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Eastman RT, Rusinova R, Herold KF, Huang XP, Dranchak P, Voss TC, Rana S, Shrimp JH, White AD, Hemmings HC, Roth BL, Inglese J, Andersen OS, Dahlin JL. Nonspecific membrane bilayer perturbations by ivermectin underlie SARS-CoV-2 in vitro activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563088. [PMID: 37961094 PMCID: PMC10634736 DOI: 10.1101/2023.10.23.563088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in in vitro models at low micromolar concentrations, five- to ten-fold higher than the reported toxic clinical concentration. At similar concentrations, ivermectin also decreased cell viability and increased biomarkers of cytotoxicity and apoptosis. Further mechanistic and profiling studies revealed that ivermectin nonspecifically perturbs membrane bilayers at the same concentrations where it decreases the SARS-CoV-2 viral burden, resulting in nonspecific modulation of membrane-based targets such as G-protein coupled receptors and ion channels. These results suggest that a primary molecular mechanism for the in vitro antiviral activity of ivermectin may be nonspecific membrane perturbation, indicating that ivermectin is unlikely to be translatable into a safe and effective antiviral agent. These results and experimental workflow provide a useful paradigm for performing preclinical studies on (pandemic-related) drug repurposing candidates.
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Affiliation(s)
- Richard T. Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Karl F. Herold
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Patricia Dranchak
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Ty C. Voss
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Sandeep Rana
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jonathan H. Shrimp
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Alex D. White
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Hugh C. Hemmings
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
- Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jayme L. Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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Joyce RL, Tibbs GR, David Warren J, Costa CJ, Aromolaran K, Lea Sanford R, Andersen OS, Li Z, Zhang G, Willis DE, Goldstein PA. Probucol is anti-hyperalgesic in a mouse peripheral nerve injury model of neuropathic pain. NEUROBIOLOGY OF PAIN (CAMBRIDGE, MASS.) 2023; 14:100141. [PMID: 38099280 PMCID: PMC10719523 DOI: 10.1016/j.ynpai.2023.100141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 12/17/2023]
Abstract
2,6-di-tert-butylphenol (2,6-DTBP) ameliorates mechanical allodynia and thermal hyperalgesia produced by partial sciatic nerve ligation in mice, and selectively inhibits HCN1 channel gating. We hypothesized that the clinically utilized non-anesthetic dimerized congener of 2,6-DTBP, probucol (2,6-di-tert-butyl-4-[2-(3,5-di-tert-butyl-4-hydroxyphenyl)sulfanylpropan-2-ylsulfanyl]phenol), would relieve the neuropathic phenotype that results from peripheral nerve damage, and that the anti-hyperalgesic efficacy in vivo would correlate with HCN1 channel inhibition in vitro. A single oral dose of probucol (800 mg/kg) relieved mechanical allodynia and thermal hyperalgesia in a mouse spared-nerve injury neuropathic pain model. While the low aqueous solubility of probucol precluded assessment of its possible interaction with HCN1 channels, our results, in conjunction with recent data demonstrating that probucol reduces lipopolysaccharide-induced mechanical allodynia and thermal hyperalgesia, support the testing/development of probucol as a non-opioid, oral antihyperalgesic albeit one of unknown mechanistic action.
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Affiliation(s)
- Rebecca L. Joyce
- Dept. of Anesthesiology, 1300 York Ave., Weill Cornell Medicine, New York, NY, USA
| | - Gareth R. Tibbs
- Dept. of Anesthesiology, 1300 York Ave., Weill Cornell Medicine, New York, NY, USA
| | - J. David Warren
- Dept. of Biochemistry, 413 E. 69th Street, Weill Cornell Medicine, New York, NY, USA
| | | | - Kelly Aromolaran
- Dept. of Anesthesiology, 1300 York Ave., Weill Cornell Medicine, New York, NY, USA
| | - R. Lea Sanford
- Dept. of Physiology & Biophysics, 1300 York Ave., Weill Cornell Medicine, New York, NY, USA
| | - Olaf S. Andersen
- Dept. of Physiology & Biophysics, 1300 York Ave., Weill Cornell Medicine, New York, NY, USA
| | - Zhucui Li
- Dept. of Biochemistry, 413 E. 69th Street, Weill Cornell Medicine, New York, NY, USA
| | - Guoan Zhang
- Dept. of Biochemistry, 413 E. 69th Street, Weill Cornell Medicine, New York, NY, USA
| | - Dianna E. Willis
- Burke Neurological Institute, 785 Mamaroneck Avenue, White Plains, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, NY, USA
| | - Peter A. Goldstein
- Dept. of Anesthesiology, 1300 York Ave., Weill Cornell Medicine, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, NY, USA
- Dept. of Medicine, Weill Cornell Medicine, New York, NY, USA
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3
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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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Schmidpeter PAM, Wu D, Rheinberger J, Riegelhaupt PM, Tang H, Robinson CV, Nimigean CM. Anionic lipids unlock the gates of select ion channels in the pacemaker family. Nat Struct Mol Biol 2022; 29:1092-1100. [PMID: 36352139 PMCID: PMC10022520 DOI: 10.1038/s41594-022-00851-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/25/2022] [Indexed: 11/11/2022]
Abstract
Lipids play important roles in regulating membrane protein function, but the molecular mechanisms used are elusive. Here we investigated how anionic lipids modulate SthK, a bacterial pacemaker channel homolog, and HCN2, whose activity contributes to pacemaking in the heart and brain. Using SthK allowed the reconstitution of purified channels in controlled lipid compositions for functional and structural assays that are not available for the eukaryotic channels. We identified anionic lipids bound tightly to SthK and their exact binding locations and determined that they potentiate channel activity. Cryo-EM structures in the most potentiating lipids revealed an open state and identified a nonannular lipid bound with its headgroup near an intersubunit salt bridge that clamps the intracellular channel gate shut. Breaking this conserved salt bridge abolished lipid modulation in SthK and eukaryotic HCN2 channels, indicating that anionic membrane lipids facilitate channel opening by destabilizing these interactions. Our findings underline the importance of state-dependent protein-lipid interactions.
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Affiliation(s)
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | | | - Haiping Tang
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
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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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Mechanisms underlying drug-mediated regulation of membrane protein function. Proc Natl Acad Sci U S A 2021; 118:2113229118. [PMID: 34753824 DOI: 10.1073/pnas.2113229118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 11/18/2022] Open
Abstract
The hydrophobic coupling between membrane proteins and their host lipid bilayer provides a mechanism by which bilayer-modifying drugs may alter protein function. Drug regulation of membrane protein function thus may be mediated by both direct interactions with the protein and drug-induced alterations of bilayer properties, in which the latter will alter the energetics of protein conformational changes. To tease apart these mechanisms, we examine how the prototypical, proton-gated bacterial potassium channel KcsA is regulated by bilayer-modifying drugs using a fluorescence-based approach to quantify changes in both KcsA function and lipid bilayer properties (using gramicidin channels as probes). All tested drugs inhibited KcsA activity, and the changes in the different gating steps varied with bilayer thickness, suggesting a coupling to the bilayer. Examining the correlations between changes in KcsA gating steps and bilayer properties reveals that drug-induced regulation of membrane protein function indeed involves bilayer-mediated mechanisms. Both direct, either specific or nonspecific, binding and bilayer-mediated mechanisms therefore are likely to be important whenever there is overlap between the concentration ranges at which a drug alters membrane protein function and bilayer properties. Because changes in bilayer properties will impact many diverse membrane proteins, they may cause indiscriminate changes in protein function.
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Sabirovas T, Valiūnienė A, Valincius G. Hybrid bilayer membranes on metallurgical polished aluminum. Sci Rep 2021; 11:9648. [PMID: 33958658 PMCID: PMC8102548 DOI: 10.1038/s41598-021-89150-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/15/2021] [Indexed: 11/09/2022] Open
Abstract
In this work we describe the functionalization of metallurgically polished aluminum surfaces yielding biomimetic electrodes suitable for probing protein/phospholipid interactions. The functionalization involves two simple steps: silanization of the aluminum and subsequent fusion of multilamellar vesicles which leads to the formation of a hybrid bilayer lipid membrane (hBLM). The vesicle fusion was followed in real-time by fast Fourier transform electrochemical impedance spectroscopy (FFT EIS). The impedance-derived complex capacitance of the hBLMs was approximately 0.61 µF cm−2, a value typical for intact phospholipid bilayers. We found that the hBLMs can be readily disrupted if exposed to > 400 nM solutions of the pore-forming peptide melittin. However, the presence of cholesterol at 40% (mol) in hBLMs exhibited an inhibitory effect on the membrane-damaging capacity of the peptide. The melittin-membrane interaction was concentration dependent decreasing with concentration. The hBLMs on Al surface can be regenerated multiple times, retaining their dielectric and functional properties essentially intact.
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Affiliation(s)
- Tomas Sabirovas
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio ave. 7, 10257, Vilnius, Lithuania
| | - Aušra Valiūnienė
- Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, 03225, Vilnius, Lithuania.
| | - Gintaras Valincius
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio ave. 7, 10257, Vilnius, Lithuania
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Schmidpeter PAM, Nimigean CM. Correlating ion channel structure and function. Methods Enzymol 2021; 652:3-30. [PMID: 34059287 DOI: 10.1016/bs.mie.2021.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Recent developments in cryogenic electron microscopy (cryo-EM) led to an exponential increase in high-resolution structures of membrane proteins, and in particular ion channels. However, structures alone can only provide limited information about the workings of these proteins. In order to understand ion channel function and regulation in molecular detail, the obtained structural data need to be correlated to functional states of the same protein. Here, we describe several techniques that can be employed to study ion channel structure and function in vitro and under defined, similar conditions. Lipid nanodiscs provide a native-like environment for membrane proteins and have become a valuable tool in membrane protein structural biology and biophysics. Combined with liposome-based flux assays for the kinetic analysis of ion channel activity as well as electrophysiological recordings, researchers now have access to an array of experimental techniques allowing for detailed structure-function correlations using purified components. Two examples are presented where we put emphasis on the lipid environment and time-resolved techniques together with mutations and protein engineering to interpret structural data obtained from single particle cryo-EM on cyclic nucleotide-gated or Ca2+-gated K+ channels. Furthermore, we provide short protocols for all the assays used in our work so that others can adapt these techniques to their experimental needs. Comprehensive structure-function correlations are essential in order to pharmacologically target channelopathies.
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Affiliation(s)
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States.
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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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Bosquesi PL, Melchior ACB, Pavan AR, Lanaro C, de Souza CM, Rusinova R, Chelucci RC, Barbieri KP, Fernandes GFDS, Carlos IZ, Andersen OS, Costa FF, Dos Santos JL. Synthesis and evaluation of resveratrol derivatives as fetal hemoglobin inducers. Bioorg Chem 2020; 100:103948. [PMID: 32450391 PMCID: PMC8052979 DOI: 10.1016/j.bioorg.2020.103948] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/29/2022]
Abstract
Resveratrol (RVT) derivatives (10a-i) were designed, synthesized, and evaluated for their potential as gamma-globin inducers in treating Sickle Cell Disease (SCD) symptoms. All compounds were able to release NO at different levels ranging from 0 to 26.3%, while RVT did not demonstrate this effect. In vivo, the antinociceptive effect was characterized using an acetic acid-induced abdominal contortion model. All compounds exhibited different levels of protection, ranging from 5.9 to 37.3%; the compound 10a was the most potent among the series. At concentrations between 3.13 and 12.5 µM, the derivative 10a resulted in a reduction of 41.1-64.3% in the TNF-α levels in the supernatants of macrophages that were previously LPS-stimulated. This inhibitory effect was higher than that of RVT used as the control. In addition, the compound 10a and RVT induced double the production of the gamma-globin chains (γG + γA), compared to the vehicle, using CD34+ cells. Compound 10a also did not induce membrane perturbation and it was not mutagenic in the in vivo assay. Thus, compound 10a emerged as a new prototype of the gamma-globin-inducer group with additional analgesic and anti-inflammatory activities and proving to be a useful alternative to treat SCD symptoms.
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Affiliation(s)
| | | | - Aline Renata Pavan
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara 14800-903, Brazil
| | - Carolina Lanaro
- University of Campinas (UNICAMP), Hematology and Hemotherapy Center, Campinas 13083-878, Brazil
| | | | - Radda Rusinova
- Weill Cornell Medical College, Department of Physiology and Biophysics, New York, NY 10065-489, United States
| | - Rafael Consolin Chelucci
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara 14800-903, Brazil
| | - Karina Pereira Barbieri
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara 14800-903, Brazil
| | | | - Iracilda Zepone Carlos
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara 14800-903, Brazil
| | - Olaf Sparre Andersen
- Weill Cornell Medical College, Department of Physiology and Biophysics, New York, NY 10065-489, United States
| | - Fernando Ferreira Costa
- University of Campinas (UNICAMP), Hematology and Hemotherapy Center, Campinas 13083-878, Brazil
| | - Jean Leandro Dos Santos
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara 14800-903, Brazil.
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11
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Efimova SS, Zakharova AA, Ostroumova OS. Alkaloids Modulate the Functioning of Ion Channels Produced by Antimicrobial Agents via an Influence on the Lipid Host. Front Cell Dev Biol 2020; 8:537. [PMID: 32695785 PMCID: PMC7339123 DOI: 10.3389/fcell.2020.00537] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/08/2020] [Indexed: 12/22/2022] Open
Abstract
It is widely recognized that an alteration in membrane physical properties induced by the adsorption of various drugs and biologically active compounds might greatly affect the functioning of peptides and proteins embedded in the membrane, in particular various ion channels. This study aimed to obtain deep insight into the diversity of the molecular mechanisms of membrane action of one of the most numerous and extremely important class of phytochemicals, the alkaloids. Protoalkaloids (derivatives of β-phenylethylamine, benzylamines, and colchicines), heterocyclic alkaloids (derivatives of purine, quinolysidine, piperidine, pyridine, quinoline, and isoquinoline), and steroid alkaloids were tested. We evaluated the effects of 22 compounds on lipid packing by investigating the thermotropic behavior of membrane lipids and the leakage of a fluorescent marker from unilamellar lipid vesicles. The alteration in the transmembrane distribution of the electrical potential was estimated by measuring the alkaloid induced changes in the boundary potential of planar lipid bilayers. We found that benzylamines, the chili pepper active components, capsaicin and dihydrocapsaicin, strongly affect not only the elastic properties of the lipid host, but also its electrostatics by dramatic decrease in membrane dipole potential. We concluded that the increase in the conductance and lifetime of gramicidin A channels induced by benzylamines was related to alteration in membrane dipole potential not to decrease in membrane stiffness. A sharp decrease in the lifetime of single ion pores induced by the antifungal lipopeptide syringomycin E, after addition of benzylamines and black pepper alkaloid piperine, was also mainly due to the reduction in dipole potential. At the same time, we showed that the disordering of membrane lipids in the presence of benzylamines and piperine plays a decisive role in the regulation of the conductance induced by the antifungal polyene macrolide antibiotic nystatin, while the inhibition of steady-state transmembrane current produced by the antimicrobial peptide cecropin A was attributed to both the dipole potential drop and membrane lipid disordering in the presence of pepper alkaloids. These data might lead to a better understanding of the biological activity of alkaloids, especially their action on voltage-gated and mechanosensitive ion channels in cell membranes.
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Affiliation(s)
- Svetlana S Efimova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Anastasiia A Zakharova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Olga S Ostroumova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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12
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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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13
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Efimova SS, Tertychnaya TE, Lavrenov SN, Ostroumova OS. The Mechanisms of Action of Triindolylmethane Derivatives on Lipid Membranes. Acta Naturae 2019; 11:38-45. [PMID: 31720015 PMCID: PMC6826156 DOI: 10.32607/20758251-2019-11-3-38-45] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The effects of new synthetic antibacterial agents – tris(1-pentyl-1H-indol-3-yl)methylium chloride
(LCTA-1975) and (1-(4-(dimethylamino)-2,5-dioxo-2,5-dihydro-1H-pyrrol-3-yl)-1H-indol-3-yl)bis(1-propyl-
1H-indol-3-yl)methylium chloride (LCTA-2701 – on model lipid membranes were studied. The ability of
the tested agents to form ion-conductive transmembrane pores, influence the electrical stability of lipid
bilayers and the phase transition of membrane lipids, and cause the deformation and fusion of lipid vesicles
was investigated. It was established that both compounds exert a strong detergent effect on model membranes.
The results of differential scanning microcalorimetry and measuring of the threshold transmembrane voltage
that caused membrane breakdown before and after adsorption of LCTA-1975 and LCTA-2701 indicated that both
agents cause disordering of membrane lipids. Synergism of the uncoupling action of antibiotics and the
alkaloid capsaicin on model lipid membranes was shown. The threshold concentration of the antibiotic that
caused an increase in the ion permeability of the lipid bilayer depended on the membrane lipid composition.
It was lower by an order of magnitude in the case of negatively charged lipid bilayers than for the uncharged
membranes. This can be explained by the positive charge of the tested agents. At the same time, LCTA-2701 was
characterized by greater efficiency than LCTA-1975. In addition to its detergent action, LCTA-2701 can induce
ion-permeable transmembrane pores: step-like current fluctuations corresponding to the opening and closing of
individual ion channels were observed. The difference in the mechanisms of action might be related to the
structural features of the antibiotic molecules: in the LCTA-1975 molecule, all three substituents at the
nitrogen atoms of the indole rings are identical and represent n-alkyl (pentyl) groups, while LCTA-2701
contains a maleimide group, along with two alkyl substituents (n-propyl). The obtained results might be
relevant to our understanding of the mechanism of action of new antibacterial agents, explaining the
difference in the selectivity of action of the tested agents on the target microorganisms and their
toxicity to human cells. Model lipid membranes should be used in further studies of the trends in
the modification and improvement of the structures of new antibacterial agents.
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Affiliation(s)
- S. S. Efimova
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - T. E. Tertychnaya
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - S. N. Lavrenov
- Gause Institute of New Antibiotics, Russian Academy of Medical Sciences, Bolshaya Pirogovskaya Str. 11, Moscow, 119021, Russia
| | - O. S. Ostroumova
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
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14
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Gutzeit VA, Thibado J, Stor DS, Zhou Z, Blanchard SC, Andersen OS, Levitz J. Conformational dynamics between transmembrane domains and allosteric modulation of a metabotropic glutamate receptor. eLife 2019; 8:45116. [PMID: 31172948 PMCID: PMC6588349 DOI: 10.7554/elife.45116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/06/2019] [Indexed: 01/01/2023] Open
Abstract
Metabotropic glutamate receptors (mGluRs) are class C, synaptic G-protein-coupled receptors (GPCRs) that contain large extracellular ligand binding domains (LBDs) and form constitutive dimers. Despite the existence of a detailed picture of inter-LBD conformational dynamics and structural snapshots of both isolated domains and full-length receptors, it remains unclear how mGluR activation proceeds at the level of the transmembrane domains (TMDs) and how TMD-targeting allosteric drugs exert their effects. Here, we use time-resolved functional and conformational assays to dissect the mechanisms by which allosteric drugs activate and modulate mGluR2. Single-molecule subunit counting and inter-TMD fluorescence resonance energy transfer measurements in living cells reveal LBD-independent conformational rearrangements between TMD dimers during receptor modulation. Using these assays along with functional readouts, we uncover heterogeneity in the magnitude, direction, and the timing of the action of both positive and negative allosteric drugs. Together our experiments lead to a three-state model of TMD activation, which provides a framework for understanding how inter-subunit rearrangements drive class C GPCR activation.
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Affiliation(s)
- Vanessa A Gutzeit
- Neuroscience Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States
| | - Jordana Thibado
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States
| | - Daniel Starer Stor
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States
| | - Scott C Blanchard
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States.,Tri-Institutional PhD Program in Chemical Biology, New York, United States
| | - Olaf S Andersen
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States
| | - Joshua Levitz
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States.,Tri-Institutional PhD Program in Chemical Biology, New York, United States.,Department of Biochemistry, Weill Cornell Medicine, New York, United States
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15
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Biomimetic Membranes with Transmembrane Proteins: State-of-the-Art in Transmembrane Protein Applications. Int J Mol Sci 2019; 20:ijms20061437. [PMID: 30901910 PMCID: PMC6472214 DOI: 10.3390/ijms20061437] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/26/2019] [Accepted: 03/13/2019] [Indexed: 12/14/2022] Open
Abstract
In biological cells, membrane proteins are the most crucial component for the maintenance of cell physiology and processes, including ion transportation, cell signaling, cell adhesion, and recognition of signal molecules. Therefore, researchers have proposed a number of membrane platforms to mimic the biological cell environment for transmembrane protein incorporation. The performance and selectivity of these transmembrane proteins based biomimetic platforms are far superior to those of traditional material platforms, but their lack of stability and scalability rule out their commercial presence. This review highlights the development of transmembrane protein-based biomimetic platforms for four major applications, which are biosensors, molecular interaction studies, energy harvesting, and water purification. We summarize the fundamental principles and recent progress in transmembrane protein biomimetic platforms for each application, discuss their limitations, and present future outlooks for industrial implementation.
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16
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Kapoor R, Peyear TA, Koeppe RE, Andersen OS. Antidepressants are modifiers of lipid bilayer properties. J Gen Physiol 2019; 151:342-356. [PMID: 30796095 PMCID: PMC6400527 DOI: 10.1085/jgp.201812263] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/17/2019] [Indexed: 12/28/2022] Open
Abstract
The two major classes of antidepressants, tricyclic antidepressants (TCAs) and selective serotonin reuptake inhibitors (SSRIs), inhibit neurotransmitter reuptake at synapses. They also have off-target effects on proteins other than neurotransmitter transporters, which may contribute to both desired changes in brain function and the development of side effects. Many proteins modulated by antidepressants are bilayer spanning and coupled to the bilayer through hydrophobic interactions such that the conformational changes underlying their function will perturb the surrounding lipid bilayer, with an energetic cost (ΔG def) that varies with changes in bilayer properties. Here, we test whether changes in ΔG def caused by amphiphilic antidepressants partitioning into the bilayer are sufficient to alter membrane protein function. Using gramicidin A (gA) channels to probe whether TCAs and SSRIs alter the bilayer contribution to the free energy difference for the gramicidin monomer⇔dimer equilibrium (representing a well-defined conformational transition), we find that antidepressants alter gA channel activity with varying potency and no stereospecificity but with different effects on bilayer elasticity and intrinsic curvature. Measuring the antidepressant partition coefficients using isothermal titration calorimetry (ITC) or cLogP shows that the bilayer-modifying potency is predicted quite well by the ITC-determined partition coefficients, and channel activity is doubled at an antidepressant/lipid mole ratio of 0.02-0.07. These results suggest a mechanism by which antidepressants could alter the function of diverse membrane proteins by partitioning into cell membranes and thereby altering the bilayer contribution to the energetics of membrane protein conformational changes.
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Affiliation(s)
- Ruchi Kapoor
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY
| | - Thasin A Peyear
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY
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17
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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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18
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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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19
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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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20
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Schmidpeter PAM, Gao X, Uphadyay V, Rheinberger J, Nimigean CM. Ligand binding and activation properties of the purified bacterial cyclic nucleotide-gated channel SthK. J Gen Physiol 2018; 150:821-834. [PMID: 29752414 PMCID: PMC5987880 DOI: 10.1085/jgp.201812023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/09/2018] [Indexed: 11/20/2022] Open
Abstract
SthK is a bacterial cyclic nucleotide–gated ion channel from Spirochaeta thermophila. By optimizing the expression and purification of SthK, Schmidpeter et al. show that cAMP and cGMP bind to the channel with similar affinity but activate it with different efficacy. Cyclic nucleotide–modulated ion channels play several essential physiological roles. They are involved in signal transduction in photoreceptors and olfactory sensory neurons as well as pacemaking activity in the heart and brain. Investigations of the molecular mechanism of their actions, including structural and electrophysiological characterization, are restricted by the availability of stable, purified protein obtained from accessible systems. Here, we establish that SthK, a cyclic nucleotide–gated (CNG) channel from Spirochaeta thermophila, is an excellent model for investigating the gating of eukaryotic CNG channels at the molecular level. The channel has high sequence similarity with its eukaryotic counterparts and was previously reported to be activated by cyclic nucleotides in patch-clamp experiments with Xenopus laevis oocytes. We optimized protein expression and purification to obtain large quantities of pure, homogeneous, and active recombinant SthK protein from Escherichia coli. A negative-stain electron microscopy (EM) single-particle analysis indicated that this channel is a promising candidate for structural studies with cryo-EM. Using radioactivity and fluorescence flux assays, as well as single-channel recordings in lipid bilayers, we show that the protein is partially activated by micromolar concentrations of cyclic adenosine monophosphate (cAMP) and that channel activity is increased by depolarization. Unlike previous studies, we find that cyclic guanosine monophosphate (cGMP) is also able to activate SthK, but with much lower efficiency than cAMP. The distinct sensitivities to different ligands resemble eukaryotic CNG and hyperpolarization-activated and cyclic nucleotide–modulated channels. Using a fluorescence binding assay, we show that cGMP and cAMP bind to SthK with similar apparent affinities, suggesting that the large difference in channel activation by cAMP or cGMP is caused by the efficacy with which each ligand promotes the conformational changes toward the open state. We conclude that the functional characteristics of SthK reported here will permit future studies to analyze ligand gating and discrimination in CNG channels.
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Affiliation(s)
| | - Xiaolong Gao
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY
| | - Vikrant Uphadyay
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY .,Department of Biochemistry, Weill Cornell Medicine, New York, NY.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
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21
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Dockendorff C, Gandhi DM, Kimball IH, Eum KS, Rusinova R, Ingólfsson HI, Kapoor R, Peyear T, Dodge MW, Martin SF, Aldrich RW, Andersen OS, Sack JT. Synthetic Analogues of the Snail Toxin 6-Bromo-2-mercaptotryptamine Dimer (BrMT) Reveal That Lipid Bilayer Perturbation Does Not Underlie Its Modulation of Voltage-Gated Potassium Channels. Biochemistry 2018; 57:2733-2743. [PMID: 29616558 PMCID: PMC6007853 DOI: 10.1021/acs.biochem.8b00292] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Drugs do not act solely by canonical ligand-receptor binding interactions. Amphiphilic drugs partition into membranes, thereby perturbing bulk lipid bilayer properties and possibly altering the function of membrane proteins. Distinguishing membrane perturbation from more direct protein-ligand interactions is an ongoing challenge in chemical biology. Herein, we present one strategy for doing so, using dimeric 6-bromo-2-mercaptotryptamine (BrMT) and synthetic analogues. BrMT is a chemically unstable marine snail toxin that has unique effects on voltage-gated K+ channel proteins, making it an attractive medicinal chemistry lead. BrMT is amphiphilic and perturbs lipid bilayers, raising the question of whether its action against K+ channels is merely a manifestation of membrane perturbation. To determine whether medicinal chemistry approaches to improve BrMT might be viable, we synthesized BrMT and 11 analogues and determined their activities in parallel assays measuring K+ channel activity and lipid bilayer properties. Structure-activity relationships were determined for modulation of the Kv1.4 channel, bilayer partitioning, and bilayer perturbation. Neither membrane partitioning nor bilayer perturbation correlates with K+ channel modulation. We conclude that BrMT's membrane interactions are not critical for its inhibition of Kv1.4 activation. Further, we found that alkyl or ether linkages can replace the chemically labile disulfide bond in the BrMT pharmacophore, and we identified additional regions of the scaffold that are amenable to chemical modification. Our work demonstrates a strategy for determining if drugs act by specific interactions or bilayer-dependent mechanisms, and chemically stable modulators of Kv1 channels are reported.
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Affiliation(s)
- Chris Dockendorff
- Department of Chemistry , Marquette University , P.O. Box 1881, Milwaukee , Wisconsin 53201-1881 , United States
| | - Disha M Gandhi
- Department of Chemistry , Marquette University , P.O. Box 1881, Milwaukee , Wisconsin 53201-1881 , United States
| | - Ian H Kimball
- Department of Physiology & Membrane Biology , University of California , 1 Shields Avenue , Davis , California 95616 , United States
| | - Kenneth S Eum
- Department of Physiology & Membrane Biology , University of California , 1 Shields Avenue , Davis , California 95616 , United States
| | - Radda Rusinova
- Department of Physiology and Biophysics , Weill Cornell Medical College , New York , New York 10065 , United States
| | - Helgi I Ingólfsson
- Department of Physiology and Biophysics , Weill Cornell Medical College , New York , New York 10065 , United States
| | - Ruchi Kapoor
- Department of Physiology and Biophysics , Weill Cornell Medical College , New York , New York 10065 , United States
| | - Thasin Peyear
- Department of Physiology and Biophysics , Weill Cornell Medical College , New York , New York 10065 , United States
| | - Matthew W Dodge
- Department of Chemistry , Marquette University , P.O. Box 1881, Milwaukee , Wisconsin 53201-1881 , United States
| | - Stephen F Martin
- Department of Chemistry , University of Texas at Austin , 1 University Station , Austin , Texas 78712 , United States
| | - Richard W Aldrich
- Department of Neuroscience , University of Texas at Austin , 1 University Station , Austin , Texas 78712 , United States
| | - Olaf S Andersen
- Department of Physiology and Biophysics , Weill Cornell Medical College , New York , New York 10065 , United States
| | - Jon T Sack
- Department of Physiology & Membrane Biology , University of California , 1 Shields Avenue , Davis , California 95616 , United States
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22
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Posson DJ, Rusinova R, Andersen OS, Nimigean CM. Stopped-Flow Fluorometric Ion Flux Assay for Ligand-Gated Ion Channel Studies. Methods Mol Biol 2018; 1684:223-235. [PMID: 29058195 DOI: 10.1007/978-1-4939-7362-0_17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Quantitative investigations into functional properties of purified ion channel proteins using standard electrophysiological methods are challenging, in particular for the determination of average ion channel behavior following rapid changes in experimental conditions (e.g., ligand concentration). Here, we describe a method for determining the functional activity of liposome-reconstituted K+ channels using a stopped-flow fluorometric ion flux assay. Channel activity is quantified by measuring the rate of fluorescence decrease of a liposome-encapsulated fluorophore, specifically quenched by thallium ions entering the liposomes via open channels. This method is well suited for studying the lipid bilayer dependence of channel activity, the activation and desensitization kinetics of ligand-dependent K+ channels, and channel modulation by channel agonists, blockers, or other antagonists.
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Affiliation(s)
- David J Posson
- Department of Anesthesiology, Weill Cornell Medical College, 1300 York Ave., New York, NY, 10065, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Ave., New York, NY, 10065, USA.,Vertex Pharmaceuticals Inc., 50 Northern Ave., Boston, MA, 02210, USA
| | - Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Ave., New York, NY, 10065, USA
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Ave., New York, NY, 10065, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, 1300 York Ave., New York, NY, 10065, USA. .,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Ave., New York, NY, 10065, USA. .,Department of Biochemistry, Weill Cornell Medical College, 1300 York Ave., New York, NY, 10065, USA.
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23
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Lum K, Ingólfsson HI, Koeppe RE, Andersen OS. Exchange of Gramicidin between Lipid Bilayers: Implications for the Mechanism of Channel Formation. Biophys J 2017; 113:1757-1767. [PMID: 29045870 DOI: 10.1016/j.bpj.2017.08.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/25/2017] [Accepted: 08/30/2017] [Indexed: 11/30/2022] Open
Abstract
The canonical mechanism of gramicidin (gA) channel formation is transmembrane dimerization of nonconducting subunits that reside in opposite bilayer leaflets. The channels do not open and close; they appear and disappear due to subunit association and dissociation. Many different types of experiments support this monomer ↔ dimer mechanism. Recently, however, this mechanism was challenged, based on experiments with lipid vesicle-incorporated gA under conditions where vesicle fusion could be controlled. In these experiments, sustained channel activity was observed long after fusion had been terminated, which led to the proposal that gA single-channel current transitions result from closed-open transitions in long-lived bilayer-spanning dimers. This proposal is at odds with 40 years of experiments, but involves the key assumption that gA monomers do not exchange between bilayers. We tested the possibility of peptide exchange between bilayers using three different types of experiments. First, we demonstrated the exchange of gA between 1,2-dierucoyl-sn-glycero-3-phosphocholine (DC22:1PC) or 1,2-dioleoyl-sn-glycero-3-phosphocholine (DC18:1PC) lipid vesicles using a fluorescence assay for gA channel activity. Second, we added gA-free DC22:1PC vesicles to both sides of planar DC18:1PC bilayers preincubated with gA, which reduced channel activity up to 10-fold. Third, we added gA-containing DC22:1PC vesicles to one or both sides of DC18:1PC planar bilayers, which produced much higher channel activity when the gA-containing vesicles were added to both sides of the bilayer, as compared to one side only. All three types of experiments show that gA subunits can exchange between lipid bilayers. The exchange of subunits between bilayers thus is firmly established, which becomes a crucial consideration with respect to the mechanism of channel formation.
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Affiliation(s)
- Kevin Lum
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Helgi I Ingólfsson
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
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24
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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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25
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Timing and Reset Mechanism of GTP Hydrolysis-Driven Conformational Changes of Atlastin. Structure 2017; 25:997-1010.e4. [PMID: 28602821 DOI: 10.1016/j.str.2017.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/12/2017] [Accepted: 05/10/2017] [Indexed: 01/09/2023]
Abstract
The endoplasmic reticulum (ER) forms a branched, dynamic membrane tubule network that is vital for cellular function. Branching arises from membrane fusion facilitated by the GTPase atlastin (ATL). Many metazoan genomes encode for three ATL isoforms that appear to fulfill partially redundant function despite differences in their intrinsic GTPase activity and localization within the ER; however, the underlying mechanistic differences between the isoforms are poorly understood. Here, we identify discrete temporal steps in the catalytic cycle for the two most dissimilar isoforms, ATL1 and ATL3, revealing an overall conserved progression of molecular events from nucleotide binding and hydrolysis to ATL dimerization and phosphate release. A crystal structure of ATL3 suggests a mechanism for the displacement of the catalytic Mg2+ ion following guanosine triphosphate (GTP) hydrolysis. Together, the data extend the mechanistic framework for how GTP hydrolysis drives conformational changes in ATL and how the cycle is reset for subsequent rounds of catalysis.
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26
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Koyanagi T, Cao KJ, Leriche G, Onofrei D, Holland GP, Mayer M, Sept D, Yang J. Hybrid Lipids Inspired by Extremophiles and Eukaryotes Afford Serum‐Stable Membranes with Low Leakage. Chemistry 2017; 23:6757-6762. [DOI: 10.1002/chem.201701378] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Takaoki Koyanagi
- Department of Chemistry and Biochemistry University of California San Diego La Jolla California 92093-0358 USA
| | - Kevin J. Cao
- Department of Chemistry and Biochemistry University of California San Diego La Jolla California 92093-0358 USA
| | - Geoffray Leriche
- Department of Chemistry and Biochemistry University of California San Diego La Jolla California 92093-0358 USA
| | - David Onofrei
- Department of Chemistry and Biochemistry San Diego State University San Diego California 92182-1030 USA
| | - Gregory P. Holland
- Department of Chemistry and Biochemistry San Diego State University San Diego California 92182-1030 USA
| | - Michael Mayer
- Adolphe Merkle Institute University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
| | - David Sept
- Department of Biomedical Engineering University of Michigan Ann Arbor Michigan 48109-2110 USA
| | - Jerry Yang
- Department of Chemistry and Biochemistry University of California San Diego La Jolla California 92093-0358 USA
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27
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Menny A, Lefebvre SN, Schmidpeter PA, Drège E, Fourati Z, Delarue M, Edelstein SJ, Nimigean CM, Joseph D, Corringer PJ. Identification of a pre-active conformation of a pentameric channel receptor. eLife 2017; 6. [PMID: 28294942 PMCID: PMC5398890 DOI: 10.7554/elife.23955] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/14/2017] [Indexed: 11/26/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate fast chemical signaling through global allosteric transitions. Despite the existence of several high-resolution structures of pLGICs, their dynamical properties remain elusive. Using the proton-gated channel GLIC, we engineered multiple fluorescent reporters, each incorporating a bimane and a tryptophan/tyrosine, whose close distance causes fluorescence quenching. We show that proton application causes a global compaction of the extracellular subunit interface, coupled to an outward motion of the M2-M3 loop near the channel gate. These movements are highly similar in lipid vesicles and detergent micelles. These reorganizations are essentially completed within 2 ms and occur without channel opening at low proton concentration, indicating that they report a pre-active intermediate state in the transition pathway toward activation. This provides a template to investigate the gating of eukaryotic neurotransmitter receptors, for which intermediate states also participate in activation. DOI:http://dx.doi.org/10.7554/eLife.23955.001 In the nervous system, proteins of the pLGIC family are found in the membrane that surrounds each neuron. These proteins have channels that can allow ions to pass through the membrane and are responsible for transmitting electrical signals from one neuron to the next. Small molecules called neurotransmitters interact with the pLGICs to open or close the ion channel. If the ability of the pLGIC channels to open is altered, it can lead to behavioral changes like addiction, or diseases such as schizophrenia or epilepsy. For a pLGIC channel to switch between the “open” and “closed” states, specific parts of the protein need to move in relation to each other. However, to study these transitions researchers have previously relied on comparing the three-dimensional structures of open and closed pLGICs extracted out of the cell membrane. Different techniques are needed to directly follow these movements within membranes. Bacteria also have proteins belonging to the pLGIC family, and Menny et al. have now investigated one such bacterial protein to understand how pLGICs open. First, a small fluorescent molecule that glows differently if the environment around it changes was attached to various parts of the bacterial channel. These fluorescent markers revealed how several parts of the protein move and they also made it possible to measure how quickly these movements take place. Some of these movements happen before the channel opens, suggesting that the activation of this pLGIC protein happens in stages and involves the protein adopting a temporary intermediate state. The next step will be to better understand the structure of the intermediate state, which could help us to understand how pLGICs work in the nervous systems of animals. In future this may aid the design of new drugs that can modify the activity of these channels in patients with neurological conditions or addictions. DOI:http://dx.doi.org/10.7554/eLife.23955.002
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Affiliation(s)
- Anaïs Menny
- Channel Receptors Unit, Institut Pasteur, Paris, France.,Unité Mixte de Recherche 3571, Centre National de la Recherche Scientifique, Paris, France.,Université Pierre et Marie Curie, Cellule Pasteur, Paris, France
| | - Solène N Lefebvre
- Channel Receptors Unit, Institut Pasteur, Paris, France.,Unité Mixte de Recherche 3571, Centre National de la Recherche Scientifique, Paris, France.,Université Pierre et Marie Curie, Cellule Pasteur, Paris, France
| | - Philipp Am Schmidpeter
- Departments of Anesthesiology, Physiology and Biophysics, Biochemistry, Weill Cornell Medicine, New York, United States
| | - Emmanuelle Drège
- BioCIS, Université Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Zaineb Fourati
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, Paris, France.,Unité Mixte de Recherche 3528, Centre National de la Recherche Scientifique, Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, Paris, France.,Unité Mixte de Recherche 3528, Centre National de la Recherche Scientifique, Paris, France
| | - Stuart J Edelstein
- Biologie Cellulaire de la Synapse, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Crina M Nimigean
- Departments of Anesthesiology, Physiology and Biophysics, Biochemistry, Weill Cornell Medicine, New York, United States
| | - Delphine Joseph
- BioCIS, Université Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Pierre-Jean Corringer
- Channel Receptors Unit, Institut Pasteur, Paris, France.,Unité Mixte de Recherche 3571, Centre National de la Recherche Scientifique, Paris, France
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28
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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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29
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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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30
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Abstract
Because of the perpetual development of resistance to current therapies for malaria, the Medicines for Malaria Venture developed the Malaria Box to facilitate the drug development process. We tested the 80 most potent compounds from the box for bilayer-mediated effects on membrane protein conformational changes (a measure of likely toxicity) in a gramicidin-based stopped flow fluorescence assay. Among the Malaria Box compounds tested, four compounds altered membrane properties (p< 0.05); MMV007384 stood out as a potent bilayer-perturbing compound that is toxic in many cell-based assays, suggesting that testing for membrane perturbation could help identify toxic compounds. In any case, MMV007384 should be approached with caution, if at all.
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31
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Posson DJ, Rusinova R, Andersen OS, Nimigean CM. Calcium ions open a selectivity filter gate during activation of the MthK potassium channel. Nat Commun 2015; 6:8342. [PMID: 26395539 PMCID: PMC4580985 DOI: 10.1038/ncomms9342] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 08/11/2015] [Indexed: 12/25/2022] Open
Abstract
Ion channel opening and closing are fundamental to cellular signalling and homeostasis. Gates that control K+ channel activity were found both at an intracellular pore constriction and within the selectivity filter near the extracellular side but the specific location of the gate that opens Ca2+-activated K+ channels has remained elusive. Using the Methanobacterium thermoautotrophicum homologue (MthK) and a stopped-flow fluorometric assay for fast channel activation, we show that intracellular quaternary ammonium blockers bind to closed MthK channels. Since the blockers are known to bind inside a central channel cavity, past the intracellular entryway, the gate must be within the selectivity filter. Furthermore, the blockers access the closed channel slower than the open channel, suggesting that the intracellular entryway narrows upon pore closure, without preventing access of either the blockers or the smaller K+. Thus, Ca2+-dependent gating in MthK occurs at the selectivity filter with coupled movement of the intracellular helices. Ion channels open and close to allow the regulated passage of ions through the membrane. Here the authors use selective ion channel blockers to analyse this regulation in a potassium channel and show that the gate is in the selectivity filter, past the entrance to the channel.
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Affiliation(s)
- David J Posson
- Department of Anesthesiology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
| | - Radda Rusinova
- Department of Anesthesiology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
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32
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Lomora M, Garni M, Itel F, Tanner P, Spulber M, Palivan CG. Polymersomes with engineered ion selective permeability as stimuli-responsive nanocompartments with preserved architecture. Biomaterials 2015; 53:406-14. [DOI: 10.1016/j.biomaterials.2015.02.080] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 10/23/2022]
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33
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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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34
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Rusinova R, Kim DM, Nimigean CM, Andersen OS. Regulation of ion channel function by the host lipid bilayer examined by a stopped-flow spectrofluorometric assay. Biophys J 2014; 106:1070-8. [PMID: 24606931 DOI: 10.1016/j.bpj.2014.01.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 01/16/2023] Open
Abstract
To examine the function of ligand-gated ion channels in a defined membrane environment, we developed a robust sequential-mixing fluorescence-based stopped-flow assay. Channel activity is determined using a channel-permeable quencher (e.g., thallium, Tl(+)) of a water-soluble fluorophore (8-aminonaphthalene-1,3,6-trisulfonic acid) encapsulated in large unilamellar vesicles in which the channel of interest has been reconstituted, which allows for rapid solution changes. To validate the method, we explored the activation of wild-type KcsA channel, as well as it's noninactivating (E71A) KcsA mutant, by extravesicular protons (H(+)). For both channel types, the day-to-day variability in the reconstitution yield (as judged from the time course of fluorescence quenching) is <10%. The activation curve for E71A KcsA is similar to that obtained previously using single-channel electrophysiology, and the activation curves for wild-type and E71A KcsA are indistinguishable, indicating that channel activation and inactivation are separate processes. We then investigated the regulation of KcsA activation by changes in lipid bilayer composition. Increasing the acyl chain length (from C18:1 to C22:1 in diacylphosphatidylcholine), but not the mole fraction of POPG (>0.25) in the bilayer-forming phospholipid mixture, alters KcsA H(+) gating. The bilayer-thickness-dependent shift in the activation curve is suggestive of a decrease in an apparent H(+) affinity and cooperativity. The control over bilayer environment and time resolution makes this method a powerful assay for exploring ligand activation and inactivation of ion channels, and how channel gating varies with changes in the channels' lipid bilayer environment or other regulatory processes.
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Affiliation(s)
- Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; Department of Anesthesiology, Weill Cornell Medical College, New York, New York.
| | - Dorothy M Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York
| | - Crina M Nimigean
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; Department of Anesthesiology, Weill Cornell Medical College, New York, New York
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
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35
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Barnoud J, Rossi G, Marrink SJ, Monticelli L. Hydrophobic compounds reshape membrane domains. PLoS Comput Biol 2014; 10:e1003873. [PMID: 25299598 PMCID: PMC4191877 DOI: 10.1371/journal.pcbi.1003873] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/25/2014] [Indexed: 12/12/2022] Open
Abstract
Cell membranes have a complex lateral organization featuring domains with distinct composition, also known as rafts, which play an essential role in cellular processes such as signal transduction and protein trafficking. In vivo, perturbations of membrane domains (e.g., by drugs or lipophilic compounds) have major effects on the activity of raft-associated proteins and on signaling pathways, but they are difficult to characterize because of the small size of the domains, typically below optical resolution. Model membranes, instead, can show macroscopic phase separation between liquid-ordered and liquid-disordered domains, and they are often used to investigate the driving forces of membrane lateral organization. Studies in model membranes have shown that some lipophilic compounds perturb membrane domains, but it is not clear which chemical and physical properties determine domain perturbation. The mechanisms of domain stabilization and destabilization are also unknown. Here we describe the effect of six simple hydrophobic compounds on the lateral organization of phase-separated model membranes consisting of saturated and unsaturated phospholipids and cholesterol. Using molecular simulations, we identify two groups of molecules with distinct behavior: aliphatic compounds promote lipid mixing by distributing at the interface between liquid-ordered and liquid-disordered domains; aromatic compounds, instead, stabilize phase separation by partitioning into liquid-disordered domains and excluding cholesterol from the disordered domains. We predict that relatively small concentrations of hydrophobic species can have a broad impact on domain stability in model systems, which suggests possible mechanisms of action for hydrophobic compounds in vivo.
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Affiliation(s)
- Jonathan Barnoud
- IBCP, CNRS UMR 5086, Lyon, France
- Université Claude Bernard Lyon I, Lyon, France
| | - Giulia Rossi
- Dept of Physics, University of Genoa, Genoa, Italy
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Luca Monticelli
- IBCP, CNRS UMR 5086, Lyon, France
- Université Claude Bernard Lyon I, Lyon, France
- * E-mail:
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36
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Ashrafuzzaman M. Aptamers as both drugs and drug-carriers. BIOMED RESEARCH INTERNATIONAL 2014; 2014:697923. [PMID: 25295268 PMCID: PMC4177733 DOI: 10.1155/2014/697923] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 08/04/2014] [Accepted: 08/22/2014] [Indexed: 11/17/2022]
Abstract
Aptamers are short nucleic acid oligos. They may serve as both drugs and drug-carriers. Their use as diagnostic tools is also evident. They can be generated using various experimental, theoretical, and computational techniques. The systematic evolution of ligands by exponential enrichment which uses iterative screening of nucleic acid libraries is a popular experimental technique. Theory inspired methodology entropy-based seed-and-grow strategy that designs aptamer templates to bind specifically to targets is another one. Aptamers are predicted to be highly useful in producing general drugs and theranostic drugs occasionally for certain diseases like cancer, Alzheimer's disease, and so on. They bind to various targets like lipids, nucleic acids, proteins, small organic compounds, and even entire organisms. Aptamers may also serve as drug-carriers or nanoparticles helping drugs to get released in specific target regions. Due to better target specific physical binding properties aptamers cause less off-target toxicity effects. Therefore, search for aptamer based drugs, drug-carriers, and even diagnostic tools is expanding fast. The biophysical properties in relation to the target specific binding phenomena of aptamers, energetics behind the aptamer transport of drugs, and the consequent biological implications will be discussed. This review will open up avenues leading to novel drug discovery and drug delivery.
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Affiliation(s)
- Md. Ashrafuzzaman
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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37
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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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38
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Lenaeus MJ, Burdette D, Wagner T, Focia PJ, Gross A. Structures of KcsA in complex with symmetrical quaternary ammonium compounds reveal a hydrophobic binding site. Biochemistry 2014; 53:5365-73. [PMID: 25093676 PMCID: PMC4139162 DOI: 10.1021/bi500525s] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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Potassium channels allow for the
passive movement of potassium
ions across the cell membrane and are instrumental in controlling
the membrane potential in all cell types. Quaternary ammonium (QA)
compounds block potassium channels and have long been used to study
the functional and structural properties of these channels. Here we
describe the interaction between three symmetrical hydrophobic QAs
and the prokaryotic potassium channel KcsA. The structures demonstrate
the presence of a hydrophobic pocket between the inner helices of
KcsA and provide insight into the binding site and blocking mechanism
of hydrophobic QAs. The structures also reveal a structurally hidden
pathway between the central cavity and the outside membrane environment
reminiscent of the lateral fenestration observed in sodium channels
that can be accessed through small conformational changes in the pore
wall. We propose that the hydrophobic binding pocket stabilizes the
alkyl chains of long-chain QA molecules and may play a key role in
hydrophobic drug binding in general.
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Affiliation(s)
- Michael J Lenaeus
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
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39
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McCoy JG, Rusinova R, Kim DM, Kowal J, Banerjee S, Jaramillo Cartagena A, Thompson AN, Kolmakova-Partensky L, Stahlberg H, Andersen OS, Nimigean CM. A KcsA/MloK1 chimeric ion channel has lipid-dependent ligand-binding energetics. J Biol Chem 2014; 289:9535-46. [PMID: 24515111 DOI: 10.1074/jbc.m113.543389] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cyclic nucleotide-modulated ion channels play crucial roles in signal transduction in eukaryotes. The molecular mechanism by which ligand binding leads to channel opening remains poorly understood, due in part to the lack of a robust method for preparing sufficient amounts of purified, stable protein required for structural and biochemical characterization. To overcome this limitation, we designed a stable, highly expressed chimeric ion channel consisting of the transmembrane domains of the well characterized potassium channel KcsA and the cyclic nucleotide-binding domains of the prokaryotic cyclic nucleotide-modulated channel MloK1. This chimera demonstrates KcsA-like pH-sensitive activity which is modulated by cAMP, reminiscent of the dual modulation in hyperpolarization-activated and cyclic nucleotide-gated channels that display voltage-dependent activity that is also modulated by cAMP. Using this chimeric construct, we were able to measure for the first time the binding thermodynamics of cAMP to an intact cyclic nucleotide-modulated ion channel using isothermal titration calorimetry. The energetics of ligand binding to channels reconstituted in lipid bilayers are substantially different from those observed in detergent micelles, suggesting that the conformation of the chimera's transmembrane domain is sensitive to its (lipid or lipid-mimetic) environment and that ligand binding induces conformational changes in the transmembrane domain. Nevertheless, because cAMP on its own does not activate these chimeric channels, cAMP binding likely has a smaller energetic contribution to gating than proton binding suggesting that there is only a small difference in cAMP binding energy between the open and closed states of the channel.
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40
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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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41
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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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42
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Darby CM, Ingólfsson HI, Jiang X, Shen C, Sun M, Zhao N, Burns K, Liu G, Ehrt S, Warren JD, Anderson OS, Brickner SJ, Nathan C. Whole cell screen for inhibitors of pH homeostasis in Mycobacterium tuberculosis. PLoS One 2013; 8:e68942. [PMID: 23935911 PMCID: PMC3728290 DOI: 10.1371/journal.pone.0068942] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/05/2013] [Indexed: 12/17/2022] Open
Abstract
Bacterial pathogens like Mycobacterium tuberculosis (Mtb) encounter acidic microenvironments in the host and must maintain their acid-base homeostasis to survive. A genetic screen identified two Mtb strains that cannot control intrabacterial pH (pHIB) in an acidic environment; infection with either strain led to severe attenuation in mice. To search for additional proteins that Mtb requires to survive at low pH, we introduced a whole-cell screen for compounds that disrupt pHIB, along with counter-screens that identify ionophores and membrane perturbors. Application of these methods to a natural product library identified four compounds of interest, one of which may inhibit novel pathway(s). This approach yields compounds that may lead to the identification of pathways that allow Mtb to survive in acidic environments, a setting in which Mtb is resistant to most of the drugs currently used to treat tuberculosis.
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Affiliation(s)
- Crystal M. Darby
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Helgi I. Ingólfsson
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
| | - Xiuju Jiang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Chun Shen
- Milstein Chemistry Core Facility, Weill Cornell Medical College, New York, New York, United States of America
| | - Mingna Sun
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Nan Zhao
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Kristin Burns
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Gang Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Tsinghua-Peking Center for Life Sciences and Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing, P. R. China
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - J. David Warren
- Milstein Chemistry Core Facility, Weill Cornell Medical College, New York, New York, United States of America
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, United States of America
| | - Olaf S. Anderson
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
| | - Steven J. Brickner
- SJ Brickner Consulting, LLC, Ledyard, Connecticut, United States of America
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
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43
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Abstract
The lack of small-molecule inhibitors for anion-selective transporters and channels has impeded our understanding of the complex mechanisms that underlie ion passage. The ubiquitous CLC "Chloride Channel" family represents a unique target for biophysical and biochemical studies because its distinctive protein fold supports both passive chloride channels and secondary-active chloride-proton transporters. Here, we describe the synthesis and characterization of a specific small-molecule inhibitor directed against a CLC antiporter (ClC-ec1). This compound, 4,4'-octanamidostilbene-2,2'-disulfonate (OADS), inhibits ClC-ec1 with low micromolar affinity and has no specific effect on a CLC channel (ClC-1). Inhibition of ClC-ec1 occurs by binding to two distinct intracellular sites. The location of these sites and the lipid dependence of inhibition suggest potential mechanisms of action. This compound will empower research to elucidate differences between antiporter and channel mechanisms and to develop treatments for CLC-mediated disorders.
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44
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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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45
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Tibbs GR, Rowley TJ, Sanford RL, Herold KF, Proekt A, Hemmings HC, Andersen OS, Goldstein PA, Flood PD. HCN1 channels as targets for anesthetic and nonanesthetic propofol analogs in the amelioration of mechanical and thermal hyperalgesia in a mouse model of neuropathic pain. J Pharmacol Exp Ther 2013; 345:363-73. [PMID: 23549867 DOI: 10.1124/jpet.113.203620] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Chronic pain after peripheral nerve injury is associated with afferent hyperexcitability and upregulation of hyperpolarization-activated, cyclic nucleotide-regulated (HCN)-mediated IH pacemaker currents in sensory neurons. HCN channels thus constitute an attractive target for treating chronic pain. HCN channels are ubiquitously expressed; analgesics targeting HCN1-rich cells in the peripheral nervous system must spare the cardiac pacemaker current (carried mostly by HCN2 and HCN4) and the central nervous system (where all four isoforms are expressed). The alkylphenol general anesthetic propofol (2,6-di-iso-propylphenol) selectively inhibits HCN1 channels versus HCN2-HCN4 and exhibits a modest pharmacokinetic preference for the periphery. Consequently, we hypothesized that propofol, and congeners, should be antihyperalgesic. Alkyl-substituted propofol analogs have different rank-order potencies with respect to HCN1 inhibition, GABA(A) receptor (GABA(A)-R) potentiation, and general anesthesia. Thus, 2,6- and 2,4-di-tertbutylphenol (2,6- and 2,4-DTBP, respectively) are more potent HCN1 antagonists than propofol, whereas 2,6- and 2,4-di-sec-butylphenol (2,6- and 2,4-DSBP, respectively) are less potent. In contrast, DSBPs, but not DTBPs, enhance GABA(A)-R function and are general anesthetics. 2,6-DTBP retained propofol's selectivity for HCN1 over HCN2-HCN4. In a peripheral nerve ligation model of neuropathic pain, 2,6-DTBP and subhypnotic propofol are antihyperalgesic. The findings are consistent with these alkylphenols exerting analgesia via non-GABA(A)-R targets and suggest that antagonism of central HCN1 channels may be of limited importance to general anesthesia. Alkylphenols are hydrophobic, and thus potential modifiers of lipid bilayers, but their effects on HCN channels are due to direct drug-channel interactions because they have little bilayer-modifying effect at therapeutic concentrations. The alkylphenol antihyperalgesic target may be HCN1 channels in the damaged peripheral nervous system.
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Affiliation(s)
- Gareth R Tibbs
- Department of Anesthesiology, College of Physicians & Surgeons, Columbia University, New York, New York, USA
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46
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Lee KI, Pastor RW, Andersen OS, Im W. Assessing smectic liquid-crystal continuum models for elastic bilayer deformations. Chem Phys Lipids 2013; 169:19-26. [PMID: 23348553 DOI: 10.1016/j.chemphyslip.2013.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/08/2013] [Accepted: 01/10/2013] [Indexed: 10/27/2022]
Abstract
For four decades, since W. Helfrich's pioneering study of smectic A liquid crystals in 1973, continuum elastic models (CEMs) have been employed as tools to understand the energetics of protein-induced lipid bilayer deformations. Among the assumptions underlying this use is that all relevant protein-lipid interactions can be included in the continuum representation of the protein-bilayer interactions through the physical parameters determined for protein-free bilayers and the choice of boundary conditions at the protein/bilayer interface. To better understand this assumption, we review the general structure of CEMs, examine how different choices of boundary conditions and physical moduli profiles alter the predicted bilayer thickness profiles around gramicidin A (gA) and mitochondrial voltage-dependent anion channels (VDAC), respectively, and compare these profiles with those obtained from all-atom molecular dynamics simulations. We find that the profiles differ qualitatively in the first lipid shell around the channels, indicating that the CEMs do not capture accurately the consequences of the protein-induced local changes in lipid bilayer dynamics. Therefore, one needs to be careful when interpreting the results of CEM-based analyses of lipid bilayer-membrane protein interactions.
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Affiliation(s)
- Kyu Ii Lee
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, KS 66047, USA
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47
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Bruno MJ, Rusinova R, Gleason NJ, Koeppe RE, Andersen OS. Interactions of drugs and amphiphiles with membranes: modulation of lipid bilayer elastic properties by changes in acyl chain unsaturation and protonation. Faraday Discuss 2013; 161:461-80; discussion 563-89. [PMID: 23805753 PMCID: PMC3703894 DOI: 10.1039/c2fd20092a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Poly-unsaturated fatty acids (PUFAs) alter the function of many membrane proteins, whereas monounsatured fatty acids generally are inert. We previously showed that docosahexaenoic acid (DHA) at pH 7 decreases the bilayer stiffness, consistent with an amphiphile-induced increase in elasticity, but not with a negative change in curvature; oleic acid (OA) was inert (Bruno, Koeppe and Andersen, Proc. Natl. Acad. Sci., 2007, 104, 9638-9643). To further explore how PUFAs and other amphiphiles may alter lipid bilayer properties, and thus membrane protein function, we examined how changes in acyl chain unsaturation and head group charge and size alter bilayer properties, as sensed by bilayer-spanning gramicidin A (gA) channels of different lengths. Compared to DHA, the neutral DHA-methyl ester has reduced effects on bilayer properties and 1-palmitoyl-2-docosahexaenoyl-phosphatidylcholine (PDPC) forms bilayers that are softer than dioleoylphosphatidylcholine (DOPC). The changes in channel function are larger for the short gA channels, indicating that changes in elasticity dominate over changes in curvature. We altered the fatty acid protonation by titration: docosahexaenoic acid (DHA) is more potent at pH 9 (relative to pH 7) and is inert at pH 4; OA, which was inert at pH 7, becomes a potent modifier of bilayer properties at pH 9. At both pH 7 and 9, DHA and OA produced larger changes in the lifetimes of the short gA channels, demonstrating that they increase lipid bilayer elasticity when deprotonated--though OA promotes the formation of inverted hexagonal phases at pH 7. The positively charged oleylamine (OAm), which has a small head-group and therefore should be a negative curvature promoter, inhibited gA channel function with similar reductions in the lifetimes of the short and long gA channels, indicating a curvature-dominated effect. Monitoring the single-channel conductance, we find that the negatively charged fatty acids increase the conductance by increasing the local negative charge around the channel, whereas the positively charged OAm has no effect. These results suggest that deprotonated fatty acids increase bilayer elasticity by reversibly adsorbing at the bilayer/solution interface.
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Affiliation(s)
- Michael J. Bruno
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA
- Department of Chemistry, Guilford College, Greensboro, NC 27410, USA
| | - Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA
| | - Nicholas J. Gleason
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Roger E. Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA
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48
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Kim T, Lee KI, Morris P, Pastor RW, Andersen OS, Im W. Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers. Biophys J 2012; 102:1551-60. [PMID: 22500755 DOI: 10.1016/j.bpj.2012.03.014] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 02/14/2012] [Accepted: 03/05/2012] [Indexed: 11/19/2022] Open
Abstract
Gramicidin A (gA) is a 15-amino-acid antibiotic peptide with an alternating L-D sequence, which forms (dimeric) bilayer-spanning, monovalent cation channels in biological membranes and synthetic bilayers. We performed molecular dynamics simulations of gA dimers and monomers in all-atom, explicit dilauroylphosphatidylcholine (DLPC), dimyristoylphosphatidylcholine (DMPC), dioleoylphosphatidylcholine (DOPC), and 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayers. The variation in acyl chain length among these different phospholipids provides a way to alter gA-bilayer interactions by varying the bilayer hydrophobic thickness, and to determine the influence of hydrophobic mismatch on the structure and dynamics of both gA channels (and monomeric subunits) and the host bilayers. The simulations show that the channel structure varied little with changes in hydrophobic mismatch, and that the lipid bilayer adapts to the bilayer-spanning channel to minimize the exposure of hydrophobic residues. The bilayer thickness, however, did not vary monotonically as a function of radial distance from the channel. In all simulations, there was an initial decrease in thickness within 4-5 Å from the channel, which was followed by an increase in DOPC and POPC or a further decrease in DLPC and DMPC bilayers. The bilayer thickness varied little in the monomer simulations-except one of three independent simulations for DMPC and all three DLPC simulations, where the bilayer thinned to allow a single subunit to form a bilayer-spanning water-permeable pore. The radial dependence of local lipid area and bilayer compressibility is also nonmonotonic in the first shell around gA dimers due to gA-phospholipid interactions and the hydrophobic mismatch. Order parameters, acyl chain dynamics, and diffusion constants also differ between the lipids in the first shell and the bulk. The lipid behaviors in the first shell around gA dimers are more complex than predicted from a simple mismatch model, which has implications for understanding the energetics of membrane protein-lipid interactions.
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Affiliation(s)
- Taehoon Kim
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, USA
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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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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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