1
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Fan C, Flood E, Sukomon N, Agarwal S, Allen TW, Nimigean CM. Calcium-gated potassium channel blockade via membrane-facing fenestrations. Nat Chem Biol 2024; 20:52-61. [PMID: 37653172 PMCID: PMC10847966 DOI: 10.1038/s41589-023-01406-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
Quaternary ammonium blockers were previously shown to bind in the pore to block both open and closed conformations of large-conductance calcium-activated potassium (BK and MthK) channels. Because blocker entry was assumed through the intracellular entryway (bundle crossing), closed-pore access suggested that the gate was not at the bundle crossing. Structures of closed MthK, a Methanobacterium thermoautotrophicum homolog of BK channels, revealed a tightly constricted intracellular gate, leading us to investigate the membrane-facing fenestrations as alternative pathways for blocker access directly from the membrane. Atomistic free energy simulations showed that intracellular blockers indeed access the pore through the fenestrations, and a mutant channel with narrower fenestrations displayed no closed-state TPeA block at concentrations that blocked the wild-type channel. Apo BK channels display similar fenestrations, suggesting that blockers may use them as access paths into closed channels. Thus, membrane fenestrations represent a non-canonical pathway for selective targeting of specific channel conformations, opening novel ways to selectively drug BK channels.
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Affiliation(s)
- Chen Fan
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria, Australia
- Schrödinger, Inc., New York, NY, USA
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Shubhangi Agarwal
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Victoria, Australia.
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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2
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Lansky S, Betancourt JM, Zhang J, Jiang Y, Kim ED, Paknejad N, Nimigean CM, Yuan P, Scheuring S. A pentameric TRPV3 channel with a dilated pore. Nature 2023; 621:206-214. [PMID: 37648856 PMCID: PMC10584365 DOI: 10.1038/s41586-023-06470-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/21/2023] [Indexed: 09/01/2023]
Abstract
Transient receptor potential (TRP) channels are a large, eukaryotic ion channel superfamily that control diverse physiological functions, and therefore are attractive drug targets1-5. More than 210 structures from more than 20 different TRP channels have been determined, and all are tetramers4. Despite this wealth of structures, many aspects concerning TRPV channels remain poorly understood, including the pore-dilation phenomenon, whereby prolonged activation leads to increased conductance, permeability to large ions and loss of rectification6,7. Here, we used high-speed atomic force microscopy (HS-AFM) to analyse membrane-embedded TRPV3 at the single-molecule level and discovered a pentameric state. HS-AFM dynamic imaging revealed transience and reversibility of the pentamer in dynamic equilibrium with the canonical tetramer through membrane diffusive protomer exchange. The pentamer population increased upon diphenylboronic anhydride (DPBA) addition, an agonist that has been shown to induce TRPV3 pore dilation. On the basis of these findings, we designed a protein production and data analysis pipeline that resulted in a cryogenic-electron microscopy structure of the TRPV3 pentamer, showing an enlarged pore compared to the tetramer. The slow kinetics to enter and exit the pentameric state, the increased pentamer formation upon DPBA addition and the enlarged pore indicate that the pentamer represents the structural correlate of pore dilation. We thus show membrane diffusive protomer exchange as an additional mechanism for structural changes and conformational variability. Overall, we provide structural evidence for a non-canonical pentameric TRP-channel assembly, laying the foundation for new directions in TRP channel research.
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Affiliation(s)
- Shifra Lansky
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - John Michael Betancourt
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Neuroscience Graduate Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Jingying Zhang
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yining Jiang
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Elizabeth D Kim
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Navid Paknejad
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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3
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Pan Y, Pohjolainen E, Schmidpeter PAM, Vaiana AC, Nimigean CM, Grubmüller H, Scheuring S. Discrimination between cyclic nucleotides in a cyclic nucleotide-gated ion channel. Nat Struct Mol Biol 2023; 30:512-520. [PMID: 36973509 DOI: 10.1038/s41594-023-00955-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 02/24/2023] [Indexed: 03/29/2023]
Abstract
Cyclic nucleotide-gated ion channels are crucial in many physiological processes such as vision and pacemaking in the heart. SthK is a prokaryotic homolog with high sequence and structure similarities to hyperpolarization-activated and cyclic nucleotide-modulated and cyclic nucleotide-gated channels, especially at the level of the cyclic nucleotide binding domains (CNBDs). Functional measurements showed that cyclic adenosine monophosphate (cAMP) is a channel activator while cyclic guanosine monophosphate (cGMP) barely leads to pore opening. Here, using atomic force microscopy single-molecule force spectroscopy and force probe molecular dynamics simulations, we unravel quantitatively and at the atomic level how CNBDs discriminate between cyclic nucleotides. We find that cAMP binds to the SthK CNBD slightly stronger than cGMP and accesses a deep-bound state that a cGMP-bound CNBD cannot reach. We propose that the deep binding of cAMP is the discriminatory state that is essential for cAMP-dependent channel activation.
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Affiliation(s)
- Yangang Pan
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Emmi Pohjolainen
- Max Planck Institute for Multidisciplinary Sciences, Theoretical and Computational Biophysics Department, Goettingen, Germany
| | | | - Andrea C Vaiana
- Max Planck Institute for Multidisciplinary Sciences, Theoretical and Computational Biophysics Department, Goettingen, Germany
- Institute of Biophysics, National Research Council, Palermo, Italy
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Helmut Grubmüller
- Max Planck Institute for Multidisciplinary Sciences, Theoretical and Computational Biophysics Department, Goettingen, Germany
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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4
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Schmidpeter PAM, Petroff JT, Khajoueinejad L, Wague A, Frankfater C, Cheng WWL, Nimigean CM, Riegelhaupt PM. Membrane phospholipids control gating of the mechanosensitive potassium leak channel TREK1. Nat Commun 2023; 14:1077. [PMID: 36841877 PMCID: PMC9968290 DOI: 10.1038/s41467-023-36765-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023] Open
Abstract
Tandem pore domain (K2P) potassium channels modulate resting membrane potentials and shape cellular excitability. For the mechanosensitive subfamily of K2Ps, the composition of phospholipids within the bilayer strongly influences channel activity. To examine the molecular details of K2P lipid modulation, we solved cryo-EM structures of the TREK1 K2P channel bound to either the anionic lipid phosphatidic acid (PA) or the zwitterionic lipid phosphatidylethanolamine (PE). At the extracellular face of TREK1, a PA lipid inserts its hydrocarbon tail into a pocket behind the selectivity filter, causing a structural rearrangement that recapitulates mutations and pharmacology known to activate TREK1. At the cytoplasmic face, PA and PE lipids compete to modulate the conformation of the TREK1 TM4 gating helix. Our findings demonstrate two distinct pathways by which anionic lipids enhance TREK1 activity and provide a framework for a model that integrates lipid gating with the effects of other mechanosensitive K2P modulators.
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Affiliation(s)
| | - John T Petroff
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Leila Khajoueinejad
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Aboubacar Wague
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Cheryl Frankfater
- Department of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA
| | - Paul M Riegelhaupt
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
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5
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Kim ED, Falzone ME, Tibbs GR, Ferrer M, Goldstein PA, Nimigean CM. Perturbation of HCN1 response to small molecule modulation. Biophys J 2023; 122:519a-520a. [PMID: 36784681 DOI: 10.1016/j.bpj.2022.11.2761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
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6
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Sukomon N, Fan C, Nimigean CM. Ball-and-Chain Inactivation in Potassium Channels. Annu Rev Biophys 2023; 52:91-111. [PMID: 36626766 DOI: 10.1146/annurev-biophys-100322-072921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Carefully orchestrated opening and closing of ion channels controls the diffusion of ions across cell membranes, generating the electrical signals required for fast transmission of information throughout the nervous system. Inactivation is a parsimonious means for channels to restrict ion conduction without the need to remove the activating stimulus. Voltage-gated channel inactivation plays crucial physiological roles, such as controlling action potential duration and firing frequency in neurons. The ball-and-chain moniker applies to a type of inactivation proposed first for sodium channels and later shown to be a universal mechanism. Still, structural evidence for this mechanism remained elusive until recently. We review the ball-and-chain inactivation research starting from its introduction as a crucial component of sodium conductance during electrical signaling in the classical Hodgkin and Huxley studies, through the discovery of its simple intuitive mechanism in potassium channels during the molecular cloning era, to the eventual elucidation of a potassium channel structure in a ball-and-chain inactivated state. Expected final online publication date for the Annual Review of Biophysics, Volume 52 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York, USA;
| | - Chen Fan
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York, USA;
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York, USA; .,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
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7
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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9
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Pan Y, Schmidpeter P, Pohjolainen E, Vaiana AC, Grubmuller H, Nimigean CM, Scheuring S. Mechanism by which a cyclic-nucleotide gated ion channel discriminates between nucleotides revealed by AFM force spectroscopy and molecular dynamics simulations. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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10
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Schmidpeter P, Wague A, Petroff JT, Cheng WW, Nimigean CM, Riegelhaupt PM. Membrane phospholipids control activity of the mechanosensitive K2P channel TREK1. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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11
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Schmidpeter P, Wu D, Rheinberger J, Riegelhaupt PM, Tang H, Robinson CV, Nimigean CM. Anionic lipids unlock the gate of pacemaker channels. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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12
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Sanganna Gari RR, Montalvo-Acosta JJ, Heath GR, Jiang Y, Gao X, Nimigean CM, Chipot C, Scheuring S. Correlation of membrane protein conformational and functional dynamics. Nat Commun 2021; 12:4363. [PMID: 34272395 PMCID: PMC8285522 DOI: 10.1038/s41467-021-24660-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/28/2021] [Indexed: 11/09/2022] Open
Abstract
Conformational changes in ion channels lead to gating of an ion-conductive pore. Ion flux has been measured with high temporal resolution by single-channel electrophysiology for decades. However, correlation between functional and conformational dynamics remained difficult, lacking experimental techniques to monitor sub-millisecond conformational changes. Here, we use the outer membrane protein G (OmpG) as a model system where loop-6 opens and closes the β-barrel pore like a lid in a pH-dependent manner. Functionally, single-channel electrophysiology shows that while closed states are favored at acidic pH and open states are favored at physiological pH, both states coexist and rapidly interchange in all conditions. Using HS-AFM height spectroscopy (HS-AFM-HS), we monitor sub-millisecond loop-6 conformational dynamics, and compare them to the functional dynamics from single-channel recordings, while MD simulations provide atomistic details and energy landscapes of the pH-dependent loop-6 fluctuations. HS-AFM-HS offers new opportunities to analyze conformational dynamics at timescales of domain and loop fluctuations.
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Affiliation(s)
- Raghavendar Reddy Sanganna Gari
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA.,Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA
| | - Joel José Montalvo-Acosta
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - George R Heath
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA.,Astbury Centre for Structural Molecular Biology, School of Physics & Astronomy, University of Leeds, Leeds, UK
| | - Yining Jiang
- Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA
| | - Xiaolong Gao
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA
| | - Crina M Nimigean
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA.,Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Université de Lorraine, Vandœuvre-lès-Nancy, France. .,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA. .,Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA.
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Kim ED, Nimigean CM. Towards Understanding HCN1 Inhibition by Small Molecules. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.2121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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15
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Tada T, Fan C, Chen JS, Kaur R, Stapleford KA, Gristick H, Dcosta BM, Wilen CB, Nimigean CM, Landau NR. An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. Cell Rep 2020; 33:108528. [PMID: 33326798 PMCID: PMC7705358 DOI: 10.1016/j.celrep.2020.108528] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/26/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022] Open
Abstract
Soluble forms of angiotensin-converting enzyme 2 (ACE2) have recently been shown to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We report on an improved soluble ACE2, termed a "microbody," in which the ACE2 ectodomain is fused to Fc domain 3 of the immunoglobulin (Ig) heavy chain. The protein is smaller than previously described ACE2-Ig Fc fusion proteins and contains an H345A mutation in the ACE2 catalytic active site that inactivates the enzyme without reducing its affinity for the SARS-CoV-2 spike. The disulfide-bonded ACE2 microbody protein inhibits entry of SARS-CoV-2 spike protein pseudotyped virus and replication of live SARS-CoV-2 in vitro and in a mouse model. Its potency is 10-fold higher than soluble ACE2, and it can act after virus bound to the cell. The microbody inhibits the entry of β coronaviruses and virus with the variant D614G spike. The ACE2 microbody may be a valuable therapeutic for coronavirus disease 2019 (COVID-19) that is active against viral variants and future coronaviruses.
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Chen Fan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jennifer S Chen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ramanjit Kaur
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA
| | | | - Harry Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Belinda M Dcosta
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA.
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16
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Wague A, Joseph TT, Woll KA, Bu W, Vaidya KA, Bhanu NV, Garcia BA, Nimigean CM, Eckenhoff RG, Riegelhaupt PM. Mechanistic insights into volatile anesthetic modulation of K2P channels. eLife 2020; 9:59839. [PMID: 33345771 PMCID: PMC7781597 DOI: 10.7554/elife.59839] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/19/2020] [Indexed: 01/01/2023] Open
Abstract
K2P potassium channels are known to be modulated by volatile anesthetic (VA) drugs and play important roles in clinically relevant effects that accompany general anesthesia. Here, we utilize a photoaffinity analog of the VA isoflurane to identify a VA-binding site in the TREK1 K2P channel. The functional importance of the identified site was validated by mutagenesis and biochemical modification. Molecular dynamics simulations of TREK1 in the presence of VA found multiple neighboring residues on TREK1 TM2, TM3, and TM4 that contribute to anesthetic binding. The identified VA-binding region contains residues that play roles in the mechanisms by which heat, mechanical stretch, and pharmacological modulators alter TREK1 channel activity and overlaps with positions found to modulate TASK K2P channel VA sensitivity. Our findings define molecular contacts that mediate VA binding to TREK1 channels and suggest a mechanistic basis to explain how K2P channels are modulated by VAs.
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Affiliation(s)
- Aboubacar Wague
- Department of Anesthesiology, Weill Cornell Medical College, New York City, United States
| | - Thomas T Joseph
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, United States
| | - Kellie A Woll
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, United States
| | - Weiming Bu
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, United States
| | - Kiran A Vaidya
- Department of Anesthesiology, Weill Cornell Medical College, New York City, United States
| | - Natarajan V Bhanu
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York City, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, United States.,Department of Biochemistry, Weill Cornell Medical College, New York City, United States
| | - Roderic G Eckenhoff
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, United States
| | - Paul M Riegelhaupt
- Department of Anesthesiology, Weill Cornell Medical College, New York City, United States
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17
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Schmidpeter PAM, Rheinberger J, Nimigean CM. Prolyl isomerization controls activation kinetics of a cyclic nucleotide-gated ion channel. Nat Commun 2020; 11:6401. [PMID: 33328472 PMCID: PMC7744796 DOI: 10.1038/s41467-020-20104-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/11/2020] [Indexed: 01/21/2023] Open
Abstract
SthK, a cyclic nucleotide-modulated ion channel from Spirochaeta thermophila, activates slowly upon cAMP increase. This is reminiscent of the slow, cAMP-induced activation reported for the hyperpolarization-activated and cyclic nucleotide-gated channel HCN2 in the family of so-called pacemaker channels. Here, we investigate slow cAMP-induced activation in purified SthK channels using stopped-flow assays, mutagenesis, enzymatic catalysis and inhibition assays revealing that the cis/trans conformation of a conserved proline in the cyclic nucleotide-binding domain determines the activation kinetics of SthK. We propose that SthK exists in two forms: trans Pro300 SthK with high ligand binding affinity and fast activation, and cis Pro300 SthK with low affinity and slow activation. Following channel activation, the cis/trans equilibrium, catalyzed by prolyl isomerases, is shifted towards trans, while steady-state channel activity is unaffected. Our results reveal prolyl isomerization as a regulatory mechanism for SthK, and potentially eukaryotic HCN channels. This mechanism could contribute to electrical rhythmicity in cells.
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Affiliation(s)
- Philipp A. M. Schmidpeter
- grid.5386.8000000041936877XWeill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065 USA
| | - Jan Rheinberger
- grid.5386.8000000041936877XWeill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065 USA ,grid.4830.f0000 0004 0407 1981Present Address: University of Groningen, Groningen, Netherlands
| | - Crina M. Nimigean
- grid.5386.8000000041936877XWeill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065 USA ,grid.5386.8000000041936877XWeill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065 USA
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18
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Nimigean CM. Polyamine block of MthK potassium channels. J Gen Physiol 2020; 152:151820. [PMID: 32459330 PMCID: PMC7335008 DOI: 10.1085/jgp.202012614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Crina M. Nimigean
- Departments of Anesthesiology, and Physiology and Biophysics, Weill Cornell Medical College, New York, NY
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19
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Fan C, Sukomon N, Flood E, Rheinberger J, Allen TW, Nimigean CM. Ball-and-chain inactivation in a calcium-gated potassium channel. Nature 2020; 580:288-293. [PMID: 32269335 PMCID: PMC7153497 DOI: 10.1038/s41586-020-2116-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/15/2020] [Indexed: 01/21/2023]
Abstract
Inactivation is the process by which ion channels terminate ion flux through their pores while the opening stimulus is still present1. In neurons, inactivation of both sodium and potassium channels is crucial for the generation of action potentials and regulation of firing frequency1,2. A cytoplasmic domain of either the channel or an accessory subunit is thought to plug the open pore to inactivate the channel via a 'ball-and-chain' mechanism3-7. Here we use cryo-electron microscopy to identify the molecular gating mechanism in calcium-activated potassium channels by obtaining structures of the MthK channel from Methanobacterium thermoautotrophicum-a purely calcium-gated and inactivating channel-in a lipid environment. In the absence of Ca2+, we obtained a single structure in a closed state, which was shown by atomistic simulations to be highly flexible in lipid bilayers at ambient temperature, with large rocking motions of the gating ring and bending of pore-lining helices. In Ca2+-bound conditions, we obtained several structures, including multiple open-inactivated conformations, further indication of a highly dynamic protein. These different channel conformations are distinguished by rocking of the gating rings with respect to the transmembrane region, indicating symmetry breakage across the channel. Furthermore, in all conformations displaying open channel pores, the N terminus of one subunit of the channel tetramer sticks into the pore and plugs it, with free energy simulations showing that this is a strong interaction. Deletion of this N terminus leads to functionally non-inactivating channels and structures of open states without a pore plug, indicating that this previously unresolved N-terminal peptide is responsible for a ball-and-chain inactivation mechanism.
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Affiliation(s)
- Chen Fan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
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20
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Sanganna Gari RR, Heath GR, Nimigean CM, Scheuring S. Correlation of High-Speed AFM and Electrophysiology Measurements to Study Ion Channel Structure-Function Relationships. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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21
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Gao X, Fan C, Nimigean CM. Ligand Binding and Voltage Modulation Open a Cyclic-Nucleotide Gated Ion Channel. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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22
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Schmidpeter PA, Nimigean CM. Native-state Prolyl Isomerization is Involved in the Activation of a CNG Channel. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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23
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Fan C, Sukomon N, Rheinberger J, Nimigean CM. Mechanism of Calcium Gating and Inactivation in a Potassium Channel. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.3161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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24
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Abstract
Integral membrane proteins have historically been challenging targets for biophysical research due to their low solubility in aqueous solution. Their importance for chemical and electrical signaling between cells, however, makes them fascinating targets for investigators interested in the regulation of cellular and physiological processes. Since membrane proteins shunt the barrier imposed by the cell membrane, they also serve as entry points for drugs, adding pharmaceutical research and development to the interests. In recent years, detailed understanding of membrane protein function has significantly increased due to high-resolution structural information obtained from single-particle cryo-EM, X-ray crystallography, and NMR. In order to further advance our mechanistic understanding on membrane proteins as well as foster drug development, it is crucial to generate more biophysical and functional data on these proteins under defined conditions. To that end, different techniques have been developed to stabilize integral membrane proteins in native-like environments that allow both structural and biophysical investigations-amphipols, lipid bicelles, and lipid nanodiscs. In this chapter, we provide detailed protocols for the reconstitution of membrane proteins according to these three techniques. We also outline some of the possible applications of each technique and discuss their advantages and possible caveats.
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Affiliation(s)
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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25
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Tong A, Petroff JT, Hsu FF, Schmidpeter PA, Nimigean CM, Sharp L, Brannigan G, Cheng WW. Direct binding of phosphatidylglycerol at specific sites modulates desensitization of a ligand-gated ion channel. eLife 2019; 8:50766. [PMID: 31724949 PMCID: PMC6855808 DOI: 10.7554/elife.50766] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/09/2019] [Indexed: 12/31/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are essential determinants of synaptic transmission, and are modulated by specific lipids including anionic phospholipids. The exact modulatory effect of anionic phospholipids in pLGICs and the mechanism of this effect are not well understood. Using native mass spectrometry, coarse-grained molecular dynamics simulations and functional assays, we show that the anionic phospholipid, 1-palmitoyl-2-oleoyl phosphatidylglycerol (POPG), preferentially binds to and stabilizes the pLGIC, Erwinia ligand-gated ion channel (ELIC), and decreases ELIC desensitization. Mutations of five arginines located in the interfacial regions of the transmembrane domain (TMD) reduce POPG binding, and a subset of these mutations increase ELIC desensitization. In contrast, a mutation that decreases ELIC desensitization, increases POPG binding. The results support a mechanism by which POPG stabilizes the open state of ELIC relative to the desensitized state by direct binding at specific sites.
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Affiliation(s)
- Ailing Tong
- Department of Anesthesiology, Washington University, Saint Louis, United States
| | - John T Petroff
- Department of Anesthesiology, Washington University, Saint Louis, United States
| | - Fong-Fu Hsu
- Department of Internal Medicine, Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Washington University, Saint Louis, United States
| | | | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, United States
| | - Liam Sharp
- Center for Computational and Integrative Biology, Rutgers University, Camden, United States
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, United States.,Department of Physics, Rutgers University, Camden, United States
| | - Wayland Wl Cheng
- Department of Anesthesiology, Washington University, Saint Louis, United States
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26
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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Rheinberger J, Gao X, Schmidpeter PA, Nimigean CM. Ligand discrimination and gating in cyclic nucleotide-gated ion channels from apo and partial agonist-bound cryo-EM structures. eLife 2018; 7:39775. [PMID: 30028291 PMCID: PMC6093708 DOI: 10.7554/elife.39775] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/19/2018] [Indexed: 12/11/2022] Open
Abstract
Cyclic nucleotide-modulated channels have important roles in visual signal transduction and pacemaking. Binding of cyclic nucleotides (cAMP/cGMP) elicits diverse functional responses in different channels within the family despite their high sequence and structure homology. The molecular mechanisms responsible for ligand discrimination and gating are unknown due to lack of correspondence between structural information and functional states. Using single particle cryo-electron microscopy and single-channel recording, we assigned functional states to high-resolution structures of SthK, a prokaryotic cyclic nucleotide-gated channel. The structures for apo, cAMP-bound, and cGMP-bound SthK in lipid nanodiscs, correspond to no, moderate, and low single-channel activity, respectively, consistent with the observation that all structures are in resting, closed states. The similarity between apo and ligand-bound structures indicates that ligand-binding domains are strongly coupled to pore and SthK gates in an allosteric, concerted fashion. The different orientations of cAMP and cGMP in the ‘resting’ and ‘activated’ structures suggest a mechanism for ligand discrimination. Ion channels are essential for transmitting signals in the nervous system and brain. One large group of ion channels includes members that are activated by cyclic nucleotides, small molecules used to transmit signals within cells. These cyclic nucleotide-gated channels play an important role in regulating our ability to see and smell. The activity of these ion channels has been studied for years, but scientists have only recently been able to look into their structure. Since structural biology methods require purified, well-behaved proteins, the members of this ion channel family selected for structural studies do not necessarily match those whose activity has been well established. There is a need for a good model that would allow both the structure and activity of a cyclic nucleotide-gated ion channel to be characterized. The cyclic nucleotide-gated ion channel, SthK, from bacteria called Spirochaeta thermophila, was identified as such model because both its activity and its structure are accessible. Rheinberger et al. have used cryo electron microscopy to solve several high-resolution structures of SthK channels. In two of the structures, SthK was bound to either one of two types of activating cyclic nucleotides – cAMP or cGMP – and in another structure, no cyclic nucleotides were bound. Separately recording the activity of individual channels allowed the activity states likely to be represented by these structures to be identified. Combining the results of the experiments revealed no activity from channels in an unbound state, low levels of activity for channels bound to cGMP, and moderate activity for channels bound to cAMP. Rheinberger et al. show that the channel, under the conditions experienced in cryo electron microscopy, is closed in all of the states studied. Unexpectedly, the binding of cyclic nucleotides produced no structural change even in the cyclic nucleotide-binding pocket of the channel, a region that was previously observed to undergo such changes when this region alone was crystallized. Rheinberger et al. deduce from this that the four subunits that make up the channel likely undergo the conformational change towards an open state all at once, rather than one by one. The structures and the basic functional characterization of SthK channels provide a strong starting point for future research into determining the entire opening and closing cycle for a cyclic nucleotide-gated channel. Human equivalents of the channel are likely to work in similar ways. The results presented by Rheinberger et al. could therefore be built upon to help address diseases that result from deficiencies in cyclic nucleotide-gated channels, such as loss of vision due to retinal degradation (retinitis pigmentosa or progressive cone dystrophy) and achromatopsia.
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Affiliation(s)
- Jan Rheinberger
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States
| | - Xiaolong Gao
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States
| | | | - Crina M Nimigean
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Department of Biochemistry, Weill Cornell Medical College, New York, United States
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28
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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29
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Gao X, Schmidpeter PA, Nimigean CM. Functional Characterization of the Cyclic Nucleotide-Gated Channel SthK. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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30
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Riegelhaupt PM, Woll KA, Joseph TT, Vaidya KA, Nimigean CM, Eckenhoff RG. Identification of a Modulatory Site of Action for the Volatile Anesthetic Isoflurane in TREK1 Tandem Pore Potassium Channels. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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31
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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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32
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Schmidpeter PAM, Nimigean CM. Fluorescence Titrations to Determine the Binding Affinity of Cyclic Nucleotides to SthK Ion Channels. Bio Protoc 2018; 8:e3041. [PMID: 30417032 DOI: 10.21769/bioprotoc.3041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The cyclic-nucleotide modulated ion channel family includes cyclic nucleotide-gated (CNG) and hyperpolarization-activated and cyclic nucleotide-modulated (HCN) channels, which play essential roles in visual and olfactory signaling and the heart pacemaking activity. Functionally, these channels have been extensively characterized by electrophysiological techniques from protein heterologously expressed in Xenopus oocytes and mammalian cells. On the other hand, expression and purification of these proteins for biophysical and structural analyses in vitro is problematic and expensive and, accordingly, only limited information on the purified channels is available in the literature. Here we describe a protocol for binding studies of fluorescently labeled cyclic nucleotides to a homologue of eukaryotic CNG channels. Furthermore, we describe how to directly probe binding of unlabeled cyclic nucleotides in a competition assay. The use of fluorescence as a sensitive probe for ligand binding reduces the amount of protein needed and enables fast and easy measurements using standard laboratory equipment.
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Affiliation(s)
| | - Crina M Nimigean
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA
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33
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Kowal J, Biyani N, Chami M, Scherer S, Rzepiela AJ, Baumgartner P, Upadhyay V, Nimigean CM, Stahlberg H. High-Resolution Cryoelectron Microscopy Structure of the Cyclic Nucleotide-Modulated Potassium Channel MloK1 in a Lipid Bilayer. Structure 2017; 26:20-27.e3. [PMID: 29249605 DOI: 10.1016/j.str.2017.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 09/16/2017] [Accepted: 11/15/2017] [Indexed: 01/26/2023]
Abstract
Eukaryotic cyclic nucleotide-modulated channels perform their diverse physiological roles by opening and closing their pores to ions in response to cyclic nucleotide binding. We here present a structural model for the cyclic nucleotide-modulated potassium channel homolog from Mesorhizobium loti, MloK1, determined from 2D crystals in the presence of lipids. Even though crystals diffract electrons to only ∼10 Å, using cryoelectron microscopy (cryo-EM) and recently developed computational methods, we have determined a 3D map of full-length MloK1 in the presence of cyclic AMP (cAMP) at ∼4.5 Å isotropic 3D resolution. The structure provides a clear picture of the arrangement of the cyclic nucleotide-binding domains with respect to both the pore and the putative voltage sensor domains when cAMP is bound, and reveals a potential gating mechanism in the context of the lipid-embedded channel.
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Affiliation(s)
- Julia Kowal
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, WRO-1058, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Nikhil Biyani
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, WRO-1058, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, WRO-1058, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Sebastian Scherer
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, WRO-1058, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Andrzej J Rzepiela
- SIB, Biozentrum, University of Basel, Klingelbergstrasse, 4056 Basel, Switzerland
| | - Paul Baumgartner
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, WRO-1058, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Vikrant Upadhyay
- Weill Cornell Medical College, Department of Anesthesiology, Box 124, 525 East 68th Street, Room A-1050, New York, NY 10065, USA
| | - Crina M Nimigean
- Weill Cornell Medical College, Department of Anesthesiology, Box 124, 525 East 68th Street, Room A-1050, New York, NY 10065, USA.
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, WRO-1058, Mattenstrasse 26, 4058 Basel, Switzerland.
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Heer FT, Posson DJ, Wojtas-Niziurski W, Nimigean CM, Bernèche S. Mechanism of activation at the selectivity filter of the KcsA K + channel. eLife 2017; 6:25844. [PMID: 28994652 PMCID: PMC5669632 DOI: 10.7554/elife.25844] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 10/05/2017] [Indexed: 12/26/2022] Open
Abstract
Potassium channels are opened by ligands and/or membrane potential. In voltage-gated K+ channels and the prokaryotic KcsA channel, conduction is believed to result from opening of an intracellular constriction that prevents ion entry into the pore. On the other hand, numerous ligand-gated K+ channels lack such gate, suggesting that they may be activated by a change within the selectivity filter, a narrow region at the extracellular side of the pore. Using molecular dynamics simulations and electrophysiology measurements, we show that ligand-induced conformational changes in the KcsA channel removes steric restraints at the selectivity filter, thus resulting in structural fluctuations, reduced K+ affinity, and increased ion permeation. Such activation of the selectivity filter may be a universal gating mechanism within K+ channels. The occlusion of the pore at the level of the intracellular gate appears to be secondary. Potassium channels are proteins found in almost all living organisms and are vital for many different biological processes. These proteins contain a pore that allows potassium ions to flow through cell membranes, but only when the channel is open. Most channels have a narrowing at the inward side of the pore, which was proposed to form a gate that controls the flow of ions. This gate only opens when the channel activates. Nearer the outward side of the pore is another narrow region called the selectivity filter. This region interacts selectively with potassium ions as they pass through the channel. Not all channels form a tight constriction at the inward end of their pore, yet they still only allow potassium ions to flow through when activated. This suggested that these channels might instead use the selectivity filter as a gate. It would also mean that whilst different potassium channels have similar structures, they do not share a common gating mechanism that controls the flow of ions. Heer et al. studied the bacterial channel called KcsA, which was thought to control the flow of potassium ions via a traditional inward gate. Computer simulations based on this protein’s structure, and experiments with purified KcsA in artificial membranes, showed that the selectivity filter was also involved when KcsA was activated. When the activated channel changed shape, the selectivity filter – which had been constrained by regions forming the pore – could now move and allow potassium ions to flow through the pore. Heer et al. confirmed using a mutant KcsA that the motion of the inward side of the pore upon activation affected the movement of the selectivity filter gate as predicted by the simulation. These findings show that the KcsA channel opens and closes at the selectivity filter. The changes at the inward side of the pore, previously believed to be the gate, firstly enable the selectivity filter to serve as a gate while also forming a secondary gate. Heer et al. propose that most if not all potassium channels may also use this mechanism. These findings illustrate that molecular simulations can be powerful for predicting how changes in the structure of a protein will affect its behavior. This and future studies of other potassium channels will help scientists to better understand the subtle differences between the diverse range of channels found across different organisms.
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Affiliation(s)
- Florian T Heer
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland.,Biozentrum, University of Basel, Basel, Switzerland
| | - David J Posson
- Department of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States
| | - Wojciech Wojtas-Niziurski
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland.,Biozentrum, University of Basel, Basel, Switzerland
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Department of Biochemistry, Weill Cornell Medical College, New York, United States
| | - Simon Bernèche
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland.,Biozentrum, University of Basel, Basel, Switzerland
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35
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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: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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36
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Rangl M, Miyagi A, Kowal J, Stahlberg H, Nimigean CM, Scheuring S. Real-time visualization of conformational changes within single MloK1 cyclic nucleotide-modulated channels. Nat Commun 2016; 7:12789. [PMID: 27647260 PMCID: PMC5034309 DOI: 10.1038/ncomms12789] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/01/2016] [Indexed: 01/11/2023] Open
Abstract
Eukaryotic cyclic nucleotide-modulated (CNM) ion channels perform various physiological roles by opening in response to cyclic nucleotides binding to a specialized cyclic nucleotide-binding domain. Despite progress in structure-function analysis, the conformational rearrangements underlying the gating of these channels are still unknown. Here, we image ligand-induced conformational changes in single CNM channels from Mesorhizobium loti (MloK1) in real-time, using high-speed atomic force microscopy. In the presence of cAMP, most channels are in a stable conformation, but a few molecules dynamically switch back and forth (blink) between at least two conformations with different heights. Upon cAMP depletion, more channels start blinking, with blinking heights increasing over time, suggestive of slow, progressive loss of ligands from the tetramer. We propose that during gating, MloK1 transitions from a set of mobile conformations in the absence to a stable conformation in the presence of ligand and that these conformations are central for gating the pore.
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Affiliation(s)
- Martina Rangl
- INSERM U1006, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, Marseille 13009, France
| | - Atsushi Miyagi
- INSERM U1006, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, Marseille 13009, France
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, Basel CH-4058, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, Basel CH-4058, Switzerland
| | - Crina M Nimigean
- INSERM U1006, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, Marseille 13009, France.,Departments of Anesthesiology, Physiology and Biophysics, and Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Simon Scheuring
- INSERM U1006, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, Marseille 13009, France
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37
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Kim DM, Dikiy I, Upadhyay V, Posson DJ, Eliezer D, Nimigean CM. Conformational heterogeneity in closed and open states of the KcsA potassium channel in lipid bicelles. J Gen Physiol 2016; 148:119-32. [PMID: 27432996 PMCID: PMC4969796 DOI: 10.1085/jgp.201611602] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/27/2016] [Indexed: 12/27/2022] Open
Abstract
The process of ion channel gating-opening and closing-involves local and global structural changes in the channel in response to external stimuli. Conformational changes depend on the energetic landscape that underlies the transition between closed and open states, which plays a key role in ion channel gating. For the prokaryotic, pH-gated potassium channel KcsA, closed and open states have been extensively studied using structural and functional methods, but the dynamics within each of these functional states as well as the transition between them is not as well understood. In this study, we used solution nuclear magnetic resonance (NMR) spectroscopy to investigate the conformational transitions within specific functional states of KcsA. We incorporated KcsA channels into lipid bicelles and stabilized them into a closed state by using either phosphatidylcholine lipids, known to favor the closed channel, or mutations designed to trap the channel shut by disulfide cross-linking. A distinct state, consistent with an open channel, was uncovered by the addition of cardiolipin lipids. Using selective amino acid labeling at locations within the channel that are known to move during gating, we observed at least two different slowly interconverting conformational states for both closed and open channels. The pH dependence of these conformations and the predictable disruptions to this dependence observed in mutant channels with altered pH sensing highlight the importance of conformational heterogeneity for KcsA gating.
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Affiliation(s)
- Dorothy M Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - Igor Dikiy
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065
| | - Vikrant Upadhyay
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - David J Posson
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065 Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY 10065
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065 Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065
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38
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Abstract
Voltage-gated potassium channels play a fundamental role in the generation and propagation of the action potential. The discovery of these channels began with predictions made by early pioneers, and has culminated in their extensive functional and structural characterization by electrophysiological, spectroscopic, and crystallographic studies. With the aid of a variety of crystal structures of these channels, a highly detailed picture emerges of how the voltage-sensing domain reports changes in the membrane electric field and couples this to conformational changes in the activation gate. In addition, high-resolution structural and functional studies of K(+) channel pores, such as KcsA and MthK, offer a comprehensive picture on how selectivity is achieved in K(+) channels. Here, we illustrate the remarkable features of voltage-gated potassium channels and explain the mechanisms used by these machines with experimental data.
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Affiliation(s)
- Dorothy M Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York 10065
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York 10065
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39
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Kowal J, Chami M, Baumgartner P, Arheit M, Chiu PL, Rangl M, Scheuring S, Schröder GF, Nimigean CM, Stahlberg H. Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nat Commun 2015; 5:3106. [PMID: 24469021 PMCID: PMC4086158 DOI: 10.1038/ncomms4106] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/13/2013] [Indexed: 12/25/2022] Open
Abstract
Cyclic nucleotide-modulated ion channels are important for signal transduction and pacemaking in eukaryotes. The molecular determinants of ligand gating in these channels are still unknown, mainly because of a lack of direct structural information. Here we report ligand-induced conformational changes in full-length MloK1, a cyclic nucleotide-modulated potassium channel from the bacterium Mesorhizobium loti, analysed by electron crystallography and atomic force microscopy. Upon cAMP binding, the cyclic nucleotide-binding domains move vertically towards the membrane, and directly contact the S1–S4 voltage sensor domains. This is accompanied by a significant shift and tilt of the voltage sensor domain helices. In both states, the inner pore-lining helices are in an ‘open’ conformation. We propose a mechanism in which ligand binding can favour pore opening via a direct interaction between the cyclic nucleotide-binding domains and voltage sensors. This offers a simple mechanistic hypothesis for the coupling between ligand gating and voltage sensing in eukaryotic HCN channels. The molecular determinants underlying ligand gating of cyclic nucleotide-modulated ion channels remain unclear. Kowal et al. determine the conformational changes underlying cAMP binding to the bacterial channel MloK1, and propose a mechanism for coupling of ligand gating and voltage sensing in eukaryotic HCN channels.
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Affiliation(s)
- Julia Kowal
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Paul Baumgartner
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Marcel Arheit
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | | | - Martina Rangl
- U1006 INSERM, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13009 Marseille, France
| | - Simon Scheuring
- U1006 INSERM, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13009 Marseille, France
| | - Gunnar F Schröder
- 1] Forschungszentrum Jülich, Institute of Complex Systems, ICS-6: Structural Biochemistry, 52425 Jülich, Germany [2] Department of Physics, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Crina M Nimigean
- Departments of Anesthesiology, Physiology and Biophysics, and Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, New York 10065, USA
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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40
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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41
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Posson DJ, Boiteux C, Allen TW, Nimigean CM. Structure and Dynamics of the Mthk K+ Channel Selectivity Filter during Gating. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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42
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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43
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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44
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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 Spectrofluorimetric Assay. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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45
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Posson DJ, Rusinova R, Andersen OS, Nimigean CM. Calcium-Dependent Gating in MthK K+ Channels Occurs at the Selectivity Filter. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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46
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Abstract
The bacterial potassium channel KcsA is gated open by the binding of protons to amino acids on the intracellular side of the channel. We have identified, via channel mutagenesis and x-ray crystallography, two pH-sensing amino acids and a set of nearby residues involved in molecular interactions that influence gating. We found that the minimal mutation of one histidine (H25) and one glutamate (E118) near the cytoplasmic gate completely abolished pH-dependent gating. Mutation of nearby residues either alone or in pairs altered the channel's response to pH. In addition, mutations of certain pairs of residues dramatically increased the energy barriers between the closed and open states. We proposed a Monod-Wyman-Changeux model for proton binding and pH-dependent gating in KcsA, where H25 is a "strong" sensor displaying a large shift in pKa between closed and open states, and E118 is a "weak" pH sensor. Modifying model parameters that are involved in either the intrinsic gating equilibrium or the pKa values of the pH-sensing residues was sufficient to capture the effects of all mutations.
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Affiliation(s)
- David J Posson
- Department of Anesthesiology, 2 Department of Physiology and Biophysics, and 3 Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065
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47
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Affiliation(s)
- Crina M Nimigean
- Department of Anesthesiology, Weill Medical College, Cornell University, New York, NY 10065, USA. crn2002@med.cornell.edu
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48
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Abstract
Discoidal lipoproteins are a novel class of nanoparticles for studying membrane proteins (MPs) in a soluble, native lipid environment, using assays that have not been traditionally applied to transmembrane proteins. Here, we report the successful delivery of an ion channel from these particles, called nanoscale apolipoprotein-bound bilayers (NABBs), to a distinct, continuous lipid bilayer that will allow both ensemble assays, made possible by the soluble NABB platform, and single-molecule assays, to be performed from the same biochemical preparation. We optimized the incorporation and verified the homogeneity of NABBs containing a prototypical potassium channel, KcsA. We also evaluated the transfer of KcsA from the NABBs to lipid bilayers using single-channel electrophysiology and found that the functional properties of the channel remained intact. NABBs containing KcsA were stable, homogeneous, and able to spontaneously deliver the channel to black lipid membranes without measurably affecting the electrical properties of the bilayer. Our results are the first to demonstrate the transfer of a MP from NABBs to a different lipid bilayer without involving vesicle fusion.
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Affiliation(s)
- Sourabh Banerjee
- Department of Anesthesiology and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10021, USA
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McCoy JG, Cheng W, Thompson AN, Nimigean CM, Nichols CG. Mechanism for Selectivity-Inactivation Coupling in KcsA Potassium Channels. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.3277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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50
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Banerjee S, Nimigean CM. Nanoparticles used to Study Allosteric Control of Ion Channels. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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