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Fahanik-Babaei J, Bagheri M, Salari S. Characterization of a novel Ca 2+-Activated potassium channel in rat brain rough endoplasmic reticulum. Arch Biochem Biophys 2024; 759:110105. [PMID: 39059600 DOI: 10.1016/j.abb.2024.110105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 07/28/2024]
Abstract
OBJECTIVES Potassium channels in the endoplasmic reticulum (ER) are crucial for maintaining calcium balance during calcium fluxes. Disruption in ER calcium balance leads to ER stress, implicated in diseases like diabetes and Alzheimer's disease (AD). However, limited data exists on ER potassium channels in excitable tissues such as the brain. To fill this gap, we aimed to evaluate potassium currents in rat brain rough endoplasmic reticulum (RER). METHODS Rats were euthanized under deep anesthesia and their brains were immediately removed. The brains were then homogenized in ice-cold sucrose buffer, followed by the extraction of RER microsomes through a series of centrifugation processes. Purity of sample was evaluated using western blotting technique. Single channel recordings were done in voltage steps from +50 to -60 mV following incorporation of rat brain RER vesicles into planar bilayers. RESULTS We observed a voltage-dependent potassium channel with an approximate conductance of 188 pS. Channel open probability was low at negative voltages, increasing at positive voltages. The channel was blocked by Charybdotoxin but not by Iberiotoxin. Additionally, TRAM-34, a specific KCa3.1 channel blocker, suppressed channel current amplitude and open probability. Western blot analysis revealed specific bands for anti-KCa3.1 antibody, approximately 50 kDa in brain homogenate and RER fraction. CONCLUSION Our study provides strong evidence for the presence of an KCa3.1 channel on the RER membrane in rat brain, exhibiting distinct electro-pharmacological profile compared to plasma membrane and other organelles.
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Affiliation(s)
- Javad Fahanik-Babaei
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Bagheri
- Department of Physiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Sajjad Salari
- Department of Physiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran.
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Eisenhauer K, Weber W, Kemp P, Gebhardt C, Kaufmann M, Tewes N, Zhdanova H, Tietze A, Rauh O, Stein V. Scaling the Functional Nanopore (FuN) Screen: Systematic Evaluation of Self-Assembling Membrane Peptides and Extension with a K +-Responsive Fluorescent Protein Sensor. ACS Synth Biol 2024; 13:1382-1392. [PMID: 38598783 DOI: 10.1021/acssynbio.3c00671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The functional analysis of protein nanopores is typically conducted in planar lipid bilayers or liposomes exploiting high-resolution but low-throughput electrical and optical read-outs. Yet, the reconstitution of protein nanopores in vitro still constitutes an empiric and low-throughput process. Addressing these limitations, nanopores can now be analyzed using the functional nanopore (FuN) screen exploiting genetically encoded fluorescent protein sensors that resolve distinct nanopore-dependent Ca2+ in- and efflux patterns across the inner membrane of Escherichia coli. With a primary proof-of-concept established for the S2168 holin, and thereof based recombinant nanopore assemblies, the question arises to what extent alternative nanopores can be analyzed with the FuN screen and to what extent alternative fluorescent protein sensors can be adapted. Focusing on self-assembling membrane peptides, three sets of 13 different nanopores are assessed for their capacity to form nanopores in the context of the FuN screen. Nanopores tested comprise both natural and computationally designed nanopores. Further, the FuN screen is extended to K+-specific fluorescent protein sensors and now provides a capacity to assess the specificity of a nanopore or ion channel. Finally, a comparison to high-resolution biophysical and electrophysiological studies in planar lipid bilayers provides an experimental benchmark for future studies.
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Affiliation(s)
- Klara Eisenhauer
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Wadim Weber
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Philipp Kemp
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Carolin Gebhardt
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Marwan Kaufmann
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Noel Tewes
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
| | - Hanna Zhdanova
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 412 96 Göteborg, Sweden
| | - Alesia Tietze
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 412 96 Göteborg, Sweden
| | - Oliver Rauh
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
| | - Viktor Stein
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
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Wei C, Pohorille A. Multi-oligomeric states of alamethicin ion channel: Assemblies and conductance. Biophys J 2023; 122:2531-2543. [PMID: 37161094 PMCID: PMC10323028 DOI: 10.1016/j.bpj.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/03/2023] [Accepted: 05/04/2023] [Indexed: 05/11/2023] Open
Abstract
Transmembrane assemblies of the peptaibol alamethicin (ALM) are among the most extensively studied ion channels not only because of their antimicrobial activity but also as models for channel structure and aggregation. In this study, several oligomeric states of ALM are investigated with molecular dynamics simulations to establish properties of the channel and obtain free energy profiles for ion transport and the corresponding values of conductance. The hexamer, heptamer, and octamer of ALM in phospholipid membrane are found to be stable but highly dynamic in barrel-stave structures, with calculated conductance equal to 18, 195, and 1270 pS, respectively, in 1 M KCl ion solution. The corresponding free energy profiles, reported for the first time, are reconstructed from simulations at applied voltage of 200 mV with the aid of the electrodiffusion model both with and without the knowledge of diffusivity. The calculated free energy barriers are equal to 2.5, 1.5, and 0.5 kcal/mol for K+ and 4.0, 2.2, and 1.5 kcal/mol for Cl-, for hexamer, heptamer, and octamer, respectively. The calculated conductance and the ratio between conductance in consecutive states are in good agreement with those measured experimentally. This suggests that the hexamer is the lowest conducting state, with measured conductance equal to 19 pS. The selectivity of K+ over Cl- is calculated as 1.5 and 2.3 for the octameric and heptameric channels, close to the selectivity measured for high-conductance states. Selectivity increases to 13 in the hexameric channel in which the narrowest Gln7 site has a pore radius of only ∼1.6 Å, again in accord with experiment. A good agreement found between calculated and measured conductance through a hexamer templated on cyclodextrin lands additional support for the results of our simulations, and the comparison with ALM reveals the dependence of conductance on the nature of phospholipid membrane.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Moffett Field, California; SETI Institute, Mountain View, California.
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Rauh O, Opper J, Sturm M, Drexler N, Scheub DD, Hansen UP, Thiel G, Schroeder I. Role of ion distribution and energy barriers for concerted motion of subunits in selectivity filter gating of a K+ channel. J Mol Biol 2022; 434:167522. [DOI: 10.1016/j.jmb.2022.167522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/04/2022] [Accepted: 02/28/2022] [Indexed: 11/25/2022]
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Cheng WWL, Arcario MJ, Petroff JT. Druggable Lipid Binding Sites in Pentameric Ligand-Gated Ion Channels and Transient Receptor Potential Channels. Front Physiol 2022; 12:798102. [PMID: 35069257 PMCID: PMC8777383 DOI: 10.3389/fphys.2021.798102] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
Lipids modulate the function of many ion channels, possibly through direct lipid-protein interactions. The recent outpouring of ion channel structures by cryo-EM has revealed many lipid binding sites. Whether these sites mediate lipid modulation of ion channel function is not firmly established in most cases. However, it is intriguing that many of these lipid binding sites are also known sites for other allosteric modulators or drugs, supporting the notion that lipids act as endogenous allosteric modulators through these sites. Here, we review such lipid-drug binding sites, focusing on pentameric ligand-gated ion channels and transient receptor potential channels. Notable examples include sites for phospholipids and sterols that are shared by anesthetics and vanilloids. We discuss some implications of lipid binding at these sites including the possibility that lipids can alter drug potency or that understanding protein-lipid interactions can guide drug design. Structures are only the first step toward understanding the mechanism of lipid modulation at these sites. Looking forward, we identify knowledge gaps in the field and approaches to address them. These include defining the effects of lipids on channel function in reconstituted systems using asymmetric membranes and measuring lipid binding affinities at specific sites using native mass spectrometry, fluorescence binding assays, and computational approaches.
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Affiliation(s)
- Wayland W L Cheng
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
| | - Mark J Arcario
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
| | - John T Petroff
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
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Jin R, He S, Black KA, Clarke OB, Wu D, Bolla JR, Johnson P, Periasamy A, Wardak A, Czabotar P, Colman PM, Robinson CV, Laver D, Smith BJ, Gulbis JM. Ion currents through Kir potassium channels are gated by anionic lipids. Nat Commun 2022; 13:490. [PMID: 35079013 PMCID: PMC8789855 DOI: 10.1038/s41467-022-28148-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
AbstractIon currents through potassium channels are gated. Constriction of the ion conduction pathway at the inner helix bundle, the textbook gate of Kir potassium channels, has been shown to be an ineffective permeation control, creating a rift in our understanding of how these channels are gated. Here we present evidence that anionic lipids act as interactive response elements sufficient to gate potassium conduction. We demonstrate the limiting barrier to K+ permeation lies within the ion conduction pathway and show that this gate is operated by the fatty acyl tails of lipids that infiltrate the conduction pathway via fenestrations in the walls of the pore. Acyl tails occupying a surface groove extending from the cytosolic interface to the conduction pathway provide a potential means of relaying cellular signals, mediated by anionic lipid head groups bound at the canonical lipid binding site, to the internal gate.
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Conti Nibali S, Di Rosa MC, Rauh O, Thiel G, Reina S, De Pinto V. Cell-free electrophysiology of human VDACs incorporated into nanodiscs: An improved method. ACTA ACUST UNITED AC 2021; 1:None. [PMID: 34568862 PMCID: PMC8448298 DOI: 10.1016/j.bpr.2021.100002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/25/2021] [Indexed: 12/15/2022]
Abstract
Voltage-dependent anion-selective channel (VDAC) is one of the main proteins of the outer mitochondrial membrane of all eukaryotes, where it forms aqueous, voltage-sensitive, and ion-selective channels. Its electrophysiological properties have been thoroughly analyzed with the planar lipid bilayer technique. To date, however, available results are based on isolations of VDACs from tissue or from recombinant VDACs produced in bacterial systems. It is well known that the cytosolic overexpression of highly hydrophobic membrane proteins often results in the formation of inclusion bodies containing insoluble aggregates. Purification of properly folded proteins and restoration of their full biological activity requires several procedures that considerably lengthen experimental times. To overcome these restraints, we propose a one-step reaction that combines in vitro cell-free protein expression with nanodisc technology to obtain human VDAC isoforms directly integrated in a native-like lipid bilayer. Reconstitution assays into artificial membranes confirm the reliability of this new methodological approach and provide results comparable to those of VDACs prepared with traditional protein isolation and reconstitution protocols. The use of membrane-mimicking nanodisc systems represents a breakthrough in VDAC electrophysiology and may be adopted to further structural studies.
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Affiliation(s)
- Stefano Conti Nibali
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Maria Carmela Di Rosa
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Oliver Rauh
- Membrane Biophysics and Center for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerhard Thiel
- Membrane Biophysics and Center for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Simona Reina
- Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, Catania, Italy.,we.MitoBiotech.srl, Catania, Italy
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,we.MitoBiotech.srl, Catania, Italy
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Rauh O, Kukovetz K, Winterstein L, Introini B, Thiel G. Combining in vitro translation with nanodisc technology and functional reconstitution of channels in planar lipid bilayers. Methods Enzymol 2021; 652:293-318. [PMID: 34059286 DOI: 10.1016/bs.mie.2021.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Experimental studies on membrane proteins have been recently enriched by two promising method developments: protocols for cell-free protein synthesis and the use of soluble nanoscale lipid bilayers, so called nanodiscs, as membrane mimics for keeping these proteins in a soluble form. Here, we show how the advantages of these techniques can be combined with the classical planar lipid bilayer method for a functional reconstitution of channel activity. The present data demonstrate that the combination of these methods offers a very rapid and reliable way of recording channel activity in different bilayer systems. This approach has additional advantages in that it strongly lowers the propensity of contamination from the expression system and allows the simultaneous reconstitution of thousands of channel proteins for macroscopic current measurements without compromising bilayer stability.
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Affiliation(s)
- Oliver Rauh
- Membrane Biophysics and Center for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Kerri Kukovetz
- Membrane Biophysics and Center for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Laura Winterstein
- Membrane Biophysics and Center for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Bianca Introini
- Department of Biosciences and CNR IBF-Mi, Università degli Studi di Milano, Milano, Italy
| | - Gerhard Thiel
- Membrane Biophysics and Center for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany.
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