1
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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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2
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Maer AM, Rusinova R, Providence LL, Ingólfsson HI, Collingwood SA, Lundbæk JA, Andersen OS. Regulation of Gramicidin Channel Function Solely by Changes in Lipid Intrinsic Curvature. Front Physiol 2022; 13:836789. [PMID: 35350699 PMCID: PMC8957996 DOI: 10.3389/fphys.2022.836789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Membrane protein function is regulated by the lipid bilayer composition. In many cases the changes in function correlate with changes in the lipid intrinsic curvature (c 0), and c 0 is considered a determinant of protein function. Yet, water-soluble amphiphiles that cause either negative or positive changes in curvature have similar effects on membrane protein function, showing that changes in lipid bilayer properties other than c 0 are important-and may be dominant. To further investigate the mechanisms underlying the bilayer regulation of protein function, we examined how maneuvers that alter phospholipid head groups effective "size"-and thereby c 0-alter gramicidin (gA) channel function. Using dioleoylphospholipids and planar bilayers, we varied the head groups' physical volume and the electrostatic repulsion among head groups (and thus their effective size). When 1,2-dioleyol-sn-glycero-3-phosphocholine (DOPC), was replaced by 1,2-dioleyol-sn-glycero-3-phosphoethanolamine (DOPE) with a smaller head group (causing a more negative c 0), the channel lifetime (τ) is decreased. When the pH of the solution bathing a 1,2-dioleyol-sn-glycero-3-phosphoserine (DOPS) bilayer is decreased from 7 to 3 (causing decreased head group repulsion and a more negative c 0), τ is decreased. When some DOPS head groups are replaced by zwitterionic head groups, τ is similarly decreased. These effects do not depend on the sign of the change in surface charge. In DOPE:DOPC (3:1) bilayers, pH changes from 5→9 to 5→0 (both increasing head group electrostatic repulsion, thereby causing a less negative c 0) both increase τ. Nor do the effects depend on the use of planar, hydrocarbon-containing bilayers, as similar changes were observed in hydrocarbon-free lipid vesicles. Altering the interactions among phospholipid head groups may alter also other bilayer properties such as thickness or elastic moduli. Such changes could be excluded using capacitance measurements and single channel measurements on gA channels of different lengths. We conclude that changes gA channel function caused by changes in head group effective size can be predicted from the expected changes in c 0.
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Affiliation(s)
| | | | | | | | | | | | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States
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3
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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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4
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Zykova VA, Adichtchev SV, Surovtsev NV. Effect of the Hydrocarbon Chain Disorder in Phosphatidylcholine Bilayers on Gigahertz Sound Velocity. J Phys Chem B 2020; 124:9079-9085. [PMID: 32970434 DOI: 10.1021/acs.jpcb.0c06043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Suspensions of multilamellar vesicles of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and hydrated and dehydrated aligned multilamellar samples of DMPC were studied by Brillouin spectroscopy in the temperature range from 90 to 333 K. The sound velocity of the longitudinal acoustic wave was evaluated from the Brillouin spectra. It was found that phase transition, hydration state, and planar or vesicular form of bilayers affect the gigahertz sound velocity. Usually, the temperature dependence of the sound velocity is weak in solid substances. Amazingly, the sound velocity of hydrated DMPC samples showed significant temperature-induced changes of up to 1.8 times, even within the solid-like gel phase. We explained this effect by temperature-induced excitations of the disordered conformational states of the hydrocarbon chains as well as anharmonic effects. In addition, the relevance of the gigahertz sound velocity to the description of subterahertz Raman features was demonstrated.
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Affiliation(s)
- V A Zykova
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - S V Adichtchev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - N V Surovtsev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
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5
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Doktorova M, Heberle FA, Marquardt D, Rusinova R, Sanford RL, Peyear TA, Katsaras J, Feigenson GW, Weinstein H, Andersen OS. Gramicidin Increases Lipid Flip-Flop in Symmetric and Asymmetric Lipid Vesicles. Biophys J 2019; 116:860-873. [PMID: 30755300 PMCID: PMC6400823 DOI: 10.1016/j.bpj.2019.01.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/03/2019] [Accepted: 01/09/2019] [Indexed: 01/06/2023] Open
Abstract
Unlike most transmembrane proteins, phospholipids can migrate from one leaflet of the membrane to the other. Because this spontaneous lipid translocation (flip-flop) tends to be very slow, cells facilitate the process with enzymes that catalyze the transmembrane movement and thereby regulate the transbilayer lipid distribution. Nonenzymatic membrane-spanning proteins with unrelated primary functions have also been found to accelerate lipid flip-flop in a nonspecific manner and by various hypothesized mechanisms. Using deuterated phospholipids, we examined the acceleration of flip-flop by gramicidin channels, which have well-defined structures and known functions, features that make them ideal candidates for probing the protein-membrane interactions underlying lipid flip-flop. To study compositionally and isotopically asymmetric proteoliposomes containing gramicidin, we expanded a recently developed protocol for the preparation and characterization of lipid-only asymmetric vesicles. Channel incorporation, conformation, and function were examined with small angle x-ray scattering, circular dichroism, and a stopped-flow spectrofluorometric assay, respectively. As a measure of lipid scrambling, we used differential scanning calorimetry to monitor the effect of gramicidin on the melting transition temperatures of the two bilayer leaflets. The two calorimetric peaks of the individual leaflets merged into a single peak over time, suggestive of scrambling, and the effect of the channel on the transbilayer lipid distribution in both symmetric 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and asymmetric 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles was quantified from proton NMR measurements. Our results show that gramicidin increases lipid flip-flop in a complex, concentration-dependent manner. To determine the molecular mechanism of the process, we used molecular dynamics simulations and further computational analysis of the trajectories to estimate the extent of membrane deformation. Together, the experimental and computational approaches were found to constitute an effective means for studying the effects of transmembrane proteins on lipid distribution in both symmetric and asymmetric model membranes.
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Affiliation(s)
- Milka Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York.
| | - Frederick A Heberle
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas; The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee
| | | | - Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - R Lea Sanford
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Thasin A Peyear
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - John Katsaras
- Large Scale Structures Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Gerald W Feigenson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Greenberg Center, New York, New York
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
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6
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Falzone ME, Rheinberger J, Lee BC, Peyear T, Sasset L, Raczkowski AM, Eng ET, Di Lorenzo A, Andersen OS, Nimigean CM, Accardi A. Structural basis of Ca 2+-dependent activation and lipid transport by a TMEM16 scramblase. eLife 2019; 8:43229. [PMID: 30648972 PMCID: PMC6355197 DOI: 10.7554/elife.43229] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022] Open
Abstract
The lipid distribution of plasma membranes of eukaryotic cells is asymmetric and phospholipid scramblases disrupt this asymmetry by mediating the rapid, nonselective transport of lipids down their concentration gradients. As a result, phosphatidylserine is exposed to the outer leaflet of membrane, an important step in extracellular signaling networks controlling processes such as apoptosis, blood coagulation, membrane fusion and repair. Several TMEM16 family members have been identified as Ca2+-activated scramblases, but the mechanisms underlying their Ca2+-dependent gating and their effects on the surrounding lipid bilayer remain poorly understood. Here, we describe three high-resolution cryo-electron microscopy structures of a fungal scramblase from Aspergillus fumigatus, afTMEM16, reconstituted in lipid nanodiscs. These structures reveal that Ca2+-dependent activation of the scramblase entails global rearrangement of the transmembrane and cytosolic domains. These structures, together with functional experiments, suggest that activation of the protein thins the membrane near the transport pathway to facilitate rapid transbilayer lipid movement.
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Affiliation(s)
- Maria E Falzone
- Department of Biochemistry, Weill Cornell Medical College, New York, United States
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medical College, New York, United States
| | - Byoung-Cheol Lee
- Department of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Structure and Function on Neural Network, Korea Brain Research Institute, Deagu, Republic of Korea
| | - Thasin Peyear
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States
| | - Linda Sasset
- Department of Pathology, Weill Cornell Medical College, New York, United States
| | - Ashleigh M Raczkowski
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Edward T Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Annarita Di Lorenzo
- Department of Pathology, Weill Cornell Medical College, New York, United States
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States
| | - Crina M Nimigean
- Department of Biochemistry, Weill Cornell Medical College, New York, United States.,Department of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States
| | - Alessio Accardi
- Department of Biochemistry, Weill Cornell Medical College, New York, United States.,Department of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States
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7
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Zhang M, Peyear T, Patmanidis I, Greathouse DV, Marrink SJ, Andersen OS, Ingólfsson HI. Fluorinated Alcohols' Effects on Lipid Bilayer Properties. Biophys J 2018; 115:679-689. [PMID: 30077334 PMCID: PMC6104562 DOI: 10.1016/j.bpj.2018.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/23/2018] [Accepted: 07/02/2018] [Indexed: 12/21/2022] Open
Abstract
Fluorinated alcohols (fluoroalcohols) have physicochemical properties that make them excellent solvents of peptides, proteins, and other compounds. Like other alcohols, fluoroalcohols also alter membrane protein function and lipid bilayer properties and stability. Thus, the questions arise: how potent are fluoroalcohols as lipid-bilayer-perturbing compounds, could small residual amounts that remain after adding compounds dissolved in fluoroalcohols alter lipid bilayer properties sufficiently to affect membranes and membrane protein function, and do they behave like other alcohols? To address these questions, we used a gramicidin-based fluorescence assay to determine the bilayer-modifying potency of selected fluoroalcohols: trifluoroethanol (TFE), HFIP, and perfluoro-tert-butanol (PFTB). These fluoroalcohols alter bilayer properties in the low (PFTB) to high (TFE) mM range. Using the same assay, we determined the bilayer partitioning of the alcohols. When referenced to the aqueous concentrations, the fluoroalcohols are more bilayer perturbing than their nonfluorinated counterparts, with the largest fluoroalcohol, PFTB, being the most potent and the smallest, TFE, the least. When referenced to the mole fractions in the membrane, however, the fluoroalcohols have equal or lesser bilayer-perturbing potency than their nonfluorinated counterparts, with TFE being more bilayer perturbing than PFTB. We compared the fluoroalcohols' molecular level bilayer interactions using atomistic molecular dynamics simulations and showed how, at higher concentrations, they can cause bilayer breakdown using absorbance measurements and 31P nuclear magnetic resonance.
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Affiliation(s)
- Mike Zhang
- Department Physiology and Biophysics, Weill Cornell Medicine, New York City, New York; The Bronx High School of Science, New York City, New York
| | - Thasin Peyear
- Department Physiology and Biophysics, Weill Cornell Medicine, New York City, New York
| | - Ilias Patmanidis
- Groningen Biomolecular Science and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Siewert J Marrink
- Groningen Biomolecular Science and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Olaf S Andersen
- Department Physiology and Biophysics, Weill Cornell Medicine, New York City, New York.
| | - Helgi I Ingólfsson
- Department Physiology and Biophysics, Weill Cornell Medicine, New York City, New York; Groningen Biomolecular Science and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands; Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California.
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8
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Weinrich M, Worcester DL, Bezrukov SM. Lipid nanodomains change ion channel function. NANOSCALE 2017; 9:13291-13297. [PMID: 28858358 PMCID: PMC5599369 DOI: 10.1039/c7nr03926c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Signaling proteins and neurotransmitter receptors often associate with saturated chain and cholesterol-rich domains of cell membranes, also known as lipid rafts. The saturated chains and high cholesterol environment in lipid rafts can modulate protein function, but evidence for such modulation of ion channel function in lipid rafts is lacking. Here, using raft-forming model membrane systems containing cholesterol, we show that lipid lateral phase separation at the nanoscale level directly affects the dissociation kinetics of the gramicidin dimer, a model ion channel.
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Affiliation(s)
- Michael Weinrich
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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9
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Effect of Statins on the Nanomechanical Properties of Supported Lipid Bilayers. Biophys J 2017; 111:363-372. [PMID: 27463138 DOI: 10.1016/j.bpj.2016.06.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 05/25/2016] [Accepted: 06/15/2016] [Indexed: 11/23/2022] Open
Abstract
Many drugs and other xenobiotics may reach systemic concentrations where they interact not only with the proteins that are their therapeutic targets but also modify the physicochemical properties of the cell membrane, which may lead to altered function of many transmembrane proteins beyond the intended targets. These changes in bilayer properties may contribute to nonspecific, promiscuous changes in membrane protein and cell function because membrane proteins are energetically coupled to their host lipid bilayer. It is thus important, for both pharmaceutical and biophysical reasons, to understand the bilayer-modifying effect of amphiphiles (including therapeutic agents). Here we use atomic force microscopy topography imaging and nanomechanical mapping to monitor the effect of statins, a family of hypolipidemic drugs, on synthetic lipid membranes. Our results reveal that statins alter the nanomechanical stability of the bilayers and increase their elastic moduli depending on the lipid bilayer order. Our results also suggest that statins increase bilayer heterogeneity, which may indicate that statins form nanometer-sized aggregates in the membrane. This is further evidence that changes in bilayer nanoscale mechanical properties may be a signature of lipid bilayer-mediated effects of amphiphilic drugs.
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10
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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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11
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Chadda R, Krishnamani V, Mersch K, Wong J, Brimberry M, Chadda A, Kolmakova-Partensky L, Friedman LJ, Gelles J, Robertson JL. The dimerization equilibrium of a ClC Cl(-)/H(+) antiporter in lipid bilayers. eLife 2016; 5. [PMID: 27484630 PMCID: PMC5010387 DOI: 10.7554/elife.17438] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 07/29/2016] [Indexed: 12/20/2022] Open
Abstract
Interactions between membrane protein interfaces in lipid bilayers play an important role in membrane protein folding but quantification of the strength of these interactions has been challenging. Studying dimerization of ClC-type transporters offers a new approach to the problem, as individual subunits adopt a stable and functionally verifiable fold that constrains the system to two states - monomer or dimer. Here, we use single-molecule photobleaching analysis to measure the probability of ClC-ec1 subunit capture into liposomes during extrusion of large, multilamellar membranes. The capture statistics describe a monomer to dimer transition that is dependent on the subunit/lipid mole fraction density and follows an equilibrium dimerization isotherm. This allows for the measurement of the free energy of ClC-ec1 dimerization in lipid bilayers, revealing that it is one of the strongest membrane protein complexes measured so far, and introduces it as new type of dimerization model to investigate the physical forces that drive membrane protein association in membranes.
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Affiliation(s)
- Rahul Chadda
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | | | - Kacey Mersch
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Jason Wong
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States.,Department of Natural Sciences, University of Bath, Bath, United Kingdom
| | - Marley Brimberry
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Ankita Chadda
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | | | - Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Janice L Robertson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
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12
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Rusinova R, Koeppe RE, Andersen OS. A general mechanism for drug promiscuity: Studies with amiodarone and other antiarrhythmics. ACTA ACUST UNITED AC 2015; 146:463-75. [PMID: 26573624 PMCID: PMC4664825 DOI: 10.1085/jgp.201511470] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/13/2015] [Indexed: 01/14/2023]
Abstract
Amiodarone is a widely prescribed antiarrhythmic drug used to treat the most prevalent type of arrhythmia, atrial fibrillation (AF). At therapeutic concentrations, amiodarone alters the function of many diverse membrane proteins, which results in complex therapeutic and toxicity profiles. Other antiarrhythmics, such as dronedarone, similarly alter the function of multiple membrane proteins, suggesting that a multipronged mechanism may be beneficial for treating AF, but raising questions about how these antiarrhythmics regulate a diverse range of membrane proteins at similar concentrations. One possible mechanism is that these molecules regulate membrane protein function by altering the common environment provided by the host lipid bilayer. We took advantage of the gramicidin (gA) channels' sensitivity to changes in bilayer properties to determine whether commonly used antiarrhythmics--amiodarone, dronedarone, propranolol, and pindolol, whose pharmacological modes of action range from multi-target to specific--perturb lipid bilayer properties at therapeutic concentrations. Using a gA-based fluorescence assay, we found that amiodarone and dronedarone are potent bilayer modifiers at therapeutic concentrations; propranolol alters bilayer properties only at supratherapeutic concentration, and pindolol has little effect. Using single-channel electrophysiology, we found that amiodarone and dronedarone, but not propranolol or pindolol, increase bilayer elasticity. The overlap between therapeutic and bilayer-altering concentrations, which is observed also using plasma membrane-like lipid mixtures, underscores the need to explore the role of the bilayer in therapeutic as well as toxic effects of antiarrhythmic agents.
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Affiliation(s)
- Radda Rusinova
- Department of Physiology and Biophysics and Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065 Department of Physiology and Biophysics and Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701
| | - Olaf S Andersen
- Department of Physiology and Biophysics and Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
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13
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Xie W, Wei Jun Low J, Armugam A, Jeyaseelan K, Wah Tong Y. Regulation of Aquaporin Z osmotic permeability in ABA tri-block copolymer. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.3.381] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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14
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Ingólfsson HI, Thakur P, Herold KF, Hobart EA, Ramsey NB, Periole X, de Jong DH, Zwama M, Yilmaz D, Hall K, Maretzky T, Hemmings HC, Blobel C, Marrink SJ, Koçer A, Sack JT, Andersen OS. Phytochemicals perturb membranes and promiscuously alter protein function. ACS Chem Biol 2014; 9:1788-98. [PMID: 24901212 PMCID: PMC4136704 DOI: 10.1021/cb500086e] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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A wide
variety of phytochemicals are consumed for their perceived
health benefits. Many of these phytochemicals have been found to alter
numerous cell functions, but the mechanisms underlying their biological
activity tend to be poorly understood. Phenolic phytochemicals are
particularly promiscuous modifiers of membrane protein function, suggesting
that some of their actions may be due to a common, membrane bilayer-mediated
mechanism. To test whether bilayer perturbation may underlie this
diversity of actions, we examined five bioactive phenols reported
to have medicinal value: capsaicin from chili peppers, curcumin from
turmeric, EGCG from green tea, genistein from soybeans, and resveratrol
from grapes. We find that each of these widely consumed phytochemicals
alters lipid bilayer properties and the function of diverse membrane
proteins. Molecular dynamics simulations show that these phytochemicals
modify bilayer properties by localizing to the bilayer/solution interface.
Bilayer-modifying propensity was verified using a gramicidin-based
assay, and indiscriminate modulation of membrane protein function
was demonstrated using four proteins: membrane-anchored metalloproteases,
mechanosensitive ion channels, and voltage-dependent potassium and
sodium channels. Each protein exhibited similar responses to multiple
phytochemicals, consistent with a common, bilayer-mediated mechanism.
Our results suggest that many effects of amphiphilic phytochemicals
are due to cell membrane perturbations, rather than specific protein
binding.
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Affiliation(s)
| | - Pratima Thakur
- Dept.
Physiology and Membrane Biology, University of California, Davis, California, United States
| | | | | | | | | | | | | | | | - Katherine Hall
- Hospital for Special
Surgery, New York, New York, United States
| | | | | | - Carl Blobel
- Hospital for Special
Surgery, New York, New York, United States
| | | | | | - Jon T. Sack
- Dept.
Physiology and Membrane Biology, University of California, Davis, California, United States
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15
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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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16
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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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17
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Tong J, Canty JT, Briggs MM, McIntosh TJ. The water permeability of lens aquaporin-0 depends on its lipid bilayer environment. Exp Eye Res 2013; 113:32-40. [PMID: 23680159 DOI: 10.1016/j.exer.2013.04.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/16/2013] [Accepted: 04/30/2013] [Indexed: 01/07/2023]
Abstract
Aquaporin-0 (AQP0), the primary water channel in lens fiber cells, is critical to lens development, organization, and function. In the avascular lens there is thought to be an internal microcirculation associated with fluid movement. Although AQP0 is known to be important in fluid fluxes across membranes, the water permeability of this channel has only been measured in Xenopus oocytes and in outer lens cortical membranes, but not in inner nuclear membranes, which have an increased cholesterol/phospholipid ratio. Here we measure the unit water permeability of AQP0 in different proteoliposomes with cholesterol/phospholipid ratios and external pHs similar to those found in the cortex and nucleus of the lens. Osmotic stress measurements were performed with proteoliposomes containing AQP0 and three different lipids mixtures: (1) phosphatidylcholine (PC) and phosphatidylglycerol (PG), (2) PC, PG, with 40 mol% cholesterol, and (3) sphingomyelin (SM), PG, with 40 mol% cholesterol. At pH 7.5 the unit permeabilities of AQP0 were 3.5 ± 0.5 × 10(-14) cm(3)/s (mean ± SEM), 1.1 ± 0.1 × 10(-14) cm(3)/s, and 0.50 ± 0.04 × 10(-14) cm(3)/s in PC:PG, PC:PG:cholesterol, and SM:PG:cholesterol, respectively. For lipid mixtures at pH 6.5, corresponding to conditions found in the lens nucleus, the AQP0 permeabilities were 1.5 ± 0.4 × 10(-14) cm(3)/s and 0.76 ± 0.03 × 10(-14) cm(3)/s in PC:PG:cholesterol and SM:PG:cholesterol, respectively. Thus, although AQP0 unit permeability can be modified by changes in pH, it is also sensitive to changes in bilayer lipid composition, and decreases with increasing cholesterol and SM content. These data imply that AQP0 water permeability is regulated by bilayer lipid composition, so that AQP0 permeability would be significantly less in the lens nucleus than in the lens cortex.
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Affiliation(s)
- Jihong Tong
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
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18
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Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels. Biophys J 2012; 103:1698-705. [PMID: 23083713 DOI: 10.1016/j.bpj.2012.08.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 11/22/2022] Open
Abstract
Water permeability through single-file channels is affected by intrinsic factors such as their size and polarity and by external determinants like their lipid environment in the membrane. Previous computational studies revealed that the obstruction of the channel by lipid headgroups can be long-lived, in the range of nanoseconds, and that pore-length-matching membrane mimetics could speed up water permeability. To test the hypothesis of lipid-channel interactions modulating channel permeability, we designed different gramicidin A derivatives with attached acyl chains. By combining extensive molecular-dynamics simulations and single-channel water permeation measurements, we show that by tuning lipid-channel interactions, these modifications reduce the presence of lipid headgroups in the pore, which leads to a clear and selective increase in their water permeability.
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19
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Large conductance, calcium- and voltage-gated potassium (BK) channels: regulation by cholesterol. Pharmacol Ther 2012; 135:133-50. [PMID: 22584144 DOI: 10.1016/j.pharmthera.2012.05.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 04/09/2012] [Indexed: 11/21/2022]
Abstract
Cholesterol (CLR) is an essential component of eukaryotic plasma membranes. CLR regulates the membrane physical state, microdomain formation and the activity of membrane-spanning proteins, including ion channels. Large conductance, voltage- and Ca²⁺-gated K⁺ (BK) channels link membrane potential to cell Ca²⁺ homeostasis. Thus, they control many physiological processes and participate in pathophysiological mechanisms leading to human disease. Because plasmalemma BK channels cluster in CLR-rich membrane microdomains, a major driving force for studying BK channel-CLR interactions is determining how membrane CLR controls the BK current phenotype, including its pharmacology, channel sorting, distribution, and role in cell physiology. Since both BK channels and CLR tissue levels play a pathophysiological role in human disease, identifying functional and structural aspects of the CLR-BK channel interaction may open new avenues for therapeutic intervention. Here, we review the studies documenting membrane CLR-BK channel interactions, dissecting out the many factors that determine the final BK current response to changes in membrane CLR content. We also summarize work in reductionist systems where recombinant BK protein is studied in artificial lipid bilayers, which documents a direct inhibition of BK channel activity by CLR and builds a strong case for a direct interaction between CLR and the BK channel-forming protein. Bilayer lipid-mediated mechanisms in CLR action are also discussed. Finally, we review studies of BK channel function during hypercholesterolemia, and underscore the many consequences that the CLR-BK channel interaction brings to cell physiology and human disease.
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20
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Rusinova R, Herold KF, Sanford RL, Greathouse DV, Hemmings HC, Andersen OS. Thiazolidinedione insulin sensitizers alter lipid bilayer properties and voltage-dependent sodium channel function: implications for drug discovery. ACTA ACUST UNITED AC 2012; 138:249-70. [PMID: 21788612 PMCID: PMC3149818 DOI: 10.1085/jgp.201010529] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The thiazolidinediones (TZDs) are used in the treatment of diabetes mellitus type 2. Their canonical effects are mediated by activation of the peroxisome proliferator–activated receptor γ (PPARγ) transcription factor. In addition to effects mediated by gene activation, the TZDs cause acute, transcription-independent changes in various membrane transport processes, including glucose transport, and they alter the function of a diverse group of membrane proteins, including ion channels. The basis for these off-target effects is unknown, but the TZDs are hydrophobic/amphiphilic and adsorb to the bilayer–water interface, which will alter bilayer properties, meaning that the TZDs may alter membrane protein function by bilayer-mediated mechanisms. We therefore explored whether the TZDs alter lipid bilayer properties sufficiently to be sensed by bilayer-spanning proteins, using gramicidin A (gA) channels as probes. The TZDs altered bilayer elastic properties with potencies that did not correlate with their affinity for PPARγ. At concentrations where they altered gA channel function, they also altered the function of voltage-dependent sodium channels, producing a prepulse-dependent current inhibition and hyperpolarizing shift in the steady-state inactivation curve. The shifts in the inactivation curve produced by the TZDs and other amphiphiles can be superimposed by plotting them as a function of the changes in gA channel lifetimes. The TZDs’ partition coefficients into lipid bilayers were measured using isothermal titration calorimetry. The most potent bilayer modifier, troglitazone, alters bilayer properties at clinically relevant free concentrations; the least potent bilayer modifiers, pioglitazone and rosiglitazone, do not. Unlike other TZDs tested, ciglitazone behaves like a hydrophobic anion and alters the gA monomer–dimer equilibrium by more than one mechanism. Our results provide a possible mechanism for some off-target effects of an important group of drugs, and underscore the importance of exploring bilayer effects of candidate drugs early in drug development.
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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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21
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Ingólfsson HI, Andersen OS. Alcohol's effects on lipid bilayer properties. Biophys J 2011; 101:847-55. [PMID: 21843475 DOI: 10.1016/j.bpj.2011.07.013] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/13/2011] [Accepted: 07/15/2011] [Indexed: 11/26/2022] Open
Abstract
Alcohols are known modulators of lipid bilayer properties. Their biological effects have long been attributed to their bilayer-modifying effects, but alcohols can also alter protein function through direct protein interactions. This raises the question: Do alcohol's biological actions result predominantly from direct protein-alcohol interactions or from general changes in the membrane properties? The efficacy of alcohols of various chain lengths tends to exhibit a so-called cutoff effect (i.e., increasing potency with increased chain length, which that eventually levels off). The cutoff varies depending on the assay, and numerous mechanisms have been proposed such as: limited size of the alcohol-protein interaction site, limited alcohol solubility, and a chain-length-dependent lipid bilayer-alcohol interaction. To address these issues, we determined the bilayer-modifying potency of 27 aliphatic alcohols using a gramicidin-based fluorescence assay. All of the alcohols tested (with chain lengths of 1-16 carbons) alter the bilayer properties, as sensed by a bilayer-spanning channel. The bilayer-modifying potency of the short-chain alcohols scales linearly with their bilayer partitioning; the potency tapers off at higher chain lengths, and eventually changes sign for the longest-chain alcohols, demonstrating an alcohol cutoff effect in a system that has no alcohol-binding pocket.
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Affiliation(s)
- Helgi I Ingólfsson
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.
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22
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Gu H, Lum K, Kim JH, Greathouse DV, Andersen OS, Koeppe RE. The membrane interface dictates different anchor roles for "inner pair" and "outer pair" tryptophan indole rings in gramicidin A channels. Biochemistry 2011; 50:4855-66. [PMID: 21539360 DOI: 10.1021/bi200136e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the effects of substituting two of the four tryptophans (the "inner pair" Trp(9) and Trp(11) or the "outer pair" Trp(13) and Trp(15)) in gramicidin A (gA) channels. The conformational preferences of the doubly substituted gA analogues were assessed using circular dichroism spectroscopy and size-exclusion chromatography, which show that the inner tryptophans 9 and 11 are critical for the gA's conformational preference in lipid bilayer membranes. [Phe(13,15)]gA largely retains the single-stranded helical channel structure, whereas [Phe(9,11)]gA exists primarily as double-stranded conformers. Within this context, the (2)H NMR spectra from labeled tryptophans were used to examine the changes in average indole ring orientations, induced by the Phe substitutions and by the shift in conformational preference. Using a method for deuterium labeling of already synthesized gAs, we introduced deuterium selectively onto positions C2 and C5 of the remaining tryptophan indole rings in the substituted gA analogues for solid-state (2)H NMR spectroscopy. The (least possible) changes in orientation and overall motion of each indole ring were estimated from the experimental spectra. Regardless of the mixture of backbone folds, the indole ring orientations observed in the analogues are similar to those found previously for gA channels. Both Phe-substituted analogues form single-stranded channels, as judged from the formation of heterodimeric channels with the native gA. [Phe(13,15)]gA channels have Na(+) currents that are ~50% and lifetimes that are ~80% of those of native gA channels. The double-stranded conformer(s) of [Phe(9,11)]gA do not form detectable channels. The minor single-stranded population of [Phe(9,11)]gA forms channels with Na(+) currents that are ~25% and single-channel lifetimes that are ~300% of those of native gA channels. Our results suggest that Trp(9) and Trp(11), when "reaching" for the interface, tend to drive both monomer folding (to "open" a channel) and dimer dissociation (to "close" a channel). Furthermore, the dipoles of Trp(9) and Trp(11) are relatively more important for the single-channel conductance than are the dipoles of Trp(13) and Trp(15).
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Affiliation(s)
- Hong Gu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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23
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Bukiya AN, Belani JD, Rychnovsky S, Dopico AM. Specificity of cholesterol and analogs to modulate BK channels points to direct sterol-channel protein interactions. J Gen Physiol 2011; 137:93-110. [PMID: 21149543 PMCID: PMC3010061 DOI: 10.1085/jgp.201010519] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 11/22/2010] [Indexed: 11/26/2022] Open
Abstract
The activity (Po) of large-conductance voltage/Ca(2+)-gated K(+) (BK) channels is blunted by cholesterol levels within the range found in natural membranes. We probed BK channel-forming α (cbv1) subunits in phospholipid bilayers with cholesterol and related monohydroxysterols and performed computational dynamics to pinpoint the structural requirements for monohydroxysterols to reduce BK Po and obtain insights into cholesterol's mechanism of action. Cholesterol, cholestanol, and coprostanol reduced Po by shortening mean open and lengthening mean closed times, whereas epicholesterol, epicholestanol, epicoprostanol, and cholesterol trisnorcholenic acid were ineffective. Thus, channel inhibition by monohydroxysterols requires the β configuration of the C3 hydroxyl and is favored by the hydrophobic nature of the side chain, while having lax requirements on the sterol A/B ring fusion. Destabilization of BK channel open state(s) has been previously interpreted as reflecting increased bilayer lateral stress by cholesterol. Lateral stress is controlled by the sterol molecular area and lipid monolayer lateral tension, the latter being related to the sterol ability to adopt a planar conformation in lipid media. However, we found that the differential efficacies of monohydroxysterols to reduce Po (cholesterol≥coprostanol≥cholestanol>>>epicholesterol) did not follow molecular area rank (coprostanol>>epicholesterol>cholesterol>cholestanol). In addition, computationally predicted energies for cholesterol (effective BK inhibitor) and epicholesterol (ineffective) to adopt a planar conformation were similar. Finally, cholesterol and coprostanol reduced Po, yet these sterols have opposite effects on tight lipid packing and, likely, on lateral stress. Collectively, these findings suggest that an increase in bilayer lateral stress is unlikely to underlie the differential ability of cholesterol and related steroids to inhibit BK channels. Remarkably, ent-cholesterol (cholesterol mirror image) failed to reduce Po, indicating that cholesterol efficacy requires sterol stereospecific recognition by a protein surface. The BK channel phenotype resembled that of α homotetramers. Thus, we hypothesize that a cholesterol-recognizing protein surface resides at the BK α subunit itself.
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Affiliation(s)
- Anna N. Bukiya
- Department of Pharmacology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163
| | | | - Scott Rychnovsky
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Alex M. Dopico
- Department of Pharmacology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163
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24
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Ingólfsson HI, Andersen OS. Screening for small molecules' bilayer-modifying potential using a gramicidin-based fluorescence assay. Assay Drug Dev Technol 2010; 8:427-36. [PMID: 20233091 DOI: 10.1089/adt.2009.0250] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many drugs and other small molecules used to modulate biological function are amphiphiles that adsorb at the bilayer/solution interface and thereby alter lipid bilayer properties. This is important because membrane proteins are energetically coupled to their host bilayer by hydrophobic interactions. Changes in bilayer properties thus alter membrane protein function, which provides a possible mechanism for "off-target" drug effects. We have previously shown that channels formed by the linear gramicidins are suitable probes for changes in lipid bilayer properties, as experienced by bilayer-spanning proteins. We now report a gramicidin-based fluorescence assay for changes in bilayer properties. The assay is based on measuring the time course of fluorescence quenching in fluorophore-loaded large unilamellar vesicles, due to entry of a gramicidin channel-permeable quencher. The method is scalable and suitable for both mechanistic studies and high-throughput screening for bilayer-perturbing, potential off-target effects, which we illustrate using capsaicin (Cap) and other compounds.
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Affiliation(s)
- Helgi I Ingólfsson
- Cornell/Rockefeller/Sloan-Kettering Tri-Institutional Program in Computational Biology and Medicine, New York, New York, USA
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25
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Jones TL, Fu R, Nielson F, Cross TA, Busath DD. Gramicidin channels are internally gated. Biophys J 2010; 98:1486-93. [PMID: 20409467 DOI: 10.1016/j.bpj.2009.11.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 10/20/2009] [Accepted: 11/12/2009] [Indexed: 11/25/2022] Open
Abstract
Gramicidin channels are archetypal molecular subjects for solid-state NMR studies and investigations of single-channel or cation conductance. Until now, the transitions between on and off conductance states have been thought, based on multichannel studies, to represent monomer <--> dimer reactions. Here we use a single-molecule deposition method (vesicle fusion to a planar bilayer) to show that gramicidin dimer channels do not normally dissociate when conductance terminates. Furthermore, the observation of two 13C peaks in solid-state NMR indicates very stable dichotomous conformations for both the first and second peptide bonds in the monomers, and a two-dimensional chemical exchange spectrum with a 12-s mixing time demonstrates that the Val1 carbonyl conformations exchange slowly, with lifetimes of several seconds. It is proposed that gramicidin channels are gated by small conformational changes in the channel near the permeation pathway. These studies demonstrate how regulation of conformations governing closed <--> open transitions may be achieved and studied at the molecular level.
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Affiliation(s)
- Tyson L Jones
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, Utah, USA
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26
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pH (low) insertion peptide (pHLIP) inserts across a lipid bilayer as a helix and exits by a different path. Proc Natl Acad Sci U S A 2010; 107:4081-6. [PMID: 20160113 DOI: 10.1073/pnas.0914330107] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
What are the molecular events that occur when a peptide inserts across a membrane or exits from it? Using the pH-triggered insertion of the pH low insertion peptide to enable kinetic analysis, we show that insertion occurs in several steps, with rapid (0.1 sec) interfacial helix formation, followed by a much slower (100 sec) insertion pathway to give a transmembrane helix. The reverse process of unfolding and peptide exit from the bilayer core, which can be induced by a rapid rise of the pH from acidic to basic, proceeds approximately 400 times faster than folding/insertion and through different intermediate states. In the exit pathway, the helix-coil transition is initiated while the polypeptide is still inside the membrane. The peptide starts to exit when about 30% of the helix is unfolded, and continues a rapid exit as it unfolds inside the membrane. These insights may guide understanding of membrane protein folding/unfolding and the design of medically useful peptides for imaging and drug delivery.
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27
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Hu JC, Bengrine A, Lis A, Awayda MS. Alternative mechanism of activation of the epithelial na+ channel by cleavage. J Biol Chem 2009; 284:36334-36345. [PMID: 19858199 PMCID: PMC2794749 DOI: 10.1074/jbc.m109.032870] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 10/19/2009] [Indexed: 11/06/2022] Open
Abstract
We examined activation of the human epithelial sodium channel (ENaC) by cleavage. We focused on cleavage of alphaENaC using the serine protease subtilisin. Trimeric channels formed with alphaFM, a construct with point mutations in both furin cleavage sites (R178A/R204A), exhibited marked reduction in spontaneous cleavage and an approximately 10-fold decrease in amiloride-sensitive whole cell conductance as compared with alphaWT (2.2 versus 21.2 microsiemens (microS)). Both alphaWT and alphaFM were activated to similar levels by subtilisin cleavage. Channels formed with alphaFD, a construct that deleted the segment between the two furin sites (Delta175-204), exhibited an intermediate conductance of 13.2 microS. More importantly, alphaFD retained the ability to be activated by subtilisin to 108.8 +/- 20.9 microS, a level not significantly different from that of subtilisin activated alphaWT (125.6 +/- 23.9). Therefore, removal of the tract between the two furin sites is not the main mechanism of channel activation. In these experiments the levels of the cleaved 22-kDa N-terminal fragment of alpha was low and did not match those of the C-terminal 65-kDa fragment. This indicated that cleavage may activate ENaC by the loss of the smaller fragment and the first transmembrane domain. This was confirmed in channels formed with alphaLD, a construct that extended the deleted sequence of alphaFD by 17 amino acids (Delta175-221). Channels with alphaLD were uncleaved, exhibited low baseline activity (4.1 microS), and were insensitive to subtilisin. Collectively, these data support an alternative hypothesis of ENaC activation by cleavage that may involve the loss of the first transmembrane domain from the channel complex.
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Affiliation(s)
- John Cong Hu
- Department of Physiology and Biophysics, State University of New York, Buffalo, New York 14214
| | - Abderrahmane Bengrine
- Department of Physiology and Biophysics, State University of New York, Buffalo, New York 14214
| | - Agnieszka Lis
- Department of Physiology and Biophysics, State University of New York, Buffalo, New York 14214
| | - Mouhamed S Awayda
- Department of Physiology and Biophysics, State University of New York, Buffalo, New York 14214.
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Lundbaek JA, Collingwood SA, Ingólfsson HI, Kapoor R, Andersen OS. Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes. J R Soc Interface 2009; 7:373-95. [PMID: 19940001 DOI: 10.1098/rsif.2009.0443] [Citation(s) in RCA: 226] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Membrane protein function is regulated by the host lipid bilayer composition. This regulation may depend on specific chemical interactions between proteins and individual molecules in the bilayer, as well as on non-specific interactions between proteins and the bilayer behaving as a physical entity with collective physical properties (e.g. thickness, intrinsic monolayer curvature or elastic moduli). Studies in physico-chemical model systems have demonstrated that changes in bilayer physical properties can regulate membrane protein function by altering the energetic cost of the bilayer deformation associated with a protein conformational change. This type of regulation is well characterized, and its mechanistic elucidation is an interdisciplinary field bordering on physics, chemistry and biology. Changes in lipid composition that alter bilayer physical properties (including cholesterol, polyunsaturated fatty acids, other lipid metabolites and amphiphiles) regulate a wide range of membrane proteins in a seemingly non-specific manner. The commonality of the changes in protein function suggests an underlying physical mechanism, and recent studies show that at least some of the changes are caused by altered bilayer physical properties. This advance is because of the introduction of new tools for studying lipid bilayer regulation of protein function. The present review provides an introduction to the regulation of membrane protein function by the bilayer physical properties. We further describe the use of gramicidin channels as molecular force probes for studying this mechanism, with a unique ability to discriminate between consequences of changes in monolayer curvature and bilayer elastic moduli.
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Affiliation(s)
- Jens A Lundbaek
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA.
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Transmembrane vs. non-transmembrane hydrophobic helix topography in model and natural membranes. Curr Opin Struct Biol 2009; 19:464-72. [DOI: 10.1016/j.sbi.2009.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 07/10/2009] [Indexed: 11/21/2022]
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Lundbaek JA. Lipid bilayer-mediated regulation of ion channel function by amphiphilic drugs. ACTA ACUST UNITED AC 2008; 131:421-9. [PMID: 18411332 PMCID: PMC2346573 DOI: 10.1085/jgp.200709948] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jens A Lundbaek
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA.
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Abstract
The lipid bilayer component of biological membranes is important for the distribution, organization, and function of bilayer-spanning proteins. This regulation is due to both specific lipid-protein interactions and general bilayer-protein interactions, which modulate the energetics and kinetics of protein conformational transitions, as well as the protein distribution between different membrane compartments. The bilayer regulation of membrane protein function arises from the hydrophobic coupling between the protein's hydrophobic domains and the bilayer hydrophobic core, which causes protein conformational changes that involve the protein/bilayer boundary to perturb the adjacent bilayer. Such bilayer perturbations, or deformations, incur an energetic cost, which for a given conformational change varies as a function of the bilayer material properties (bilayer thickness, intrinsic lipid curvature, and the elastic compression and bending moduli). Protein function therefore is regulated by changes in bilayer material properties, which determine the free-energy changes caused by the protein-induced bilayer deformation. The lipid bilayer thus becomes an allosteric regulator of membrane function.
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Affiliation(s)
- Olaf S Andersen
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021, USA.
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Artigas P, Al'aref SJ, Hobart EA, Díaz LF, Sakaguchi M, Straw S, Andersen OS. 2,3-butanedione monoxime affects cystic fibrosis transmembrane conductance regulator channel function through phosphorylation-dependent and phosphorylation-independent mechanisms: the role of bilayer material properties. Mol Pharmacol 2006; 70:2015-26. [PMID: 16966478 DOI: 10.1124/mol.106.026070] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
2,3-Butanedione monoxime (BDM) is widely believed to act as a chemical phosphatase. We therefore examined the effects of BDM on the cystic fibrosis transmembrane regulator (CFTR) Cl(-) channel, which is regulated by phosphorylation in a complex manner. In guinea pig ventricular myocytes, forskolin-activated whole-cell CFTR currents responded biphasically to external 20 mM BDM: a rapid approximately 2-fold current activation was followed by a slower (tau approximately 20 s) inhibition (to approximately 20% of control). The inhibitory response was abolished by intracellular dialysis with the phosphatase inhibitor microcystin, suggesting involvement of endogenous phosphatases. The BDM-induced activation was studied further in Xenopus laevis oocytes expressing human epithelial CFTR. The concentration for half-maximal BDM activation (K(0.5)) was state-dependent, approximately 2 mM for highly and approximately 20 mM for partially phosphorylated channels, suggesting a modulated receptor mechanism. Because BDM modulates many different membrane proteins with similar K(0.5) values, we tested whether BDM could alter protein function by altering lipid bilayer properties rather than by direct BDM-protein interactions. Using gramicidin channels of different lengths (different channel-bilayer hydrophobic mismatch) as reporters of bilayer stiffness, we found that BDM increases channel appearance rates and lifetimes (reduces bilayer stiffness). At 20 mM BDM, the appearance rates increase approximately 4-fold (for the longer, 15 residues/monomer, channels) to approximately 10-fold (for the shorter, 13 residues/monomer channels); the lifetimes increase approximately 50% independently of channel length. BDM thus reduces the energetic cost of bilayer deformation, an effect that may underlie the effects of BDM on CFTR and other membrane proteins; the state-dependent changes in K(0.5) are consistent with such a bilayer-mediated mechanism.
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Affiliation(s)
- Pablo Artigas
- Laboratory of Cardiac/Membrane Physiology, The Rockefeller University, 1230 York Ave., New York, NY 10021, USA.
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