lipid mixture used for membrane formation. To interpret these findings, we propose that tubulin binding redistributes the lateral pressure of lipid packing along the membrane depth, making it closer to the profile expected for lamellar lipids. This redistribution happens because tubulin perturbs the lipid headgroup spacing to reach the membrane's hydrophobic core via its amphiphilic α-helical domain. Specifically, it increases the forces of repulsion between the lipid headgroups and reduces such forces in the hydrophobic region. We suggest that the effect is reciprocal, meaning that alterations in lipid bilayer mechanics caused by membrane remodeling during cell proliferation in disease and development may also modulate tubulin membrane binding, thus exerting regulatory functions. One of those functions includes the regulation of protein-protein interactions at the membrane surface, as exemplified by VDAC complexation with tubulin.
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Affiliation(s)
- Tatiana K. Rostovtseva
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA (S.M.B.)
| | - Michael Weinrich
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Daniel Jacobs
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA (S.M.B.)
| | - William M. Rosencrans
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA (S.M.B.)
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sergey M. Bezrukov
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA (S.M.B.)
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5
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Hossain MZ, Stroberg W. Bilayer tension-induced clustering of the UPR sensor IRE1. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184262. [PMID: 38081494 DOI: 10.1016/j.bbamem.2023.184262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/19/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
The endoplasmic reticulum acts as a protein quality control center where a range of chaperones and foldases facilitates protein folding. IRE1 is a sensory transmembrane protein that transduces signals of proteotoxic stress by forming clusters and activating a cellular program called the unfolded protein response (UPR). Recently, membrane thickness variation due to membrane compositional changes have been shown to drive IRE1 cluster formation, activating the UPR even in the absence of proteotoxic stress. Here, we demonstrate a direct relationship between bilayer tension and UPR activation based on IRE1 dimer stability. The stability of the IRE1 dimer in a (50%DOPC-50%POPC) membrane at different applied bilayer tensions was analyzed via molecular dynamics simulations. The potential of mean force for IRE1 dimerization predicts a higher concentration of IRE1 dimers for both tensed and compressed ER membranes. This study shows that IRE1 may be a mechanosensitive membrane protein and establishes a direct biophysical relationship between bilayer tension and UPR activation.
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Affiliation(s)
- Md Zobayer Hossain
- Department of Mechanical Engineering, University of Alberta, 9211-116 Street NW, Edmonton, T6G 1H9, Alberta, Canada.
| | - Wylie Stroberg
- Department of Mechanical Engineering, University of Alberta, 9211-116 Street NW, Edmonton, T6G 1H9, Alberta, Canada.
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6
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Peyear TA, Andersen OS. Screening for bilayer-active and likely cytotoxic molecules reveals bilayer-mediated regulation of cell function. J Gen Physiol 2023; 155:e202213247. [PMID: 36763053 PMCID: PMC9948646 DOI: 10.1085/jgp.202213247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/06/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023] Open
Abstract
A perennial problem encountered when using small molecules (drugs) to manipulate cell or protein function is to assess whether observed changes in function result from specific interactions with a desired target or from less specific off-target mechanisms. This is important in laboratory research as well as in drug development, where the goal is to identify molecules that are unlikely to be successful therapeutics early in the process, thereby avoiding costly mistakes. We pursued this challenge from the perspective that many bioactive molecules (drugs) are amphiphiles that alter lipid bilayer elastic properties, which may cause indiscriminate changes in membrane protein (and cell) function and, in turn, cytotoxicity. Such drug-induced changes in bilayer properties can be quantified as changes in the monomer↔dimer equilibrium for bilayer-spanning gramicidin channels. Using this approach, we tested whether molecules in the Pathogen Box (a library of 400 drugs and drug-like molecules with confirmed activity against tropical diseases released by Medicines for Malaria Venture to encourage the development of therapies for neglected tropical diseases) are bilayer modifiers. 32% of the molecules in the Pathogen Box were bilayer modifiers, defined as molecules that at 10 µM shifted the monomer↔dimer equilibrium toward the conducting dimers by at least 50%. Correlation analysis of the molecules' reported HepG2 cell cytotoxicity to bilayer-modifying potency, quantified as the shift in the gramicidin monomer↔dimer equilibrium, revealed that molecules producing <25% change in the equilibrium had significantly lower probability of being cytotoxic than molecules producing >50% change. Neither cytotoxicity nor bilayer-modifying potency (quantified as the shift in the gramicidin monomer↔dimer equilibrium) was well predicted by conventional physico-chemical descriptors (hydrophobicity, polar surface area, etc.). We conclude that drug-induced changes in lipid bilayer properties are robust predictors of the likelihood of membrane-mediated off-target effects, including cytotoxicity.
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Affiliation(s)
- Thasin A. Peyear
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences. New York, NY, USA
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
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7
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Kondrashov OV, Rokitskaya TI, Batishchev OV, Kotova EA, Antonenko YN, Akimov SA. Peptide-induced membrane elastic deformations decelerate gramicidin dimer-monomer equilibration. Biophys J 2021; 120:5309-5321. [PMID: 34715080 DOI: 10.1016/j.bpj.2021.10.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/23/2021] [Accepted: 10/22/2021] [Indexed: 10/20/2022] Open
Abstract
Gramicidin A (gA) is a hydrophobic pentadecapeptide readily incorporating into a planar bilayer lipid membrane (BLM), thereby inducing a large macroscopic current across the BLM. This current results from ion-channel formation due to head-to-head transbilayer dimerization of gA monomers with rapidly established monomer-dimer equilibrium. Any disturbance of the equilibrium, e.g., by sensitized photoinactivation of a portion of gA monomers, causes relaxation toward a new equilibrium state. According to previous studies, the characteristic relaxation time of the gA-mediated electric current decreases as the current increases upon elevating the gA concentration in the membrane. Here, we report data on the current relaxation kinetics for gA analogs with N-terminal valine replaced by glycine or tyrosine. Surprisingly, the relaxation time increased rather than decreased upon elevation of the total membrane conductance induced by these gA analogs, thus contradicting the classical kinetic scheme. We developed a general theoretical model that accounts for lateral interaction of monomers and dimers mediated by membrane elastic deformations. The modified kinetic scheme of the gramicidin dimerization predicts the reverse dependence of the relaxation time on membrane conductance for gA analogs, with a decreased dimerization constant that is in a good agreement with our experimental data. The equilibration process may be also modulated by incorporation of other peptides ("impurities") into the lipid membrane.
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Affiliation(s)
- Oleg V Kondrashov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg V Batishchev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Elena A Kotova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Sergey A Akimov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia.
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8
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Pfeffermann J, Eicher B, Boytsov D, Hannesschlaeger C, Galimzyanov TR, Glasnov TN, Pabst G, Akimov SA, Pohl P. Photoswitching of model ion channels in lipid bilayers. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 224:112320. [PMID: 34600201 DOI: 10.1016/j.jphotobiol.2021.112320] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/27/2021] [Accepted: 09/20/2021] [Indexed: 11/19/2022]
Abstract
Membrane proteins can be regulated by alterations in material properties intrinsic to the hosting lipid bilayer. Here, we investigated whether the reversible photoisomerization of bilayer-embedded diacylglycerols (OptoDArG) with two azobenzene-containing acyl chains may trigger such regulatory events. We observed an augmented open probability of the mechanosensitive model channel gramicidin A (gA) upon photoisomerizing OptoDArG's acyl chains from trans to cis: integral planar bilayer conductance brought forth by hundreds of simultaneously conducting gA dimers increased by typically >50% - in good agreement with the observed increase in single-channel lifetime. Further, (i) increments in the electrical capacitance of planar lipid bilayers and protrusion length of aspirated giant unilamellar vesicles into suction pipettes, as well as (ii) changes of small-angle X-ray scattering of multilamellar vesicles indicated that spontaneous curvature, hydrophobic thickness, and bending elasticity decreased upon switching from trans- to cis-OptoDArG. Our bilayer elasticity model for gA supports the causal relationship between changes in gA activity and bilayer material properties upon photoisomerization. Thus, we conclude that photolipids are deployable for converting bilayers of potentially diverse origins into light-gated actuators for mechanosensitive proteins.
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Affiliation(s)
- Juergen Pfeffermann
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstraße 40, Linz 4020, Austria
| | - Barbara Eicher
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Austria
| | - Danila Boytsov
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstraße 40, Linz 4020, Austria
| | | | - Timur R Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy prospekt, Moscow 119071, Russia
| | - Toma N Glasnov
- University of Graz, Institute of Chemistry, NAWI Graz, Graz, Austria
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Austria
| | - Sergey A Akimov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy prospekt, Moscow 119071, Russia
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstraße 40, Linz 4020, Austria.
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9
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Ernst M, Robertson JL. The Role of the Membrane in Transporter Folding and Activity. J Mol Biol 2021; 433:167103. [PMID: 34139219 PMCID: PMC8756397 DOI: 10.1016/j.jmb.2021.167103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022]
Abstract
The synthesis, folding, and function of membrane transport proteins are critical factors for defining cellular physiology. Since the stability of these proteins evolved amidst the lipid bilayer, it is no surprise that we are finding that many of these membrane proteins demonstrate coupling of their structure or activity in some way to the membrane. More and more transporter structures are being determined with some information about the surrounding membrane, and computational modeling is providing further molecular details about these solvation structures. Thus, the field is moving towards identifying which molecular mechanisms - lipid interactions, membrane perturbations, differential solvation, and bulk membrane effects - are involved in linking membrane energetics to transporter stability and function. In this review, we present an overview of these mechanisms and the growing evidence that the lipid bilayer is a major determinant of the fold, form, and function of membrane transport proteins in membranes.
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Affiliation(s)
- Melanie Ernst
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Janice L Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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10
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Chen P, Vorobyov I, Roux B, Allen TW. Molecular Dynamics Simulations Based on Polarizable Models Show that Ion Permeation Interconverts between Different Mechanisms as a Function of Membrane Thickness. J Phys Chem B 2021; 125:1020-1035. [PMID: 33493394 DOI: 10.1021/acs.jpcb.0c08613] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Different mechanisms have been proposed to explain the permeation of charged compounds through lipid membranes. Overall, it is expected that an ion-induced defect permeation mechanism, where substantial membrane deformations accompany ion movement, should be dominant in thin membranes but that a solubility-diffusion mechanism, where ions partition into the membrane core with large associated dehydration energy costs, becomes dominant in thicker membranes. However, while this physical picture is intuitively reasonable, capturing the interconversion between these two permeation mechanisms in molecular dynamics (MD) simulations based on atomic models is challenging. In particular, simulations relying on nonpolarizable force fields are artificially unfavorable to the solubility-diffusion mechanism, as induced polarization of the nonpolar hydrocarbon is ignored, causing overestimated free energy costs for charged molecules to enter into this region of the membrane. In this study, all-atom MD simulations based on nonpolarizable and polarizable force fields are used to quantitatively characterize the permeation process for the arginine side chain analog methyl-guanidinium through bilayer membranes of mono-unsaturated phosphatidylcholine lipids with and without cholesterol, resulting in thicknesses spanning from ∼24 to ∼42 Å. With simulations based on a nonpolarizable force field, ion translocation can take place solely through an ion-induced defect mechanism, with free energy barriers increasing linearly from 14 to 40 kcal/mol, depending on the thickness. However, with simulations based on a polarizable force field, ion translocation is predominantly dominated by an ion-induced defect mechanism in thin membranes, which progressively converts to a solubility-diffusion mechanism as the membranes get thicker. The transition between the two mechanisms occurs at a thickness of ∼29 Å, with lipid tails of 22 or more carbon atoms. This situation appears to represent the upper limit for ion-induced defect permeation within the current polarizable models. Beyond this thickness, it becomes energetically preferable for the ion to dehydrate and partition into the membrane core-a phenomenon that cannot be captured using the nonpolarizable models. Induced electronic polarizability therefore leads not just to a shift in permeation energetics but to an interconversion between two strikingly different physical mechanisms. The result highlights the importance of induced polarizability in modeling lipid membranes.
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Affiliation(s)
- Peiran Chen
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Igor Vorobyov
- Department of Physiology & Membrane Biology, Department of Pharmacology, University of California, Davis, California 95616, United States
| | - Benoît Roux
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Toby W Allen
- School of Science, RMIT University, Melbourne 3001, Australia
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11
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Hirano M, Yamamoto D, Asakura M, Hayakawa T, Mise S, Matsumoto A, Ide T. A Lipid Bilayer Formed on a Hydrogel Bead for Single Ion Channel Recordings. MICROMACHINES 2020; 11:mi11121070. [PMID: 33271761 PMCID: PMC7759777 DOI: 10.3390/mi11121070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/28/2020] [Accepted: 11/29/2020] [Indexed: 02/05/2023]
Abstract
Ion channel proteins play important roles in various cell functions, making them attractive drug targets. Artificial lipid bilayer recording is a technique used to measure the ion transport activities of channel proteins with high sensitivity and accuracy. However, the measurement efficiency is low. In order to improve the efficiency, we developed a method that allows us to form bilayers on a hydrogel bead and record channel currents promptly. We tested our system by measuring the activities of various types of channels, including gramicidin, alamethicin, α-hemolysin, a voltage-dependent anion channel 1 (VDAC1), a voltage- and calcium-activated large conductance potassium channel (BK channel), and a potassium channel from Streptomyces lividans (KcsA channel). We confirmed the ability for enhanced measurement efficiency and measurement system miniaturizion.
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Affiliation(s)
- Minako Hirano
- Bio Photonics Laboratory, The Graduate School for the Creation of New Photonics Industries, Shizuoka 431-1202, Japan;
| | - Daiki Yamamoto
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan; (D.Y.); (M.A.); (T.H.)
| | - Mami Asakura
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan; (D.Y.); (M.A.); (T.H.)
| | - Tohru Hayakawa
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan; (D.Y.); (M.A.); (T.H.)
| | - Shintaro Mise
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan; (S.M.); (A.M.)
| | - Akinobu Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan; (S.M.); (A.M.)
| | - Toru Ide
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan; (D.Y.); (M.A.); (T.H.)
- Correspondence: ; Tel.: +81-86-251-8203
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12
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Sun D, Peyear TA, Bennett WFD, Holcomb M, He S, Zhu F, Lightstone FC, Andersen OS, Ingólfsson HI. Assessing the Perturbing Effects of Drugs on Lipid Bilayers Using Gramicidin Channel-Based In Silico and In Vitro Assays. J Med Chem 2020; 63:11809-11818. [PMID: 32945672 PMCID: PMC7586341 DOI: 10.1021/acs.jmedchem.0c00958] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Indexed: 01/07/2023]
Abstract
Partitioning of bioactive molecules, including drugs, into cell membranes may produce indiscriminate changes in membrane protein function. As a guide to safe drug development, it therefore becomes important to be able to predict the bilayer-perturbing potency of hydrophobic/amphiphilic drugs candidates. Toward this end, we exploited gramicidin channels as molecular force probes and developed in silico and in vitro assays to measure drugs' bilayer-modifying potency. We examined eight drug-like molecules that were found to enhance or suppress gramicidin channel function in a thick 1,2-dierucoyl-sn-glycero-3-phosphocholine (DC22:1PC) but not in thin 1,2-dioleoyl-sn-glycero-3-phosphocholine (DC18:1PC) lipid bilayer. The mechanism underlying this difference was attributable to the changes in gramicidin dimerization free energy by drug-induced perturbations of lipid bilayer physical properties and bilayer-gramicidin interactions. The combined in silico and in vitro approaches, which allow for predicting the perturbing effects of drug candidates on membrane protein function, have implications for preclinical drug safety assessment.
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Affiliation(s)
- Delin Sun
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Thasin A. Peyear
- Department
of Physiology and Biophysics, Weill Cornell
Medicine, New York, New York 10065, United States
| | - W. F. Drew Bennett
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Matthew Holcomb
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Stewart He
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Fangqiang Zhu
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Felice C. Lightstone
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Olaf S. Andersen
- Department
of Physiology and Biophysics, Weill Cornell
Medicine, New York, New York 10065, United States
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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13
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Sanver D, Sadeghpour A, Rappolt M, Di Meo F, Trouillas P. Structure and Dynamics of Dioleoyl-Phosphatidylcholine Bilayers under the Influence of Quercetin and Rutin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11776-11786. [PMID: 32911935 DOI: 10.1021/acs.langmuir.0c01484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Quercetin and rutin, two widely studied flavonoids with applications foreseen in the sectors of pharmaceutical and cosmetic industries, have been chosen as model compounds for a detailed structural and dynamical investigation onto their influence on fluid lipid bilayers. Combining global small angle X-ray scattering analysis with molecular dynamics, various changes in the properties of dioleoyl-phosphatidylcholine (DOPC) bilayers have been determined. The solubility of quercetin in DOPC membranes is assured up to 12 mol %, whereas rutin, with additional glucose and rhamnose groups, are fully soluble only up to 6 mol %. Both flavonoids induce an increase in membrane undulations and thin the bilayers slightly (<1 Å) in a concentration dependent manner, wherein quercetin shows a stronger effect. Concomitantly, in the order of 2-4%, the adjacent bilayer distance increases with the flavonoid's concentration. Partial molecular areas of quercetin and rutin are determined to be 26 and 51 Å2, respectively. Simulated averaged areas per molecule confirm these estimates. A 60° tilted orientation of quercetin is observed with respect to the bilayer normal, whereas the flavonoid moiety of rutin is oriented more perpendicular (α-angle 30°) to the membrane surface. Both flavonoid moieties are located at a depth of 12 and 16 Å for quercetin and rutin, respectively, while their anionic forms display a location closer to the polar interface. Finally, at both simulated concentrations (1.5 and 12 mol %), DOPC-rutin systems induce a stronger packing of the pure DOPC lipid bilayer, mainly due to stronger attractive electrostatic interactions in the polar lipid head region.
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Affiliation(s)
- Didem Sanver
- Faculty of Engineering and Architecture, Department of Food Engineering, Necmettin Erbakan University, Konya 42050, Turkey
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, U.K
| | - Amin Sadeghpour
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, U.K
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil 4123, Switzerland
| | - Michael Rappolt
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, U.K
| | - Florent Di Meo
- INSERM U1248 IPPRITT, University of Limoges, 2 rue du Prof. Descottes, Limoges 87000, France
| | - Patrick Trouillas
- INSERM U1248 IPPRITT, University of Limoges, 2 rue du Prof. Descottes, Limoges 87000, France
- RCPTM, Department of Physical Chemistry, Faculty of Sciences, Palacký University, Olomouc 771 47, Czech Republic
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14
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Callahan KM, Mondou B, Sasseville L, Schwartz JL, D'Avanzo N. The influence of membrane bilayer thickness on KcsA channel activity. Channels (Austin) 2020; 13:424-439. [PMID: 31608774 PMCID: PMC6802934 DOI: 10.1080/19336950.2019.1676367] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Atomic resolution structures have provided significant insight into the gating and permeation mechanisms of various ion channels, including potassium channels. However, ion channels may also be regulated by numerous factors, including the physiochemical properties of the membrane in which they are embedded. For example, the matching of the bilayer's hydrophobic region to the hydrophobic external surface of the ion channel is thought to minimize the energetic penalty needed to solvate hydrophobic residues or exposed lipid tails. To understand the molecular basis of such regulation by hydrophobic matching requires examining channels in the presence of the lipid membrane. Here we examine the role of hydrophobic matching in regulating the activity of the model potassium channel, KcsA. 86Rb+ influx assays and single-channel recordings indicate that the non-inactivating E71A KcsA channel is most active in thin bilayers (<diC18:1PC). Bilayer thickness affects the open probability of KcsA and not its unitary conductance. Molecular dynamics simulations indicate that the bilayer can sufficiently modify its dimensions to accommodate KcsA channels without major perturbations in the protein helical packing within the nanosecond timescale. Based on experimental results and MD simulations, we present a model in which bilayer thickness influences the stability of the open and closed conformations of the intracellular gate of KcsA, with minimal impact on the stability of the selectivity filter of the non-inactivating mutant, E71A.
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Affiliation(s)
- Karen M Callahan
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada
| | - Benoit Mondou
- Département de biochimie et médecine moléculaire, Université de Montréal , Montréal , Canada
| | - Louis Sasseville
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada
| | - Jean-Louis Schwartz
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada.,Département de biochimie et médecine moléculaire, Université de Montréal , Montréal , Canada.,Centre SÈVE, Université de Sherbrooke , Sherbrooke , Canada
| | - Nazzareno D'Avanzo
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada.,Département de biochimie et médecine moléculaire, Université de Montréal , Montréal , Canada
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15
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DAPTOMYCIN, its membrane-active mechanism vs. that of other antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183395. [PMID: 32526177 DOI: 10.1016/j.bbamem.2020.183395] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/04/2020] [Accepted: 06/07/2020] [Indexed: 11/23/2022]
Abstract
Over 3000 membrane-active antimicrobial peptides (AMPs) have been discovered, but only three of them have been approved by the U.S. Food and Drug Administration (FDA) for therapeutic applications, i.e., gramicidin, daptomycin and colistin. Of the three approved AMPs, daptomycin is a last-line-of-defense antibiotic for treating Gram-positive infections. However its use has already created bacterial resistance. To search for its substitutes that might counter the resistance, we need to understand its molecular mechanism. The mode of action of daptomycin appears to be causing bacterial membrane depolarization through ion leakage. Daptomycin forms a unique complex with calcium ions and phosphatidylglycerol molecules in membrane at a specific stoichiometric ratio: Dap2Ca3PG2. How does this complex promote ion conduction across the membrane? We hope that biophysics of peptide-membrane interaction can answer this question. This review summarizes the biophysical works that have been done on membrane-active AMPs to understand their mechanisms of action, including gramicidin, daptomycin, and underdeveloped pore-forming AMPs. The analysis suggests that daptomycin forms transient ionophores in the target membranes. We discuss questions that remain to be answered.
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16
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Rostovtseva TK, Queralt-Martín M, Rosencrans WM, Bezrukov SM. Targeting the Multiple Physiologic Roles of VDAC With Steroids and Hydrophobic Drugs. Front Physiol 2020; 11:446. [PMID: 32457654 PMCID: PMC7221028 DOI: 10.3389/fphys.2020.00446] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
There is accumulating evidence that endogenous steroids and non-polar drugs are involved in the regulation of mitochondrial physiology. Many of these hydrophobic compounds interact with the Voltage Dependent Anion Channel (VDAC). This major metabolite channel in the mitochondrial outer membrane (MOM) regulates the exchange of ions and water-soluble metabolites, such as ATP and ADP, across the MOM, thus governing mitochondrial respiration. Proteomics and biochemical approaches together with molecular dynamics simulations have identified an impressively large number of non-polar compounds, including endogenous, able to bind to VDAC. These findings have sparked speculation that both natural steroids and synthetic hydrophobic drugs regulate mitochondrial physiology by directly affecting VDAC ion channel properties and modulating its metabolite permeability. Here we evaluate recent studies investigating the effect of identified VDAC-binding natural steroids and non-polar drugs on VDAC channel functioning. We argue that while many compounds are found to bind to the VDAC protein, they do not necessarily affect its channel functions in vitro. However, they may modify other aspects of VDAC physiology such as interaction with its cytosolic partner proteins or complex formation with other mitochondrial membrane proteins, thus altering mitochondrial function.
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Affiliation(s)
- Tatiana K Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - María Queralt-Martín
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - William M Rosencrans
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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17
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Sun D, Peyear TA, Bennett WFD, Andersen OS, Lightstone FC, Ingólfsson HI. Molecular Mechanism for Gramicidin Dimerization and Dissociation in Bilayers of Different Thickness. Biophys J 2019; 117:1831-1844. [PMID: 31676135 PMCID: PMC7018991 DOI: 10.1016/j.bpj.2019.09.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/01/2019] [Accepted: 09/04/2019] [Indexed: 01/01/2023] Open
Abstract
Membrane protein functions can be altered by subtle changes in the host lipid bilayer physical properties. Gramicidin channels have emerged as a powerful system for elucidating the underlying mechanisms of membrane protein function regulation through changes in bilayer properties, which are reflected in the thermodynamic equilibrium distribution between nonconducting gramicidin monomers and conducting bilayer-spanning dimers. To improve our understanding of how subtle changes in bilayer thickness alter the gramicidin monomer and dimer distributions, we performed extensive atomistic molecular dynamics simulations and fluorescence-quenching experiments on gramicidin A (gA). The free-energy calculations predicted a nonlinear coupling between the bilayer thickness and channel formation. The energetic barrier inhibiting gA channel formation was sharply increased in the thickest bilayer (1,2-dierucoyl-sn-glycero-3-phosphocholine). This prediction was corroborated by experimental results on gramicidin channel activity in bilayers of different thickness. To further explore the mechanism of channel formation, we performed extensive unbiased molecular dynamics simulations, which allowed us to observe spontaneous gA dimer formation in lipid bilayers. The simulations revealed structural rearrangements in the gA subunits and changes in lipid packing, as well as water reorganization, that occur during the dimerization process. Together, the simulations and experiments provide new, to our knowledge, insights into the process and mechanism of gramicidin channel formation, as a prototypical example of the bilayer regulation of membrane protein function.
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Affiliation(s)
- Delin Sun
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Thasin A Peyear
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - W F Drew Bennett
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Felice C Lightstone
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Helgi I Ingólfsson
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California.
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18
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Park S, Yeom MS, Andersen OS, Pastor RW, Im W. Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation between Binary Bilayers. J Chem Theory Comput 2019; 15:6491-6503. [PMID: 31560853 PMCID: PMC7076909 DOI: 10.1021/acs.jctc.9b00815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using a recently developed binary bilayer system (BBS) consisting of two patches of laterally contacting bilayers, umbrella sampling molecular dynamics (MD) simulations were performed for quantitative characterization of protein-lipid interactions. The BBS is composed of 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) with an embedded model membrane protein, a gramicidin A (gA) channel. The calculated free energy difference for the transfer of a gA channel from DLPC (hydrophobic thickness ≈ 21.5 Å) to DMPC (hydrophobic thickness ≈ 25.5 Å) bilayers, ΔG(DLPC → DMPC), is -2.2 ± 0.7 kcal/mol. This value appears at odds with the traditional view that the hydrophobic length of the gA channel is ∼22 Å. To understand this discrepancy, we first note that recent MD simulations by different groups have shown that lipid bilayer thickness profiles in the vicinity of a gA channel differ qualitatively from the deformation profile predicted from continuum elastic bilayer models. Our MD simulations at low and high gA:lipid molar ratios and different membrane compositions indicate that the gA channel's effective hydrophobic length is ∼26 Å. Using this effective hydrophobic length, ΔG(DLPC → DMPC) determined here is in excellent agreement with predictions based on continuum elastic models (-3.0 to -2.2 kcal/mol) where the bilayer deformation energy is approximated as a harmonic function of the mismatch between the channel's effective hydrophobic length and the hydrophobic thickness of the bilayer. The free energy profile for gA in the BBS includes a barrier at the interface between the two bilayers which can be attributed to the line tension at the interface between two bilayers with different hydrophobic thicknesses. This observation implies that translation of a peptide between two different regions of a cell membrane (such as between the liquid ordered and disordered phases) may include effects of a barrier at the interface in addition to the relative free energies of the species far from the interface. The BBS allows for direct transfer free energy calculations between bilayers without a need of a reference medium, such as bulk water, and thus provides an efficient simulation protocol for the quantitative characterization of protein-lipid interactions at all-atom resolution.
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Affiliation(s)
- Soohyung Park
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information , Daejeon , Korea
| | - Olaf S Andersen
- Department of Physiology and Biophysics , Weill Cornell Medicine , New York , New York 10065 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States.,School of Computational Sciences , Korea Institute for Advanced Study , Seoul 02455 , Republic of Korea
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19
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Sah BK, Das K, Kundu S. pH-dependent structure, pattern and hysteresis behaviour of lipid (DMPA)-protein (BSA) monolayer complex. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2019.123663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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20
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Puiggalí-Jou A, Del Valle LJ, Alemán C. Biomimetic hybrid membranes: incorporation of transport proteins/peptides into polymer supports. SOFT MATTER 2019; 15:2722-2736. [PMID: 30869096 DOI: 10.1039/c8sm02513d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Molecular sensing, water purification and desalination, drug delivery, and DNA sequencing are some striking applications of biomimetic hybrid membranes. These devices take advantage of biomolecules, which have gained excellence in their specificity and efficiency during billions of years, and of artificial materials that load the purified biological molecules and provide technological properties, such as robustness, scalability, and suitable nanofeatures to confine the biomolecules. Recent methodological advances allow more precise control of polymer membranes that support the biomacromolecules, and are expected to improve the design of the next generation of membranes as well as their applicability. In the first section of this review we explain the biological relevance of membranes, membrane proteins, and the classification used for the latter. After this, we critically analyse the different approaches employed for the production of highly selective hybrid membranes, focusing on novel materials made of self-assembled block copolymers and nanostructured polymers. Finally, a summary of the advantages and disadvantages of the different methodologies is presented and the main characteristics of biomimetic hybrid membranes are highlighted.
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Affiliation(s)
- Anna Puiggalí-Jou
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019, Barcelona, Spain. and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019, Barcelona, Spain
| | - Luis J Del Valle
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019, Barcelona, Spain. and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019, Barcelona, Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019, Barcelona, Spain. and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019, Barcelona, Spain
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21
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Micro-Surface and -Interfacial Tensions Measured Using the Micropipette Technique: Applications in Ultrasound-Microbubbles, Oil-Recovery, Lung-Surfactants, Nanoprecipitation, and Microfluidics. MICROMACHINES 2019; 10:mi10020105. [PMID: 30717224 PMCID: PMC6413238 DOI: 10.3390/mi10020105] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 01/08/2023]
Abstract
This review presents a series of measurements of the surface and interfacial tensions we have been able to make using the micropipette technique. These include: equilibrium tensions at the air-water surface and oil-water interface, as well as equilibrium and dynamic adsorption of water-soluble surfactants and water-insoluble and lipids. At its essence, the micropipette technique is one of capillary-action, glass-wetting, and applied pressure. A micropipette, as a parallel or tapered shaft, is mounted horizontally in a microchamber and viewed in an inverted microscope. When filled with air or oil, and inserted into an aqueous-filled chamber, the position of the surface or interface meniscus is controlled by applied micropipette pressure. The position and hence radius of curvature of the meniscus can be moved in a controlled fashion from dimensions associated with the capillary tip (~5–10 μm), to back down the micropipette that can taper out to 450 μm. All measurements are therefore actually made at the microscale. Following the Young–Laplace equation and geometry of the capillary, the surface or interfacial tension value is simply obtained from the radius of the meniscus in the tapered pipette and the applied pressure to keep it there. Motivated by Franklin’s early experiments that demonstrated molecularity and monolayer formation, we also give a brief potted-historical perspective that includes fundamental surfactancy driven by margarine, the first use of a micropipette to circuitously measure bilayer membrane tensions and free energies of formation, and its basis for revolutionising the study and applications of membrane ion-channels in Droplet Interface Bilayers. Finally, we give five examples of where our measurements have had an impact on applications in micro-surfaces and microfluidics, including gas microbubbles for ultrasound contrast; interfacial tensions for micro-oil droplets in oil recovery; surface tensions and tensions-in-the surface for natural and synthetic lung surfactants; interfacial tension in nanoprecipitation; and micro-surface tensions in microfluidics.
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22
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Kondrashov OV, Galimzyanov TR, Pavlov KV, Kotova EA, Antonenko YN, Akimov SA. Membrane Elastic Deformations Modulate Gramicidin A Transbilayer Dimerization and Lateral Clustering. Biophys J 2018; 115:478-493. [PMID: 30049405 PMCID: PMC6084527 DOI: 10.1016/j.bpj.2018.07.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 01/25/2023] Open
Abstract
Gramicidin A (gA) is a short β-helical peptide known to form conducting channels in lipid membranes because of transbilayer dimerization. The gA conducting dimer, being shorter than the lipid bilayer thickness, deforms the membrane in its vicinity, and the bilayer elastic energy contributes to the gA dimer formation energy. Likewise, membrane incorporation of a gA monomer, which is shorter than the lipid monolayer thickness, creates a void, thereby forcing surrounding lipid molecules to tilt to fill it. The energy of membrane deformation was calculated in the framework of the continuum elasticity theory, taking into account splay, tilt, lateral stretching/compression, Gaussian splay deformations, and external membrane tension. We obtained the interaction energy profiles for two gA monomers located either in the same or in the opposite monolayers. The profiles demonstrated the long-range attraction and short-range repulsion behavior of the monomers resulting from the membrane deformation. Analysis of the profile features revealed conditions under which clusters of gA monomers would not dissipate because of diffusion. The calculated dependence of the dimer formation and decay energy barriers on the membrane elastic properties was in good agreement with the available experimental data and suggested an explanation for a hitherto contentious phenomenon.
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Affiliation(s)
- Oleg V Kondrashov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia; Department of Theoretical Physics, Moscow Institute of Physics and Technology, Dolgoprudniy, Moscow Region, Russia
| | - Timur R Galimzyanov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia; Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology "MISiS," Moscow, Russia
| | - Konstantin V Pavlov
- Laboratory of Electrophysiology, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Elena A Kotova
- Department of Photosynthesis and Fluorescence Research Methods, A. N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Yuri N Antonenko
- Laboratory of Membrane Biophysics, A. N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Sergey A Akimov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia; Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology "MISiS," Moscow, Russia.
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23
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Azar E, Constantin D, Warschawski DE. The effect of gramicidin inclusions on the local order of membrane components. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:44. [PMID: 29582214 PMCID: PMC7088371 DOI: 10.1140/epje/i2018-11644-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
We study the local effect of the antimicrobial peptide Gramicidin A on bilayers composed of lipids or surfactants using nuclear magnetic resonance spectroscopy and wide-angle X-ray scattering, techniques that probe the orientational and positional order of the alkyl chains, respectively. The two types of order vary with temperature and peptide concentration in complex ways which depend on the membrane composition, highlighting the subtlety of the interaction between inclusions and the host bilayer. The amplitude of the variation is relatively low, indicating that the macroscopic constants used to describe the elasticity of the bilayer are unlikely to change with the addition of peptide.
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Affiliation(s)
- Elise Azar
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Doru Constantin
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France.
| | - Dror E Warschawski
- UMR 7099, CNRS-Université Paris Diderot, Institut de Biologie Physico-Chimique, Paris, France
- Département de Chimie, Université du Québec à Montréal, Downtown Station, P.O. Box 8888, H3C 3P8, Montreal, Canada
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24
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Bories F, Constantin D, Galatola P, Fournier JB. Coupling between Inclusions and Membranes at the Nanoscale. PHYSICAL REVIEW LETTERS 2018; 120:128104. [PMID: 29694104 DOI: 10.1103/physrevlett.120.128104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 06/08/2023]
Abstract
The activity of cell membrane inclusions (such as ion channels) is influenced by the host lipid membrane, to which they are elastically coupled. This coupling concerns the hydrophobic thickness of the bilayer (imposed by the length of the channel, as per the hydrophobic matching principle) but also its slope at the boundary of the inclusion. However, this parameter has never been measured so far. We combine small-angle x-ray scattering data and a complete elastic model to measure the slope for the model gramicidin channel and show that it is surprisingly steep in two membrane systems with very different elastic properties. This conclusion is confirmed and generalized by the comparison with recent results in the simulation literature and with conductivity measurements.
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Affiliation(s)
- Florent Bories
- Laboratoire "Matière et Systèmes Complexes" (MSC), UMR 7057 CNRS, Université Paris 7 Diderot, 75205 Paris Cedex 13, France
| | - Doru Constantin
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Paolo Galatola
- Laboratoire "Matière et Systèmes Complexes" (MSC), UMR 7057 CNRS, Université Paris 7 Diderot, 75205 Paris Cedex 13, France
| | - Jean-Baptiste Fournier
- Laboratoire "Matière et Systèmes Complexes" (MSC), UMR 7057 CNRS, Université Paris 7 Diderot, 75205 Paris Cedex 13, France
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25
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Palanco ME, Skovgaard N, Hansen JS, Berg-Sørensen K, Hélix-Nielsen C. Tuning biomimetic membrane barrier properties by hydrocarbon, cholesterol and polymeric additives. BIOINSPIRATION & BIOMIMETICS 2017; 13:016005. [PMID: 29019793 DOI: 10.1088/1748-3190/aa92be] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The barrier properties of cellular membranes are increasingly attracting attention as a source of inspiration for designing biomimetic membranes. The broad range of potential technological applications makes the use of lipid and lately also polymeric materials a popular choice for constructing biomimetic membranes, where the barrier properties can be controlled by the composition of the membrane constituent elements. Here we investigate the membrane properties reported by the light-induced proton pumping activity of bacteriorhodopsin (bR) reconstituted in three vesicle systems of different membrane composition. Specifically we quantify how the resulting proton influx and efflux rates are influenced by the membrane composition using a variety of membrane modulators. We demonstrate that by adding hydrocarbons to vesicles with reconstituted bR formed from asolectin lipids the resulting transmembrane proton fluxes changes proportional to the carbon chain length when compared against control. We observe a similar proportionality in single-component 1,2-Dioleoyl-sn-glycero-3-phosphocholine model membranes when using cholesterol. Lastly we investigate the effects of adding the amphiphilic di-block co-polymer polybutadiene-polyethyleneoxide (PB12-PEO10) to phospholipid membranes formed from 1,2-Dioleoyl-sn-glycero-3-phosphocholine, 1,2-Dioleoyl-sn-glycero-3-phosphatidylethanolamine, and 1,2-Dioleoyl-sn-glycero-3-phosphatidylserine. The proton pumping activity of bR (measured as a change in extra-vesicular pH) in mixed lipid/PB12-PEO10 lipid systems is up to six-fold higher compared to that observed for bR containing vesicles made from PB12-PEO10 alone. Interestingly, bR inserts with apparent opposite orientation in pure PB12-PEO10 vesicles as compared to pure lipid vesicles. Addition of equimolar amounts of lipids to PB12-PEO10 results in bR orientation similar to that observed for pure lipids. In conclusion our results show how the barrier properties of the membranes can be controlled by the composition of the membrane. In particular the use of mixed lipid-polymer systems may pave the way for constructing biomimetic membranes tailored for optimal properties in various applications including drug delivery systems, biosensors and energy conservation technology.
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Affiliation(s)
- Marta Espina Palanco
- Department of Physics, Technical University of Denmark (DTU), 2800 Kgs. Lyngby, Denmark. These authors contributed equally to this work
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Schulze Greiving VC, de Boer HL, Bomer JG, van den Berg A, Le Gac S. Integrated microfluidic biosensing platform for simultaneous confocal microscopy and electrophysiological measurements on bilayer lipid membranes and ion channels. Electrophoresis 2017; 39:496-503. [PMID: 29193178 DOI: 10.1002/elps.201700346] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/04/2017] [Accepted: 11/05/2017] [Indexed: 01/19/2023]
Abstract
Combining high-resolution imaging and electrophysiological recordings is key for various types of experimentation on lipid bilayers and ion channels. Here, we propose an integrated biosensing platform consisting of a microfluidic cartridge and a dedicated chip-holder to conduct such dual measurements on suspended lipid bilayers, in a user-friendly manner. To illustrate the potential of the integrated platform, we characterize lipid bilayers in terms of thickness and fluidity while simultaneously monitoring single ion channel currents. For that purpose, POPC lipid bilayers are supplemented with a fluorescently-tagged phospholipid (NBD-PE, 1% mol) for Fluorescence Recovery After Photobleaching (FRAP) measurements and a model ion channel (gramicidin, 1 nM). These combined measurements reveal that NBD-PE has no effect on the lipid bilayer thickness while gramicidin induces thinning of the membrane. Furthermore, the presence of gramicidin does not alter the lipid bilayer fluidity. Surprisingly, in lipid bilayers supplemented with both probes, a reduction in gramicidin open probability and lifetime is observed compared to lipid bilayers with gramicidin only, suggesting an influence of NBD-PE on the gramicidin ion function. Altogether, our proposed microfluidic biosensing platform in combination with the herein presented multi-parametric measurement scheme paves the way to explore the interdependent relationship between lipid bilayer properties and ion channel function.
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Affiliation(s)
- Verena C Schulze Greiving
- BIOS, Lab on a chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Hans L de Boer
- BIOS, Lab on a chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Johan G Bomer
- BIOS, Lab on a chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Albert van den Berg
- BIOS, Lab on a chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Séverine Le Gac
- BIOS, Lab on a chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
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Abstract
The PhoQ/PhoP two-component system plays an essential role in the response of enterobacteria to the environment of their mammalian hosts. It is known to sense several stimuli that are potentially associated with the host, including extracellular magnesium limitation, low pH, and the presence of cationic antimicrobial peptides. Here, we show that the PhoQ/PhoP two-component systems of Escherichia coli and Salmonella can also perceive an osmotic upshift, another key stimulus to which bacteria become exposed within the host. In contrast to most previously established stimuli of PhoQ, the detection of osmotic upshift does not require its periplasmic sensor domain. Instead, we show that the activity of PhoQ is affected by the length of the transmembrane (TM) helix as well as by membrane lateral pressure. We therefore propose that osmosensing relies on a conformational change within the TM domain of PhoQ induced by a perturbation in cell membrane thickness and lateral pressure under hyperosmotic conditions. Furthermore, the response mediated by the PhoQ/PhoP two-component system was found to improve bacterial growth recovery under hyperosmotic stress, partly through stabilization of the sigma factor RpoS. Our findings directly link the PhoQ/PhoP two-component system to bacterial osmosensing, suggesting that this system can mediate a concerted response to most of the established host-related cues.
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28
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Sugawara M. Transmembrane Signaling with Lipid-Bilayer Assemblies as a Platform for Channel-Based Biosensing. CHEM REC 2017; 18:433-444. [PMID: 29135061 DOI: 10.1002/tcr.201700046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/02/2017] [Indexed: 11/08/2022]
Abstract
Artificial and natural lipid membranes that elicit transmembrane signaling is are useful as a platform for channel-based biosensing. In this account we summarize our research on the design of transmembrane signaling associated with lipid bilayer membranes containing nanopore-forming compounds. Channel-forming compounds, such as receptor ion-channels, channel-forming peptides and synthetic channels, are embedded in planar and spherical bilayer lipid membranes to develop highly sensitive and selective biosensing methods for a variety of analytes. The membrane-bound receptor approach is useful for introducing receptor sites on both planar and spherical bilayer lipid membranes. Natural receptors in biomembranes are also used for designing of biosensing methods.
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Affiliation(s)
- Masao Sugawara
- Department of chemistry, College of humanities and sciences, Nihon University, Tokyo, Japan
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Time-resolved measurements of an ion channel conformational change driven by a membrane phase transition. Proc Natl Acad Sci U S A 2017; 114:10840-10845. [PMID: 28973859 DOI: 10.1073/pnas.1708070114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using temperature-jump infrared spectroscopy, we are able to trigger a gel-to-fluid phase transition in lipid vesicles and monitor in real time how a membrane protein responds to structural changes in the membrane. The melting of lipid domains in 1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles is observed to occur in as fast as 50 ns, with a temperature dependence characteristic of critical slowing. Gramicidin D (gD) added to the membrane responds primarily to the change in thickness of the membrane on a timescale coincident with the membrane melting. Using structure-based spectral modeling, we assign the conformational changes to compression and rotation of a partially dissociated gD dimer. Free energy calculations indicate that the high rate is a result of near-barrierless diffusion on a protein energy landscape that is radically reshaped by membrane thinning. The structural changes associated with the phase transition are similar to the fluctuation modes of fluid phase membranes, highlighting the importance of understanding the dynamic nature of the membrane environment around proteins.
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Beaven AH, Sodt AJ, Pastor RW, Koeppe RE, Andersen OS, Im W. Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes. J Chem Theory Comput 2017; 13:5054-5064. [PMID: 28870079 DOI: 10.1021/acs.jctc.7b00400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Previous experiments have shown that the lifetime of a gramicidin A dimer channel (which forms from two nonconducting monomers) in a lipid bilayer is modulated by mutations of the tryptophan (Trp) residues at the bilayer-water interface. We explore this further using extensive molecular dynamics simulations of various gA dimer and monomer mutants at the Trp positions in phosphatidylcholine bilayers with different tail lengths. gA interactions with the surrounding bilayer are strongly modulated by mutating these Trp residues. There are three principal effects: eliminating residue hydrogen bonding ability (i.e., reducing the channel-monolayer coupling strength) reduces the extent of the bilayer deformation caused by the assembled dimeric channel; a residue's size and geometry affects its orientation, leading to different hydrogen bonding partners; and increasing a residue's hydrophobicity increases the depth of gA monomer insertion relative to the bilayer center, thereby increasing the lipid bending frustration.
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Affiliation(s)
- Andrew H Beaven
- Department of Chemistry, The University of Kansas , Lawrence, Kansas 66045, United States
| | | | | | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College , New York, New York 10065, United States
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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Argudo D, Bethel NP, Marcoline FV, Wolgemuth CW, Grabe M. New Continuum Approaches for Determining Protein-Induced Membrane Deformations. Biophys J 2017; 112:2159-2172. [PMID: 28538153 DOI: 10.1016/j.bpj.2017.03.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/16/2017] [Accepted: 03/27/2017] [Indexed: 01/21/2023] Open
Abstract
The influence of the membrane on transmembrane proteins is central to a number of biological phenomena, notably the gating of stretch activated ion channels. Conversely, membrane proteins can influence the bilayer, leading to the stabilization of particular membrane shapes, topological changes that occur during vesicle fission and fusion, and shape-dependent protein aggregation. Continuum elastic models of the membrane have been widely used to study protein-membrane interactions. These mathematical approaches produce physically interpretable membrane shapes, energy estimates for the cost of deformation, and a snapshot of the equilibrium configuration. Moreover, elastic models are much less computationally demanding than fully atomistic and coarse-grained simulation methodologies; however, it has been argued that continuum models cannot reproduce the distortions observed in fully atomistic molecular dynamics simulations. We suggest that this failure can be overcome by using chemically and geometrically accurate representations of the protein. Here, we present a fast and reliable hybrid continuum-atomistic model that couples the protein to the membrane. We show that the model is in excellent agreement with fully atomistic simulations of the ion channel gramicidin embedded in a POPC membrane. Our continuum calculations not only reproduce the membrane distortions produced by the channel but also accurately determine the channel's orientation. Finally, we use our method to investigate the role of membrane bending around the charged voltage sensors of the transient receptor potential cation channel TRPV1. We find that membrane deformation significantly stabilizes the energy of insertion of TRPV1 by exposing charged residues on the S4 segment to solution.
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Affiliation(s)
- David Argudo
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Neville P Bethel
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Frank V Marcoline
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Charles W Wolgemuth
- Departments of Molecular and Cellular Biology and Physics, University of Arizona, Tucson, Arizona
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.
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Herold KF, Andersen OS, Hemmings HC. Divergent effects of anesthetics on lipid bilayer properties and sodium channel function. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:617-626. [PMID: 28695248 DOI: 10.1007/s00249-017-1239-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/27/2017] [Accepted: 07/01/2017] [Indexed: 02/07/2023]
Abstract
General anesthetics revolutionized medicine by allowing surgeons to perform more complex and much longer procedures. This widely used class of drugs is essential to patient care, yet their exact molecular mechanism(s) are incompletely understood. One early hypothesis over a century ago proposed that nonspecific interactions of anesthetics with the lipid bilayer lead to changes in neuronal function via effects on membrane properties. This model was supported by the Meyer-Overton correlation between anesthetic potency and lipid solubility and despite more recent evidence for specific protein targets, in particular ion-channels, lipid bilayer-mediated effects of anesthetics is still under debate. We therefore tested a wide range of chemically diverse general anesthetics on lipid bilayer properties using a sensitive and functional gramicidin-based assay. None of the tested anesthetics altered lipid bilayer properties at clinically relevant concentrations. Some anesthetics did affect the bilayer, though only at high supratherapeutic concentrations, which are unlikely relevant for clinical anesthesia. These results suggest that anesthetics directly interact with membrane proteins without altering lipid bilayer properties at clinically relevant concentrations. Voltage-gated Na+ channels are potential anesthetic targets and various isoforms are inhibited by a wide range of volatile anesthetics. They inhibit channel function by reducing peak Na+ current and shifting steady-state inactivation toward more hyperpolarized potentials. Recent advances in crystallography of prokaryotic Na+ channels, which are sensitive to volatile anesthetics, together with molecular dynamics simulations and electrophysiological studies will help identify potential anesthetic interaction sites within the channel protein itself.
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Affiliation(s)
- Karl F Herold
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Hugh C Hemmings
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, 10065, USA. .,Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA.
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Sodt AJ, Beaven AH, Andersen OS, Im W, Pastor RW. Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model. Biophys J 2017; 112:1198-1213. [PMID: 28355547 DOI: 10.1016/j.bpj.2017.01.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/11/2017] [Accepted: 01/30/2017] [Indexed: 12/20/2022] Open
Abstract
To change conformation, a protein must deform the surrounding bilayer. In this work, a three-dimensional continuum elastic model for gramicidin A in a lipid bilayer is shown to describe the sensitivity to thickness, curvature stress, and the mechanical properties of the lipid bilayer. A method is demonstrated to extract the gramicidin-lipid boundary condition from all-atom simulations that can be used in the three-dimensional continuum model. The boundary condition affects the deformation dramatically, potentially much more than typical variations in the material stiffness do as lipid composition is changed. Moreover, it directly controls the sensitivity to curvature stress. The curvature stress and hydrophobic surfaces of the all-atom and continuum models are found to be in excellent agreement. The continuum model is applied to estimate the enrichment of hydrophobically matched lipids near the channel in a mixture, and the results agree with single-channel experiments and extended molecular dynamics simulations from the companion article by Beaven et al. in this issue of Biophysical Journal.
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Affiliation(s)
- Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| | - Andrew H Beaven
- Department of Chemistry, The University of Kansas, Lawrence, Kansas
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Beaven AH, Maer AM, Sodt AJ, Rui H, Pastor RW, Andersen OS, Im W. Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation. Biophys J 2017; 112:1185-1197. [PMID: 28355546 DOI: 10.1016/j.bpj.2017.01.028] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/11/2017] [Accepted: 01/30/2017] [Indexed: 10/19/2022] Open
Abstract
Integral membrane protein function can be modulated by the host bilayer. Because biological membranes are diverse and nonuniform, we explore the consequences of lipid diversity using gramicidin A channels embedded in phosphatidylcholine (PC) bilayers composed of equimolar mixtures of di-oleoyl-PC and di-erucoyl-PC (dC18:1+dC22:1, respectively), di-palmitoleoyl-PC and di-nervonoyl-PC (dC16:1+dC24:1, respectively), and di-eicosenoyl-PC (pure dC20:1), all of which have the same average bilayer chain length. Single-channel lifetime experiments, molecular dynamics simulations, and a simple lipid compression model are used in tandem to gain insight into lipid redistribution around the channel, which partially alleviates the bilayer deformation energy associated with channel formation. The average single-channel lifetimes in the two-component bilayers (95 ± 10 ms for dC18:1+dC22:1 and 195 ± 20 ms for dC16:1+dC24:1) were increased relative to the single-component dC20:1 control bilayer (65 ± 10 ms), implying lipid redistribution. Using a theoretical treatment of thickness-dependent changes in channel lifetimes, the effective local enrichment of lipids around the channel was estimated to be 58 ± 4% dC18:1 and 66 ± 2% dC16:1 in the dC18:1+dC22:1 and dC16:1+dC24:1 bilayers, respectively. 3.5-μs molecular dynamics simulations show 66 ± 2% dC16:1 in the first lipid shell around the channel in the dC16:1+dC24:1 bilayer, but no significant redistribution (50 ± 4% dC18:1) in the dC18:1+dC22:1 bilayer; these simulated values are within the 95% confidence intervals of the experimental averages. The strong preference for the better matching lipid (dC16:1) near the channel in the dC16:1+dC24:1 mixture and lesser redistribution in the dC18:1+dC22:1 mixture can be explained by the energetic cost associated with compressing the lipids to match the channel's hydrophobic length.
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Affiliation(s)
- Andrew H Beaven
- Department of Chemistry, The University of Kansas, Lawrence, Kansas
| | - Andreia M Maer
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Huan Rui
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania.
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Tong J, Wu Z, Briggs MM, Schulten K, McIntosh TJ. The Water Permeability and Pore Entrance Structure of Aquaporin-4 Depend on Lipid Bilayer Thickness. Biophys J 2017; 111:90-9. [PMID: 27410737 DOI: 10.1016/j.bpj.2016.05.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/13/2016] [Indexed: 12/22/2022] Open
Abstract
Aquaporin-4 (AQP4), the primary water channel in glial cells of the mammalian brain, plays a critical role in water transport in the central nervous system. Previous experiments have shown that the water permeability of AQP4 depends on the cholesterol content in the lipid bilayer, but it was not clear whether changes in permeability were due to direct cholesterol-AQP4 interactions or to indirect effects caused by cholesterol-induced changes in bilayer elasticity or bilayer thickness. To determine the effects resulting only from bilayer thickness, here we use a combination of experiments and simulations to analyze AQP4 in cholesterol-free phospholipid bilayers with similar elastic properties but different hydrocarbon core thicknesses previously determined by x-ray diffraction. The channel (unit) water permeabilities of AQP4 measured by osmotic-gradient experiments were 3.5 ± 0.2 × 10(-13) cm(3)/s (mean ± SE), 3.0 ± 0.3 × 10(-13) cm(3)/s, 2.5 ± 0.2 × 10(-13) cm(3)/s, and 0.9 ± 0.1 × 10(-13) cm(3)/s in bilayers containing (C22:1)(C22:1)PC, (C20:1)(C20:1)PC, (C16:0)(C18:1)PC, and (C13:0)(C13:0)PC, respectively. Channel permeabilities obtained by molecular dynamics (MD) simulations were 3.3 ± 0.1 × 10(-13) cm(3)/s and 2.5 ± 0.1 × 10(-13) cm(3)/s in (C22:1)(C22:1)PC and (C14:0)(C14:0)PC bilayers, respectively. Both the osmotic-gradient and MD-simulation results indicated that AQP4 channel permeability decreased with decreasing bilayer hydrocarbon thickness. The MD simulations also suggested structural modifications in AQP4 in response to changes in bilayer thickness. Although the simulations showed no appreciable changes to the radius of the pore located in the hydrocarbon region of the bilayers, the simulations indicated that there were changes in both pore length and α-helix organization near the cytoplasmic vestibule of the channel. These structural changes, caused by mismatch between the hydrophobic length of AQP4 and the bilayer hydrocarbon thickness, could explain the observed differences in water permeability with changes in bilayer thickness.
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Affiliation(s)
- Jihong Tong
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina
| | - Zhe Wu
- Center for the Physics of Living Cells and Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois
| | - Margaret M Briggs
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina
| | - Klaus Schulten
- Center for the Physics of Living Cells and Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois.
| | - Thomas J McIntosh
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina.
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Clinical concentrations of chemically diverse general anesthetics minimally affect lipid bilayer properties. Proc Natl Acad Sci U S A 2017; 114:3109-3114. [PMID: 28265069 DOI: 10.1073/pnas.1611717114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
General anesthetics have revolutionized medicine by facilitating invasive procedures, and have thus become essential drugs. However, detailed understanding of their molecular mechanisms remains elusive. A mechanism proposed over a century ago involving unspecified interactions with the lipid bilayer known as the unitary lipid-based hypothesis of anesthetic action, has been challenged by evidence for direct anesthetic interactions with a range of proteins, including transmembrane ion channels. Anesthetic concentrations in the membrane are high (10-100 mM), however, and there is no experimental evidence ruling out a role for the lipid bilayer in their ion channel effects. A recent hypothesis proposes that anesthetic-induced changes in ion channel function result from changes in bilayer lateral pressure that arise from partitioning of anesthetics into the bilayer. We examined the effects of a broad range of chemically diverse general anesthetics and related nonanesthetics on lipid bilayer properties using an established fluorescence assay that senses drug-induced changes in lipid bilayer properties. None of the compounds tested altered bilayer properties sufficiently to produce meaningful changes in ion channel function at clinically relevant concentrations. Even supra-anesthetic concentrations caused minimal bilayer effects, although much higher (toxic) concentrations of certain anesthetic agents did alter lipid bilayer properties. We conclude that general anesthetics have minimal effects on bilayer properties at clinically relevant concentrations, indicating that anesthetic effects on ion channel function are not bilayer-mediated but rather involve direct protein interactions.
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ZAMOTO T, TOMINAGA S, NISHIO M, SHOJI A, SUGAWARA M. A Planar Bilayer Lipid Membrane Sensor Using a Miniaturized Auto-patch System. ANAL SCI 2017; 33:1421-1425. [DOI: 10.2116/analsci.33.1421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Taiga ZAMOTO
- Department of Chemistry, College of Humanities and Sciences, Nihon University
| | - Satoshi TOMINAGA
- Department of Chemistry, College of Humanities and Sciences, Nihon University
| | | | | | - Masao SUGAWARA
- Department of Chemistry, College of Humanities and Sciences, Nihon University
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Choi HJ, Song JM, Bondy BJ, Compans RW, Kang SM, Prausnitz MR. Effect of Osmotic Pressure on the Stability of Whole Inactivated Influenza Vaccine for Coating on Microneedles. PLoS One 2015; 10:e0134431. [PMID: 26230936 PMCID: PMC4521748 DOI: 10.1371/journal.pone.0134431] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 07/10/2015] [Indexed: 11/18/2022] Open
Abstract
Enveloped virus vaccines can be damaged by high osmotic strength solutions, such as those used to protect the vaccine antigen during drying, which contain high concentrations of sugars. We therefore studied shrinkage and activity loss of whole inactivated influenza virus in hyperosmotic solutions and used those findings to improve vaccine coating of microneedle patches for influenza vaccination. Using stopped-flow light scattering analysis, we found that the virus underwent an initial shrinkage on the order of 10% by volume within 5 s upon exposure to a hyperosmotic stress difference of 217 milliosmolarity. During this shrinkage, the virus envelope had very low osmotic water permeability (1 - 6×10-4 cm s-1) and high Arrhenius activation energy (Ea = 15.0 kcal mol-1), indicating that the water molecules diffused through the viral lipid membranes. After a quasi-stable state of approximately 20 s to 2 min, depending on the species and hypertonic osmotic strength difference of disaccharides, there was a second phase of viral shrinkage. At the highest osmotic strengths, this led to an undulating light scattering profile that appeared to be related to perturbation of the viral envelope resulting in loss of virus activity, as determined by in vitro hemagglutination measurements and in vivo immunogenicity studies in mice. Addition of carboxymethyl cellulose effectively prevented vaccine activity loss in vitro and in vivo, believed to be due to increasing the viscosity of concentrated sugar solution and thereby reducing osmotic stress during coating of microneedles. These results suggest that hyperosmotic solutions can cause biphasic shrinkage of whole inactivated influenza virus which can damage vaccine activity at high osmotic strength and that addition of a viscosity enhancer to the vaccine coating solution can prevent osmotically driven damage and thereby enable preparation of stable microneedle coating formulations for vaccination.
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Affiliation(s)
- Hyo-Jick Choi
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Jae-Min Song
- Department of Global Medical Science, Sungshin Women's University, Seoul, Korea
| | - Brian J. Bondy
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Richard W. Compans
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Sang-Moo Kang
- Center for Inflammation, Immunity, & Infection and Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Mark R. Prausnitz
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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Modifiers of membrane dipole potentials as tools for investigating ion channel formation and functioning. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:245-97. [PMID: 25708465 DOI: 10.1016/bs.ircmb.2014.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrostatic fields generated on and within biological membranes play a fundamental role in key processes in cell functions. The role of the membrane dipole potential is of particular interest because of its powerful impact on membrane permeability and lipid-protein interactions, including protein insertion, oligomerization, and function. The membrane dipole potential is defined by the orientation of electric dipoles of lipid headgroups, fatty acid carbonyl groups, and membrane-adsorbed water. As a result, the membrane interior is several hundred millivolts more positive than the external aqueous phase. This potential decrease depends on the lipid, and especially sterol, composition of the membrane. The adsorption of certain electroneutral molecules known as dipole modifiers may also lead to significant changes in the magnitude of the potential decrease. These agents are widely used to study the effects of the dipole potential on membrane transport. This review presents a critical analysis of a variety of data from studies dedicated to ion channel formation and functioning in membranes with different dipole potentials. The types of ion channels found in cellular membranes and pores formed by antimicrobial agents and toxins in artificial lipid membranes are summarized. The mechanisms underlying the influence of the membrane dipole potential on ion channel activity, including dipole-dipole and charge-dipole interactions in the pores and in membranes, are discussed. A hypothesis, in which lipid rafts in both model and cellular membranes also modulate ion channel activity by virtue of an increased or decreased dipole potential, is also considered.
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Herold KF, Sanford RL, Lee W, Schultz MF, Ingólfsson HI, Andersen OS, Hemmings HC. Volatile anesthetics inhibit sodium channels without altering bulk lipid bilayer properties. J Gen Physiol 2014; 144:545-60. [PMID: 25385786 PMCID: PMC4242807 DOI: 10.1085/jgp.201411172] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 10/08/2014] [Indexed: 01/05/2023] Open
Abstract
Although general anesthetics are clinically important and widely used, their molecular mechanisms of action remain poorly understood. Volatile anesthetics such as isoflurane (ISO) are thought to alter neuronal function by depressing excitatory and facilitating inhibitory neurotransmission through direct interactions with specific protein targets, including voltage-gated sodium channels (Na(v)). Many anesthetics alter lipid bilayer properties, suggesting that ion channel function might also be altered indirectly through effects on the lipid bilayer. We compared the effects of ISO and of a series of fluorobenzene (FB) model volatile anesthetics on Na(v) function and lipid bilayer properties. We examined the effects of these agents on Na(v) in neuronal cells using whole-cell electrophysiology, and on lipid bilayer properties using a gramicidin-based fluorescence assay, which is a functional assay for detecting changes in lipid bilayer properties sensed by a bilayer-spanning ion channel. At clinically relevant concentrations (defined by the minimum alveolar concentration), both the FBs and ISO produced prepulse-dependent inhibition of Na(v) and shifted the voltage dependence of inactivation toward more hyperpolarized potentials without affecting lipid bilayer properties, as sensed by gramicidin channels. Only at supra-anesthetic (toxic) concentrations did ISO alter lipid bilayer properties. These results suggest that clinically relevant concentrations of volatile anesthetics alter Na(v) function through direct interactions with the channel protein with little, if any, contribution from changes in bulk lipid bilayer properties. Our findings further suggest that changes in lipid bilayer properties are not involved in clinical anesthesia.
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Affiliation(s)
- Karl F Herold
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - R Lea Sanford
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - William Lee
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Margaret F Schultz
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Helgi I Ingólfsson
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Olaf S Andersen
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Hugh C Hemmings
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065 Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
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Gurnev PA, Nestorovich EM. Channel-forming bacterial toxins in biosensing and macromolecule delivery. Toxins (Basel) 2014; 6:2483-540. [PMID: 25153255 PMCID: PMC4147595 DOI: 10.3390/toxins6082483] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 12/19/2022] Open
Abstract
To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on "Intracellular Traffic and Transport of Bacterial Protein Toxins", reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their "second life" in a variety of developing medical and technological applications.
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Affiliation(s)
- Philip A Gurnev
- Physics Department, University of Massachusetts, Amherst, MA 01003, USA.
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Assembly and stability of Salmonella enterica ser. Typhi TolC protein in POPE and DMPE. J Biol Phys 2014; 40:387-400. [PMID: 25011632 DOI: 10.1007/s10867-014-9357-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022] Open
Abstract
In this work we assessed the suitability of two different lipid membranes for the simulation of a TolC protein from Salmonella enterica serovar Typhi. The TolC protein family is found in many pathogenic Gram-negative bacteria including Vibrio cholera and Pseudomonas aeruginosa and acts as an outer membrane channel for expulsion of drug and toxin from the cell. In S. typhi, the causative agent for typhoid fever, the TolC outer membrane protein is an antigen for the pathogen. The lipid environment is an important modulator of membrane protein structure and function. We evaluated the conformation of the TolC protein in the presence of DMPE and POPE bilayers using molecular dynamics simulation. The S. typhi TolC protein exhibited similar conformational dynamics to TolC and its homologues. Conformational flexibility of the protein is seen in the C-terminal, extracellular loops, and α-helical region. Despite differences in the two lipids, significant similarities in the motion of the protein in POPE and DMPE were observed, including the rotational motion of the C-terminal residues and the partially open extracellular loops. However, analysis of the trajectories demonstrated effects of hydrophobic matching of the TolC protein in the membrane, particularly in the lengthening of the lipids and subtle movements of the protein's β-barrel towards the lower leaflet in DMPE. The study exhibited the use of molecular dynamics simulation in revealing the differential effect of membrane proteins and lipids on each other. In this study, POPE is potentially a more suitable model for future simulation of the S. typhi TolC protein.
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Sugawara M, Shoji A, Sakamoto M. Pore-forming compounds as signal transduction elements for highly sensitive biosensing. ANAL SCI 2014; 30:119-28. [PMID: 24420253 DOI: 10.2116/analsci.30.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pore-forming compounds are attracting much attention due to the signal transduction ability for the development of highly sensitive biosensing. In this review, we describe an overview of the recent advances made by our group in the design of molecular sensing interfaces of spherical and planar lipid bilayers and natural bilayers. The potential uses of pore-forming compounds, such as gramicidin and MCM-41, in lipid bilayers and natural glutamate receptor channels in biomembrane are presented.
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Affiliation(s)
- Masao Sugawara
- Department of Chemistry, College of Humanities and Sciences, Nihon University
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Alejo JL, Blanchard SC, Andersen OS. Small-molecule photostabilizing agents are modifiers of lipid bilayer properties. Biophys J 2014; 104:2410-8. [PMID: 23746513 DOI: 10.1016/j.bpj.2013.04.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022] Open
Abstract
Small-molecule photostabilizing or protective agents (PAs) provide essential support for the stability demands on fluorescent dyes in single-molecule spectroscopy and fluorescence microscopy. These agents are employed also in studies of cell membranes and model systems mimicking lipid bilayer environments, but there is little information about their possible effects on membrane structure and physical properties. Given the impact of amphipathic small molecules on bilayer properties such as elasticity and intrinsic curvature, we investigated the effects of six commonly used PAs--cyclooctatetraene (COT), para-nitrobenzyl alcohol (NBA), Trolox (TX), 1,4-diazabicyclo[2.2.2]octane (DABCO), para-nitrobenzoic acid (pNBA), and n-propyl gallate (nPG)--on bilayer properties using a gramicidin A (gA)-based fluorescence quench assay to probe for PA-induced changes in the gramicidin monomer↔dimer equilibrium. The experiments were done using fluorophore-loaded large unilamellar vesicles that had been doped with gA, and changes in the gA monomer↔dimer equilibrium were assayed using a gA channel-permeable fluorescence quencher (Tl⁺). Changes in bilayer properties caused by, e.g., PA adsorption at the bilayer/solution interface that alter the equilibrium constant for gA channel formation, and thus the number of conducting gA channels in the large unilamellar vesicle membrane, will be detectable as changes in the rate of Tl⁺ influx-the fluorescence quench rate. Over the experimentally relevant millimolar concentration range, TX, NBA, and pNBA, caused comparable increases in gA channel activity. COT, also in the millimolar range, caused a slight decrease in gA channel activity. nPG increased channel activity at submillimolar concentrations. DABCO did not alter gA activity. Five of the six tested PAs thus alter lipid bilayer properties at experimentally relevant concentrations, which becomes important for the design and analysis of fluorescence studies in cells and model membrane systems. We therefore tested combinations of COT, NBA, and TX; the combinations altered the fluorescence quench rate less than would be predicted assuming their effects on bilayer properties were additive. The combination of equimolar concentrations of COT and NBA caused minimal changes in the fluorescence quench rate.
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Affiliation(s)
- Jose L Alejo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
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Ion channel stability of Gramicidin A in lipid bilayers: Effect of hydrophobic mismatch. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:328-38. [DOI: 10.1016/j.bbamem.2013.10.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/20/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022]
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Rusinova R, Hobart EA, Koeppe RE, Andersen OS. Phosphoinositides alter lipid bilayer properties. ACTA ACUST UNITED AC 2013; 141:673-90. [PMID: 23712549 PMCID: PMC3664701 DOI: 10.1085/jgp.201310960] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Phosphatidylinositol-4,5-bisphosphate (PIP2), which constitutes ∼1% of the plasma membrane phospholipid, plays a key role in membrane-delimited signaling. PIP2 regulates structurally and functionally diverse membrane proteins, including voltage- and ligand-gated ion channels, inwardly rectifying ion channels, transporters, and receptors. In some cases, the regulation is known to involve specific lipid–protein interactions, but the mechanisms by which PIP2 regulates many of its various targets remain to be fully elucidated. Because many PIP2 targets are membrane-spanning proteins, we explored whether the phosphoinositides might alter bilayer physical properties such as curvature and elasticity, which would alter the equilibrium between membrane protein conformational states—and thereby protein function. Taking advantage of the gramicidin A (gA) channels’ sensitivity to changes in lipid bilayer properties, we used gA-based fluorescence quenching and single-channel assays to examine the effects of long-chain PIP2s (brain PIP2, which is predominantly 1-stearyl-2-arachidonyl-PIP2, and dioleoyl-PIP2) on bilayer properties. When premixed with dioleoyl-phosphocholine at 2 mol %, both long-chain PIP2s produced similar changes in gA channel function (bilayer properties); when applied through the aqueous solution, however, brain PIP2 was a more potent modifier than dioleoyl-PIP2. Given the widespread use of short-chain dioctanoyl-phosphoinositides, we also examined the effects of diC8-phosphoinositol (PI), PI(4,5)P2, PI(3,5)P2, PI(3,4)P2, and PI(3,4,5)P3. The diC8 phosphoinositides, except for PI(3,5)P2, altered bilayer properties with potencies that decreased with increasing head group charge. Nonphosphoinositide diC8 phospholipids generally were more potent bilayer modifiers than the polyphosphoinositides. These results show that physiological increases or decreases in plasma membrane PIP2 levels, as a result of activation of PI kinases or phosphatases, are likely to alter lipid bilayer properties, in addition to any other effects they may have. The results further show that exogenous PIP2, as well as structural analogues that differ in acyl chain length or phosphorylation state, alters lipid bilayer properties at the concentrations used in many cell physiological experiments.
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Affiliation(s)
- Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA.
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Peptide-induced membrane leakage by lysine derivatives of gramicidin A in liposomes, planar bilayers, and erythrocytes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2428-35. [DOI: 10.1016/j.bbamem.2013.06.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 06/10/2013] [Accepted: 06/13/2013] [Indexed: 11/21/2022]
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Watson MC, Morriss-Andrews A, Welch PM, Brown FLH. Thermal fluctuations in shape, thickness, and molecular orientation in lipid bilayers. II. Finite surface tensions. J Chem Phys 2013; 139:084706. [DOI: 10.1063/1.4818530] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Choi HJ, Ebersbacher CF, Kim MC, Kang SM, Montemagno CD. A mechanistic study on the destabilization of whole inactivated influenza virus vaccine in gastric environment. PLoS One 2013; 8:e66316. [PMID: 23776657 PMCID: PMC3679046 DOI: 10.1371/journal.pone.0066316] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 05/03/2013] [Indexed: 11/19/2022] Open
Abstract
Oral immunization using whole inactivated influenza virus vaccine promises an efficient vaccination strategy. While oral vaccination was hampered by harsh gastric environment, a systematic understanding about vaccine destabilization mechanisms was not performed. Here, we investigated the separate and combined effects of temperature, retention time, pH, and osmotic stress on the stability of influenza vaccine by monitoring the time-dependent morphological change using stopped-flow light scattering. When exposed to osmotic stress, clustering of vaccine particles was enhanced in an acidic medium (pH 2.0) at ≥25°C. Fluorescence spectroscopic studies showed that hyper-osmotic stress at pH 2.0 and 37°C caused a considerable increase in conformational change of antigenic proteins compared to that in acidic iso-osmotic medium. A structural integrity of membrane was destroyed upon exposure to hyper-osmotic stress, leading to irreversible morphological change, as observed by undulation in stopped-flow light scattering intensity and transmission electron microscopy. Consistent with these analyses, hemagglutination activity decreased more significantly with an increasing magnitude of hyper-osmotic stress than in the presence of the hypo- and iso-osmotic stresses. This study shows that the magnitude and direction of the osmotic gradient has a substantial impact on the stability of orally administrated influenza vaccine.
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Affiliation(s)
- Hyo-Jick Choi
- School of Energy, Environmental, Biological and Medical Engineering University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Charles F. Ebersbacher
- School of Energy, Environmental, Biological and Medical Engineering University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Min-Chul Kim
- Center for Inflammation, Immunity and Infection and Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Sang-Moo Kang
- Center for Inflammation, Immunity and Infection and Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Carlo D. Montemagno
- National Institute for Nanotechnology, Nanotechnology Accelerator and Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
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Stimberg VC, Bomer JG, van Uitert I, van den Berg A, Le Gac S. High yield, reproducible and quasi-automated bilayer formation in a microfluidic format. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:1076-1085. [PMID: 23139010 DOI: 10.1002/smll.201201821] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 08/27/2012] [Indexed: 05/28/2023]
Abstract
A microfluidic platform is reported for various experimentation schemes on cell membrane models and membrane proteins using a combination of electrical and optical measurements, including confocal microscopy. Bilayer lipid membranes (BLMs) are prepared in the device upon spontaneous and instantaneous thinning of the lipid solution in a 100-μm dry-etched aperture in a 12.5-μm thick Teflon foil. Using this quasi-automated approach, a remarkable 100% membrane formation yield is reached (including reflushing in 4% of the cases), and BLMs are stable for up to 36 h. Furthermore, the potential of this platform is demonstrated for (i) the in-depth characterization of BLMs comprising both synthetic and natural lipids (1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) and L-α-phosphatidylcholine (L-α-PC)/cholesterol, respectively) in terms of seal resistance, capacitance, surface area, specific capacitance, and membrane hydrophobic thickness; (ii) confocal microscopy imaging of phase separation in sphingomyelin/L-α-PC/cholesterol ternary membranes; (iii) electrical measurements of individual nanopores (α-hemolysin, gramicidin); and (iv) indirect assessment of the alteration of membrane properties upon exposure to chemical stimuli using the natural nanopore gramicidin as a sensor.
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Affiliation(s)
- Verena C Stimberg
- BIOS-Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands
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