1
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Krajewska M, Możajew M, Filipek S, Koprowski P. Interaction of ROMK2 channel with lipid kinases DGKE and AGK: Potential channel activation by localized anionic lipid synthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159443. [PMID: 38056763 DOI: 10.1016/j.bbalip.2023.159443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/20/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
In this study, we utilized enzyme-catalyzed proximity labeling with the engineered promiscuous biotin ligase Turbo-ID to identify the proxisome of the ROMK2 channel. This channel resides in various cellular membrane compartments of the cell including the plasma membrane, endoplasmic reticulum and mitochondria. Within mitochondria, ROMK2 has been suggested as a pore-forming subunit of mitochondrial ATP-regulated potassium channel (mitoKATP). We found that ROMK2 proxisome in addition to previously known protein partners included two lipid kinases: acylglycerol kinase (AGK) and diacylglycerol kinase ε (DGKE), which are localized in mitochondria and the endoplasmic reticulum, respectively. Through co-immunoprecipitation, we confirmed that these two kinases are present in complexes with ROMK2 channels. Additionally, we found that the products of AGK and DGKE, lysophosphatidic acid (LPA) and phosphatidic acid (PA), stimulated the activity of ROMK2 channels in artificial lipid bilayers. Our molecular docking studies revealed the presence of acidic lipid binding sites in the ROMK2 channel, similar to those previously identified in Kir2 channels. Based on these findings, we propose a model wherein localized lipid synthesis, mediated by channel-bound lipid kinases, contributes to the regulation of ROMK2 activity within distinct intracellular compartments, such as mitochondria and the endoplasmic reticulum.
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Affiliation(s)
- Milena Krajewska
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology PAS, Warsaw, Poland
| | - Mariusz Możajew
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology PAS, Warsaw, Poland; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Sławomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Piotr Koprowski
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology PAS, Warsaw, Poland.
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2
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Maksaev G, Bründl-Jirout M, Stary-Weinzinger A, Zangerl-Plessl EM, Lee SJ, Nichols CG. Subunit gating resulting from individual protonation events in Kir2 channels. Nat Commun 2023; 14:4538. [PMID: 37507406 PMCID: PMC10382558 DOI: 10.1038/s41467-023-40058-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Inwardly rectifying potassium (Kir) channels open at the 'helix bundle crossing' (HBC), formed by the M2 helices at the cytoplasmic end of the transmembrane pore. Introduced negative charges at the HBC (G178D) in Kir2.2 channels forces opening, allowing pore wetting and free movement of permeant ions between the cytoplasm and the inner cavity. Single-channel recordings reveal striking, pH-dependent, subconductance behaviors in G178D (or G178E and equivalent Kir2.1[G177E]) mutant channels, with well-resolved non-cooperative subconductance levels. Decreasing cytoplasmic pH shifts the probability towards lower conductance levels. Molecular dynamics simulations show how protonation of Kir2.2[G178D], or the D173 pore-lining residues, changes solvation, K+ ion occupancy, and K+ conductance. Ion channel gating and conductance are classically understood as separate processes. The present data reveal how individual protonation events change the electrostatic microenvironment of the pore, resulting in step-wise alterations of ion pooling, and hence conductance, that appear as 'gated' substates.
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Affiliation(s)
- Grigory Maksaev
- Department of Cell Biology and Physiology, and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael Bründl-Jirout
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Anna Stary-Weinzinger
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Eva-Maria Zangerl-Plessl
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, Vienna, Austria.
| | - Sun-Joo Lee
- Department of Cell Biology and Physiology, and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Colin G Nichols
- Department of Cell Biology and Physiology, and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, USA.
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3
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Krajewska M, Szewczyk A, Kulawiak B, Koprowski P. Pharmacological Characterization of a Recombinant Mitochondrial ROMK2 Potassium Channel Expressed in Bacteria and Reconstituted in Planar Lipid Bilayers. MEMBRANES 2023; 13:360. [PMID: 36984747 PMCID: PMC10052516 DOI: 10.3390/membranes13030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
In the inner mitochondrial membrane, several potassium channels that play a role in cell life and death have been identified. One of these channels is the ATP-regulated potassium channel (mitoKATP). The ROMK2 potassium channel is a potential molecular component of the mitoKATP channel. The current study aimed to investigate the pharmacological modulation of the activity of the ROMK2 potassium channel expressed in Escherichia coli bacteria. ROMK2 was solubilized in polymer nanodiscs and incorporated in planar lipid bilayers. The impact of known mitoKATP channel modulators on the activity of the ROMK2 was characterized. We found that the ROMK2 channel was activated by the mitoKATP channel opener diazoxide and blocked by mitoKATP inhibitors such as ATP/Mg2+, 5-hydroxydecanoic acid, and antidiabetic sulfonylurea glibenclamide. These results indicate that the ROMK2 potassium protein may be a pore-forming subunit of mitoKATP and that the impact of channel modulators is not related to the presence of accessory proteins.
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Affiliation(s)
- Milena Krajewska
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology PAS, 02-093 Warsaw, Poland
- Interdisciplinary Laboratory of Molecular Biology and Biophysics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Adam Szewczyk
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology PAS, 02-093 Warsaw, Poland
| | - Bogusz Kulawiak
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology PAS, 02-093 Warsaw, Poland
| | - Piotr Koprowski
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology PAS, 02-093 Warsaw, Poland
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4
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Maksaev G, Bründl-Jirout M, Stary-Weinzinger A, Zangerl-Plessl EM, Lee SJ, Nichols CG. Subunit gating resulting from individual protonation events in Kir2 channels. RESEARCH SQUARE 2023:rs.3.rs-2640647. [PMID: 36993294 PMCID: PMC10055540 DOI: 10.21203/rs.3.rs-2640647/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Inwardly rectifying potassium (Kir) channels play a critical role in stabilizing the membrane potential, thus controlling numerous physiological phenomena in multiple tissues. Channel conductance is activated by cytoplasmic modulators that open the channel at the 'helix bundle crossing' (HBC), formed by the coming together of the M2 helices from each of the four subunits, at the cytoplasmic end of the transmembrane pore. We introduced a negative charge at the bundle crossing region (G178D) in classical inward rectifier Kir2.2 channel subunits that forces channel opening, allowing pore wetting and free movement of permeant ions between the cytoplasm and the inner cavity. Single-channel recordings reveal a striking pH-dependent subconductance behavior in G178D (or G178E and equivalent Kir2.1[G177E]) mutant channels that reflects individual subunit events. These subconductance levels are well resolved temporally and occur independently, with no evidence of cooperativity. Decreasing cytoplasmic pH shifts the probability towards lower conductance levels, and molecular dynamics simulations show how protonation of Kir2.2[G178D] and, additionally, the rectification controller (D173) pore-lining residues leads to changes in pore solvation, K+ ion occupancy, and ultimately K+ conductance. While subconductance gating has long been discussed, resolution and explanation have been lacking. The present data reveals how individual protonation events change the electrostatic microenvironment of the pore, resulting in distinct, uncoordinated, and relatively long-lasting conductance states, which depend on levels of ion pooling in the pore and the maintenance of pore wetting. Gating and conductance are classically understood as separate processes in ion channels. The remarkable sub-state gating behavior of these channels reveals how intimately connected 'gating' and 'conductance' are in reality.
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Affiliation(s)
- Grigory Maksaev
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael Bründl-Jirout
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Anna Stary-Weinzinger
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Eva-Maria Zangerl-Plessl
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Sun-Joo Lee
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Colin G. Nichols
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
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5
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Lee SJ, Maeda S, Gao J, Nichols CG. Oxidation Driven Reversal of PIP 2-dependent Gating in GIRK2 Channels. FUNCTION 2023; 4:zqad016. [PMID: 37168492 PMCID: PMC10165546 DOI: 10.1093/function/zqad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/24/2023] [Accepted: 04/03/2023] [Indexed: 05/13/2023] Open
Abstract
Physiological activity of G protein gated inward rectifier K+ (GIRK, Kir3) channel, dynamically regulated by three key ligands, phosphoinositol-4,5-bisphosphate (PIP2), Gβγ, and Na+, underlies cellular electrical response to multiple hormones and neurotransmitters in myocytes and neurons. In a reducing environment, matching that inside cells, purified GIRK2 (Kir3.2) channels demonstrate low basal activity, and expected sensitivity to the above ligands. However, under oxidizing conditions, anomalous behavior emerges, including rapid loss of PIP2 and Na+-dependent activation and a high basal activity in the absence of any agonists, that is now paradoxically inhibited by PIP2. Mutagenesis identifies two cysteine residues (C65 and C190) as being responsible for the loss of PIP2 and Na+-dependent activity and the elevated basal activity, respectively. The results explain anomalous findings from earlier studies and illustrate the potential pathophysiologic consequences of oxidation on GIRK channel function, as well as providing insight to reversed ligand-dependence of Kir and KirBac channels.
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Affiliation(s)
| | - Shoji Maeda
- Department of Pharmacology, Medical School, University of Michigan, Ann Arbor, Michigan, USA
| | - Jian Gao
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Colin G Nichols
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
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6
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Jogini V, Jensen MØ, Shaw DE. Gating and modulation of an inward-rectifier potassium channel. J Gen Physiol 2022; 155:213765. [PMID: 36524993 PMCID: PMC9764021 DOI: 10.1085/jgp.202213085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Inward-rectifier potassium channels (Kirs) are lipid-gated ion channels that differ from other K+ channels in that they allow K+ ions to flow more easily into, rather than out of, the cell. Inward rectification is known to result from endogenous magnesium ions or polyamines (e.g., spermine) binding to Kirs, resulting in a block of outward potassium currents, but questions remain regarding the structural and dynamic basis of the rectification process and lipid-dependent channel activation. Here, we present the results of long-timescale molecular dynamics simulations starting from a crystal structure of phosphatidylinositol 4,5-bisphosphate (PIP2)-bound chicken Kir2.2 with a non-conducting pore. After introducing a mutation (G178R) that is known to increase the open probability of a homologous channel, we were able to observe transitions to a stably open, ion-conducting pore, during which key conformational changes occurred in the main activation gate and the cytoplasmic domain. PIP2 binding appeared to increase stability of the pore in its open and conducting state, as PIP2 removal resulted in pore closure, with a median closure time about half of that with PIP2 present. To investigate structural details of inward rectification, we simulated spermine binding to and unbinding from the open pore conformation at positive and negative voltages, respectively, and identified a spermine-binding site located near a previously hypothesized site between the pore cavity and the selectivity filter. We also studied the effects of long-range electrostatics on conduction and spermine binding by mutating charged residues in the cytoplasmic domain and found that a finely tuned charge density, arising from basic and acidic residues within the cytoplasmic domain, modulated conduction and rectification.
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Affiliation(s)
| | | | - David E. Shaw
- D. E. Shaw Research, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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7
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Yekefallah M, Rasberry CA, van Aalst EJ, Browning HP, Amani R, Versteeg DB, Wylie BJ. Mutational Insight into Allosteric Regulation of Kir Channel Activity. ACS OMEGA 2022; 7:43621-43634. [PMID: 36506180 PMCID: PMC9730464 DOI: 10.1021/acsomega.2c04456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/10/2022] [Indexed: 06/08/2023]
Abstract
Potassium (K+) channels are regulated in part by allosteric communication between the helical bundle crossing, or inner gate, and the selectivity filter, or outer gate. This network is triggered by gating stimuli. In concert, there is an allosteric network which is a conjugated set of interactions which correlate long-range structural rearrangements necessary for channel function. Inward-rectifier K+ (Kir) channels favor inward K+ conductance, are ligand-gated, and help establish resting membrane potentials. KirBac1.1 is a bacterial Kir (KirBac) channel homologous to human Kir (hKir) channels. Additionally, KirBac1.1 is gated by the anionic phospholipid ligand phosphatidylglycerol (PG). In this study, we use site-directed mutagenesis to investigate residues involved in the KirBac1.1 gating mechanism and allosteric network we previously proposed using detailed solid-state NMR (SSNMR) measurements. Using fluorescence-based K+ and sodium (Na+) flux assays, we identified channel mutants with impaired function that do not alter selectivity of the channel. In tandem, we performed coarse grain molecular dynamics simulations, observing changes in PG-KirBac1.1 interactions correlated with mutant channel activity and contacts between the two transmembrane helices and pore helix tied to this behavior. Lipid affinity is closely tied to the proximity of two tryptophan residues on neighboring subunits which lure anionic lipids to a cationic pocket formed by a cluster of arginine residues. Thus, these simulations establish a structural and functional basis for the role of each mutated site in the proposed allosteric network. The experimental and simulated data provide insight into key functional residues involved in gating and lipid allostery of K+ channels. Our findings also have direct implications on the physiology of hKir channels due to conservation of many of the residues identified in this work from KirBac1.1.
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8
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Fernandes CAH, Zuniga D, Fagnen C, Kugler V, Scala R, Péhau-Arnaudet G, Wagner R, Perahia D, Bendahhou S, Vénien-Bryan C. Cryo-electron microscopy unveils unique structural features of the human Kir2.1 channel. SCIENCE ADVANCES 2022; 8:eabq8489. [PMID: 36149965 PMCID: PMC9506730 DOI: 10.1126/sciadv.abq8489] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
We present the first structure of the human Kir2.1 channel containing both transmembrane domain (TMD) and cytoplasmic domain (CTD). Kir2.1 channels are strongly inward-rectifying potassium channels that play a key role in maintaining resting membrane potential. Their gating is modulated by phosphatidylinositol 4,5-bisphosphate (PIP2). Genetically inherited defects in Kir2.1 channels are responsible for several rare human diseases, including Andersen's syndrome. The structural analysis (cryo-electron microscopy), surface plasmon resonance, and electrophysiological experiments revealed a well-connected network of interactions between the PIP2-binding site and the G-loop through residues R312 and H221. In addition, molecular dynamics simulations and normal mode analysis showed the intrinsic tendency of the CTD to tether to the TMD and a movement of the secondary anionic binding site to the membrane even without PIP2. Our results revealed structural features unique to human Kir2.1 and provided insights into the connection between G-loop and gating and the pathological mechanisms associated with this channel.
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Affiliation(s)
- Carlos A. H. Fernandes
- UMR 7590, CNRS, Muséum National d’Histoire Naturelle, IRD, Institut de Minéralogie, Physique des Matériaux et de Cosmochimie, IMPMC, Sorbonne Université, 75005 Paris, France
| | - Dania Zuniga
- UMR 7590, CNRS, Muséum National d’Histoire Naturelle, IRD, Institut de Minéralogie, Physique des Matériaux et de Cosmochimie, IMPMC, Sorbonne Université, 75005 Paris, France
| | - Charline Fagnen
- UMR 7590, CNRS, Muséum National d’Histoire Naturelle, IRD, Institut de Minéralogie, Physique des Matériaux et de Cosmochimie, IMPMC, Sorbonne Université, 75005 Paris, France
| | - Valérie Kugler
- IMPReSs Facility, Biotechnology and Cell Signaling UMR 7242, CNRS–University of Strasbourg, Illkirch, Cedex, France
| | - Rosa Scala
- CNRS UMR7370, LP2M, Labex ICST, Faculté de Médecine, Université Côte d’Azur, Nice, France
| | - Gérard Péhau-Arnaudet
- Ultrastructural BioImaging Core Facility/UMR 3528, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Renaud Wagner
- IMPReSs Facility, Biotechnology and Cell Signaling UMR 7242, CNRS–University of Strasbourg, Illkirch, Cedex, France
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, 4 Ave. des Sciences, 91190 Gif-sur-Yvette, France
| | - Saïd Bendahhou
- CNRS UMR7370, LP2M, Labex ICST, Faculté de Médecine, Université Côte d’Azur, Nice, France
| | - Catherine Vénien-Bryan
- UMR 7590, CNRS, Muséum National d’Histoire Naturelle, IRD, Institut de Minéralogie, Physique des Matériaux et de Cosmochimie, IMPMC, Sorbonne Université, 75005 Paris, France
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9
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Kiya T, Takeshita K, Kawanabe A, Fujiwara Y. Intermolecular functional coupling between phosphoinositides and the potassium channel KcsA. J Biol Chem 2022; 298:102257. [PMID: 35839854 PMCID: PMC9396063 DOI: 10.1016/j.jbc.2022.102257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/15/2022] Open
Abstract
Biological membranes are composed of a wide variety of lipids. Phosphoinositides (PIPns) in the membrane inner leaflet only account for a small percentage of the total membrane lipids but modulate the functions of various membrane proteins, including ion channels, which play important roles in cell signaling. KcsA, a prototypical K+ channel that is small, simple, and easy to handle, has been broadly examined regarding its crystallography, in silico molecular analysis, and electrophysiology. It has been reported that KcsA activity is regulated by membrane phospholipids, such as phosphatidylglycerol. However, there has been no quantitative analysis of the correlation between direct lipid binding and the functional modification of KcsA, and it is unknown whether PIPns modulate KcsA function. Here, using contact bubble bilayer recording, we observed that the open probability of KcsA increased significantly (from about 10% to 90%) when the membrane inner leaflet contained only a small percentage of PIPns. In addition, we found an increase in the electrophysiological activity of KcsA correlated with a larger number of negative charges on PIPns. We further analyzed the affinity of the direct interaction between PIPns and KcsA using microscale thermophoresis and observed a strong correlation between direct lipid binding and the functional modification of KcsA. In conclusion, our approach was able to reconstruct the direct modification of KcsA by PIPns, and we propose that it can also be applied to elucidate the mechanism of modification of other ion channels by PIPns.
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Affiliation(s)
- Takunari Kiya
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kagawa 761-0793, Japan
| | - Kohei Takeshita
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Hyogo 679-5148, Japan
| | - Akira Kawanabe
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kagawa 761-0793, Japan.
| | - Yuichiro Fujiwara
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kagawa 761-0793, Japan.
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10
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Claveras Cabezudo A, Feriel Khoualdi A, D’Avanzo N. Computational Prediction of Phosphoinositide Binding to Hyperpolarization-Activated Cyclic-Nucleotide Gated Channels. Front Physiol 2022; 13:859087. [PMID: 35399260 PMCID: PMC8990809 DOI: 10.3389/fphys.2022.859087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/25/2022] [Indexed: 12/31/2022] Open
Abstract
Protein-lipid interactions are key regulators of ion channel function. Numerous ion channels, including hyperpolarization-activated cyclic-nucleotide gated (HCN) channels have been shown to be regulated by phosphoinositides (PIPs), with important implications in cardiac and neuronal function. Specifically, PIPs have been shown to enhance HCN activation. Using computational approaches, we aim to identify potential binding sites for HCN1-PIP interactions. Computational docking and coarse-grained simulations indicate that PIP binding to HCN1 channels is not well coordinated, but rather occurs over a broad surface of charged residues primarily in the HCN-domain, S2 and S3 helices that can be loosely organized in 2 or 3 overlapping clusters. Thus, PIP-HCN1 interactions are more resembling of electrostatic interactions that occur in myristoylated alanine-rich C kinase substrate (MARCKS) proteins, than the specifically coordinated interactions that occur in pleckstrin homology domains (PH domains) or ion channels such as inward rectifier potassium (Kir) channels. Our results also indicate that phosphatidylinositol (PI) interactions with HCN1 are even lower affinity, explaining why unphosphorylated PI have no effect on HCN1 activation unlike phosphorylated PIPs.
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Affiliation(s)
- Ainara Claveras Cabezudo
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada
| | - Asma Feriel Khoualdi
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada
| | - Nazzareno D’Avanzo
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada
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11
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Dietzen NM, Arcario MJ, Chen LJ, Petroff JT, Moreland KT, Krishnan K, Brannigan G, Covey DF, Cheng WW. Polyunsaturated fatty acids inhibit a pentameric ligand-gated ion channel through one of two binding sites. eLife 2022; 11:74306. [PMID: 34982031 PMCID: PMC8786314 DOI: 10.7554/elife.74306] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/31/2021] [Indexed: 01/01/2023] Open
Abstract
Polyunsaturated fatty acids (PUFAs) inhibit pentameric ligand-gated ion channels (pLGICs) but the mechanism of inhibition is not well understood. The PUFA, docosahexaenoic acid (DHA), inhibits agonist responses of the pLGIC, ELIC, more effectively than palmitic acid, similar to the effects observed in the GABAA receptor and nicotinic acetylcholine receptor. Using photo-affinity labeling and coarse-grained molecular dynamics simulations, we identified two fatty acid binding sites in the outer transmembrane domain (TMD) of ELIC. Fatty acid binding to the photolabeled sites is selective for DHA over palmitic acid, and specific for an agonist-bound state. Hexadecyl-methanethiosulfonate modification of one of the two fatty acid binding sites in the outer TMD recapitulates the inhibitory effect of PUFAs in ELIC. The results demonstrate that DHA selectively binds to multiple sites in the outer TMD of ELIC, but that state-dependent binding to a single intrasubunit site mediates DHA inhibition of ELIC.
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Affiliation(s)
- Noah M Dietzen
- Department of Anesthesiology, Washington University in St. Louis, St Louis, United States
| | - Mark J Arcario
- Department of Anesthesiology, Washington University in St. Louis, St Louis, United States
| | - Lawrence J Chen
- Department of Anesthesiology, Washington University in St. Louis, St Louis, United States
| | - John T Petroff
- Department of Anesthesiology, Washington University in St. Louis, St Louis, United States
| | - K Trent Moreland
- Department of Anesthesiology, Washington University in St. Louis, St Louis, United States
| | - Kathiresan Krishnan
- Department of Developmental Biology, Washington University in St. Louis, St Louis, United States
| | - Grace Brannigan
- Center for the Computational and Integrative Biology, Rutgers University, Camden, United States.,Department of Physics, Rutgers University, Camden, United States
| | - Douglas F Covey
- Department of Anesthesiology, Washington University in St. Louis, St Louis, United States.,Department of Developmental Biology, Washington University in St. Louis, St Louis, United States.,Department of Psychiatry, Washington University in St. Louis, St. Louis, United States.,Taylor Institute for Innovative Psychiatric Research, Washington University in St. Louis, St. Louis, United States
| | - Wayland Wl Cheng
- Department of Anesthesiology, Washington University in St. Louis, St Louis, United States
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12
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Insights into the Role of Membrane Lipids in the Structure, Function and Regulation of Integral Membrane Proteins. Int J Mol Sci 2021; 22:ijms22169026. [PMID: 34445730 PMCID: PMC8396450 DOI: 10.3390/ijms22169026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Membrane proteins exist within the highly hydrophobic membranes surrounding cells and organelles, playing key roles in cellular function. It is becoming increasingly clear that the membrane does not just act as an appropriate environment for these proteins, but that the lipids that make up these membranes are essential for membrane protein structure and function. Recent technological advances in cryogenic electron microscopy and in advanced mass spectrometry methods, as well as the development of alternative membrane mimetic systems, have allowed experimental study of membrane protein–lipid complexes. These have been complemented by computational approaches, exploiting the ability of Molecular Dynamics simulations to allow exploration of membrane protein conformational changes in membranes with a defined lipid content. These studies have revealed the importance of lipids in stabilising the oligomeric forms of membrane proteins, mediating protein–protein interactions, maintaining a specific conformational state of a membrane protein and activity. Here we review some of the key recent advances in the field of membrane protein–lipid studies, with major emphasis on respiratory complexes, transporters, channels and G-protein coupled receptors.
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Pipatpolkai T, Quetschlich D, Stansfeld PJ. From Bench to Biomolecular Simulation: Phospholipid Modulation of Potassium Channels. J Mol Biol 2021; 433:167105. [PMID: 34139216 PMCID: PMC8361781 DOI: 10.1016/j.jmb.2021.167105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/05/2022]
Abstract
Potassium (K+) ion channels are crucial in numerous cellular processes as they hyperpolarise a cell through K+ conductance, returning a cell to its resting potential. K+ channel mutations result in multiple clinical complications such as arrhythmia, neonatal diabetes and migraines. Since 1995, the regulation of K+ channels by phospholipids has been heavily studied using a range of interdisciplinary methods such as cellular electrophysiology, structural biology and computational modelling. As a result, K+ channels are model proteins for the analysis of protein-lipid interactions. In this review, we will focus on the roles of lipids in the regulation of K+ channels, and how atomic-level structures, along with experimental techniques and molecular simulations, have helped guide our understanding of the importance of phospholipid interactions.
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Affiliation(s)
- Tanadet Pipatpolkai
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK; Department of Physiology Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PT, UK
| | - Daniel Quetschlich
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK; Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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14
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Kir Channel Molecular Physiology, Pharmacology, and Therapeutic Implications. Handb Exp Pharmacol 2021; 267:277-356. [PMID: 34345939 DOI: 10.1007/164_2021_501] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
For the past two decades several scholarly reviews have appeared on the inwardly rectifying potassium (Kir) channels. We would like to highlight two efforts in particular, which have provided comprehensive reviews of the literature up to 2010 (Hibino et al., Physiol Rev 90(1):291-366, 2010; Stanfield et al., Rev Physiol Biochem Pharmacol 145:47-179, 2002). In the past decade, great insights into the 3-D atomic resolution structures of Kir channels have begun to provide the molecular basis for their functional properties. More recently, computational studies are beginning to close the time domain gap between in silico dynamic and patch-clamp functional studies. The pharmacology of these channels has also been expanding and the dynamic structural studies provide hope that we are heading toward successful structure-based drug design for this family of K+ channels. In the present review we focus on placing the physiology and pharmacology of this K+ channel family in the context of atomic resolution structures and in providing a glimpse of the promising future of therapeutic opportunities.
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15
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Agasid MT, Robinson CV. Probing membrane protein-lipid interactions. Curr Opin Struct Biol 2021; 69:78-85. [PMID: 33930613 DOI: 10.1016/j.sbi.2021.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/08/2021] [Accepted: 03/21/2021] [Indexed: 12/15/2022]
Abstract
Structure determination of membrane proteins has highlighted the many roles played by lipids in influencing overall protein architecture. It is now widely accepted that lipids surrounding membrane proteins play crucial roles by modulating their conformational, structural, and functional properties. Capturing often transient lipid interactions and defining their chemical identity, however, remains challenging. Recent advances in mass spectrometry have resolved questions concerning lipid interactions by providing the molecular composition of intact complexes in association with lipids. Together with other biophysical tools, a picture is emerging of the dynamic nature of lipid-mediated interactions and their effects on conformation, interactions, and signaling.
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Affiliation(s)
- Mark T Agasid
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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16
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Zangerl-Plessl EM, Lee SJ, Maksaev G, Bernsteiner H, Ren F, Yuan P, Stary-Weinzinger A, Nichols CG. Atomistic basis of opening and conduction in mammalian inward rectifier potassium (Kir2.2) channels. J Gen Physiol 2021; 152:jgp.201912422. [PMID: 31744859 PMCID: PMC7034095 DOI: 10.1085/jgp.201912422] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/30/2019] [Indexed: 12/15/2022] Open
Abstract
This paper presents the crystal structure of a forced open inward rectifier Kir2.2 channel. Molecular dynamics reveals the details of ion permeation through the open channel. Potassium ion conduction through open potassium channels is essential to control of membrane potentials in all cells. To elucidate the open conformation and hence the mechanism of K+ ion conduction in the classic inward rectifier Kir2.2, we introduced a negative charge (G178D) at the crossing point of the inner helix bundle, the location of ligand-dependent gating. This “forced open” mutation generated channels that were active even in the complete absence of phosphatidylinositol-4,5-bisphosphate (PIP2), an otherwise essential ligand for Kir channel opening. Crystal structures were obtained at a resolution of 3.6 Å without PIP2 bound, or 2.8 Å in complex with PIP2. The latter revealed a slight widening at the helix bundle crossing (HBC) through backbone movement. MD simulations showed that subsequent spontaneous wetting of the pore through the HBC gate region allowed K+ ion movement across the HBC and conduction through the channel. Further simulations reveal atomistic details of the opening process and highlight the role of pore-lining acidic residues in K+ conduction through Kir2 channels.
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Affiliation(s)
| | - Sun-Joo Lee
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO
| | - Grigory Maksaev
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO
| | - Harald Bernsteiner
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Feifei Ren
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO
| | - Peng Yuan
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO
| | | | - Colin G Nichols
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO
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17
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PIP 2: A critical regulator of vascular ion channels hiding in plain sight. Proc Natl Acad Sci U S A 2020; 117:20378-20389. [PMID: 32764146 PMCID: PMC7456132 DOI: 10.1073/pnas.2006737117] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The phosphoinositide, phosphatidylinositol 4,5-bisphosphate (PIP2), has long been established as a major contributor to intracellular signaling, primarily by virtue of its role as a substrate for phospholipase C (PLC). Signaling by Gq-protein-coupled receptors triggers PLC-mediated hydrolysis of PIP2 into inositol 1,4,5-trisphosphate and diacylglycerol, which are well known to modulate vascular ion channel activity. Often overlooked, however, is the role PIP2 itself plays in this regulation. Although numerous reports have demonstrated that PIP2 is critical for ion channel regulation, how it impacts vascular function has received scant attention. In this review, we focus on PIP2 as a regulator of ion channels in smooth muscle cells and endothelial cells-the two major classes of vascular cells. We further address the concerted effects of such regulation on vascular function and blood flow control. We close with a consideration of current knowledge regarding disruption of PIP2 regulation of vascular ion channels in disease.
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18
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Duncan AL, Corey RA, Sansom MSP. Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channels. Proc Natl Acad Sci U S A 2020. [PMID: 32213593 DOI: 10.5281/zenodo.3634884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Protein-lipid interactions are a key element of the function of many integral membrane proteins. These potential interactions should be considered alongside the complexity and diversity of membrane lipid composition. Inward rectifier potassium channel (Kir) Kir2.2 has multiple interactions with plasma membrane lipids: Phosphatidylinositol (4, 5)-bisphosphate (PIP2) activates the channel; a secondary anionic lipid site has been identified, which augments the activation by PIP2; and cholesterol inhibits the channel. Molecular dynamics simulations are used to characterize in molecular detail the protein-lipid interactions of Kir2.2 in a model of the complex plasma membrane. Kir2.2 has been simulated with multiple, functionally important lipid species. From our simulations we show that PIP2 interacts most tightly at the crystallographic interaction sites, outcompeting other lipid species at this site. Phosphatidylserine (PS) interacts at the previously identified secondary anionic lipid interaction site, in a PIP2 concentration-dependent manner. There is interplay between these anionic lipids: PS interactions are diminished when PIP2 is not present in the membrane, underlining the need to consider multiple lipid species when investigating protein-lipid interactions.
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Affiliation(s)
- Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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19
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Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channels. Proc Natl Acad Sci U S A 2020; 117:7803-7813. [PMID: 32213593 PMCID: PMC7149479 DOI: 10.1073/pnas.1918387117] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ion channels form pores that allow for the selective transport of ions across cell membranes, generating electrical signals in response to a variety of signals. Inward rectifier potassium (Kir) channels in particular are regulated by direct interactions with the complex mixture of lipids that are present in eukaryotic cell membranes. However, the molecular details of these concurrent lipid interactions with Kir channels are not clear and difficult to access via experimental methods. Here, we simulate the Kir2.2 channel in a complex lipid mixture to explore how anionic phospholipids and cholesterol dynamically organize around the membrane protein. In particular we demonstrate a synergy between binding interactions of different anionic phospholipid species which are known to activate Kir channels. Protein–lipid interactions are a key element of the function of many integral membrane proteins. These potential interactions should be considered alongside the complexity and diversity of membrane lipid composition. Inward rectifier potassium channel (Kir) Kir2.2 has multiple interactions with plasma membrane lipids: Phosphatidylinositol (4, 5)-bisphosphate (PIP2) activates the channel; a secondary anionic lipid site has been identified, which augments the activation by PIP2; and cholesterol inhibits the channel. Molecular dynamics simulations are used to characterize in molecular detail the protein–lipid interactions of Kir2.2 in a model of the complex plasma membrane. Kir2.2 has been simulated with multiple, functionally important lipid species. From our simulations we show that PIP2 interacts most tightly at the crystallographic interaction sites, outcompeting other lipid species at this site. Phosphatidylserine (PS) interacts at the previously identified secondary anionic lipid interaction site, in a PIP2 concentration-dependent manner. There is interplay between these anionic lipids: PS interactions are diminished when PIP2 is not present in the membrane, underlining the need to consider multiple lipid species when investigating protein–lipid interactions.
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20
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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: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [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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21
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Corey RA, Vickery ON, Sansom MSP, Stansfeld PJ. Insights into Membrane Protein-Lipid Interactions from Free Energy Calculations. J Chem Theory Comput 2019; 15:5727-5736. [PMID: 31476127 PMCID: PMC6785801 DOI: 10.1021/acs.jctc.9b00548] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Integral membrane proteins are regulated
by specific interactions
with lipids from the surrounding bilayer. The structures of protein–lipid
complexes can be determined through a combination of experimental
and computational approaches, but the energetic basis of these interactions
is difficult to resolve. Molecular dynamics simulations provide the
primary computational technique to estimate the free energies of these
interactions. We demonstrate that the energetics of protein–lipid
interactions may be reliably and reproducibly calculated using three
simulation-based approaches: potential of mean force calculations,
alchemical free energy perturbation, and well-tempered metadynamics.
We employ these techniques within the framework of a coarse-grained
force field and apply them to both bacterial and mammalian membrane
protein–lipid systems. We demonstrate good agreement between
the different techniques, providing a robust framework for their automated
implementation within a pipeline for annotation of newly determined
membrane protein structures.
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Affiliation(s)
- Robin A Corey
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Owen N Vickery
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Mark S P Sansom
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Phillip J Stansfeld
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
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22
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A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca 2+-activated Cl - channel ANO1 (TMEM16A). Proc Natl Acad Sci U S A 2019; 116:19952-19962. [PMID: 31515451 DOI: 10.1073/pnas.1904012116] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
ANO1 (TMEM16A) is a Ca2+-activated Cl- channel that regulates diverse cellular functions including fluid secretion, neuronal excitability, and smooth muscle contraction. ANO1 is activated by elevation of cytosolic Ca2+ and modulated by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. Here, we describe a closely concerted experimental and computational study, including electrophysiology, mutagenesis, functional assays, and extended sampling of lipid-protein interactions with molecular dynamics (MD) to characterize PI(4,5)P2 binding modes and sites on ANO1. ANO1 currents in excised inside-out patches activated by 270 nM Ca2+ at +100 mV are increased by exogenous PI(4,5)P2 with an EC50 = 1.24 µM. The effect of PI(4,5)P2 is dependent on membrane voltage and Ca2+ and is explained by a stabilization of the ANO1 Ca2+-bound open state. Unbiased atomistic MD simulations with 1.4 mol% PI(4,5)P2 in a phosphatidylcholine bilayer identified 8 binding sites with significant probability of binding PI(4,5)P2 Three of these sites captured 85% of all ANO1-PI(4,5)P2 interactions. Mutagenesis of basic amino acids near the membrane-cytosol interface found 3 regions of ANO1 critical for PI(4,5)P2 regulation that correspond to the same 3 sites identified by MD. PI(4,5)P2 is stabilized by hydrogen bonding between amino acid side chains and phosphate/hydroxyl groups on PI(4,5)P2 Binding of PI(4,5)P2 alters the position of the cytoplasmic extension of TM6, which plays a crucial role in ANO1 channel gating, and increases the accessibility of the inner vestibule to Cl- ions. We propose a model consisting of a network of 3 PI(4,5)P2 binding sites at the cytoplasmic face of the membrane allosterically regulating ANO1 channel gating.
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23
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Bernsteiner H, Zangerl-Plessl EM, Chen X, Stary-Weinzinger A. Conduction through a narrow inward-rectifier K + channel pore. J Gen Physiol 2019; 151:1231-1246. [PMID: 31511304 PMCID: PMC6785732 DOI: 10.1085/jgp.201912359] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/25/2019] [Accepted: 08/13/2019] [Indexed: 12/17/2022] Open
Abstract
G-protein–gated inwardly rectifying potassium channels are important mediators of inhibitory neurotransmission. Based on microsecond-scale molecular dynamics simulations, Bernsteiner et al. propose novel gating details that may enable K+ flux via a direct knock-on mechanism. Inwardly rectifying potassium (Kir) channels play a key role in controlling membrane potentials in excitable and unexcitable cells, thereby regulating a plethora of physiological processes. G-protein–gated Kir channels control heart rate and neuronal excitability via small hyperpolarizing outward K+ currents near the resting membrane potential. Despite recent breakthroughs in x-ray crystallography and cryo-EM, the gating and conduction mechanisms of these channels are poorly understood. MD simulations have provided unprecedented details concerning the gating and conduction mechanisms of voltage-gated K+ and Na+ channels. Here, we use multi-microsecond–timescale MD simulations based on the crystal structures of GIRK2 (Kir3.2) bound to phosphatidylinositol-4,5-bisphosphate to provide detailed insights into the channel’s gating dynamics, including insights into the behavior of the G-loop gate. The simulations also elucidate the elementary steps that underlie the movement of K+ ions through an inward-rectifier K+ channel under an applied electric field. Our simulations suggest that K+ permeation might occur via direct knock-on, similar to the mechanism recently shown for Kv channels.
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Affiliation(s)
- Harald Bernsteiner
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | | | - Xingyu Chen
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
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24
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Duncan AL, Song W, Sansom MSP. Lipid-Dependent Regulation of Ion Channels and G Protein-Coupled Receptors: Insights from Structures and Simulations. Annu Rev Pharmacol Toxicol 2019; 60:31-50. [PMID: 31506010 DOI: 10.1146/annurev-pharmtox-010919-023411] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ion channels and G protein-coupled receptors (GPCRs) are regulated by lipids in their membrane environment. Structural studies combined with biophysical and molecular simulation investigations reveal interaction sites for specific lipids on membrane protein structures. For K channels, PIP2 plays a key role in regulating Kv and Kir channels. Likewise, several recent cryo-EM structures of TRP channels have revealed bound lipids, including PIP2 and cholesterol. Among the pentameric ligand-gated ion channel family, structural and biophysical studies suggest the M4 TM helix may act as a lipid sensor, e.g., forming part of the binding sites for neurosteroids on the GABAA receptor. Structures of GPCRs have revealed multiple cholesterol sites, which may modulate both receptor dynamics and receptor oligomerization. PIP2 also interacts with GPCRs and may modulate their interactions with G proteins. Overall, it is evident that multiple lipid binding sites exist on channels and receptors that modulate their function allosterically and are potential druggable sites.
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Affiliation(s)
- Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
| | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
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25
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Robinson CV, Rohacs T, Hansen SB. Tools for Understanding Nanoscale Lipid Regulation of Ion Channels. Trends Biochem Sci 2019; 44:795-806. [PMID: 31060927 PMCID: PMC6729126 DOI: 10.1016/j.tibs.2019.04.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/23/2019] [Accepted: 04/01/2019] [Indexed: 11/17/2022]
Abstract
Anionic phospholipids are minor but prominent components of the plasma membrane that are necessary for ion channel function. Their persistence in bulk membranes, in particular phosphatidylinositol 4,5-bisphosphate (PIP2), initially suggested they act as channel cofactors. However, recent technologies have established an emerging system of nanoscale signaling to ion channels based on lipid compartmentalization (clustering), direct lipid binding, and local lipid dynamics that allow cells to harness lipid heterogeneity to gate ion channels. The new tools to study lipid binding are set to transform our view of the membrane and answer important questions surrounding ion channel-delimited processes such as mechanosensation.
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Affiliation(s)
- Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Tibor Rohacs
- Department of Pharmacology, Physiology and Neuroscience, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Scott B Hansen
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA.
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26
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Qile M, Ji Y, Houtman MJC, Veldhuis M, Romunde F, Kok B, van der Heyden MAG. Identification of a PEST Sequence in Vertebrate K IR2.1 That Modifies Rectification. Front Physiol 2019; 10:863. [PMID: 31333502 PMCID: PMC6624654 DOI: 10.3389/fphys.2019.00863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/20/2019] [Indexed: 11/13/2022] Open
Abstract
KIR2.1 potassium channels, producing inward rectifier potassium current (IK1), are important for final action potential repolarization and a stable resting membrane potential in excitable cells like cardiomyocytes. Abnormal KIR2.1 function, either decreased or increased, associates with diseases such as Andersen-Tawil syndrome, long and short QT syndromes. KIR2.1 ion channel protein trafficking and subcellular anchoring depends on intrinsic specific short amino acid sequences. We hypothesized that combining an evolutionary based sequence comparison and bioinformatics will identify new functional domains within the C-terminus of the KIR2.1 protein, which function could be determined by mutation analysis. We determined PEST domain signatures, rich in proline (P), glutamic acid (E), serine (S), and threonine (T), within KIR2.1 sequences using the “epestfind” webtool. WT and ΔPEST KIR2.1 channels were expressed in HEK293T and COS-7 cells. Patch-clamp electrophysiology measurements were performed in the inside-out mode on excised membrane patches and the whole cell mode using AxonPatch 200B amplifiers. KIR2.1 protein expression levels were determined by western blot analysis. Immunofluorescence microscopy was used to determine KIR2.1 subcellular localization. An evolutionary conserved PEST domain was identified in the C-terminus of the KIR2.1 channel protein displaying positive PEST scores in vertebrates ranging from fish to human. No similar PEST domain was detected in KIR2.2, KIR2.3, and KIR2.6 proteins. Deletion of the PEST domain in California kingsnake and human KIR2.1 proteins (ΔPEST), did not affect plasma membrane localization. Co-expression of WT and ΔPEST KIR2.1 proteins resulted in heterotetrameric channel formation. Deletion of the PEST domain did not increase protein stability in cycloheximide assays [T½ from 2.64 h (WT) to 1.67 h (ΔPEST), n.s.]. WT and ΔPEST channels, either from human or snake, produced typical IK1, however, human ΔPEST channels displayed stronger intrinsic rectification. The current observations suggest that the PEST sequence of KIR2.1 is not associated with rapid protein degradation, and has a role in the rectification behavior of IK1 channels.
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Affiliation(s)
- Muge Qile
- Department of Medical Physiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
| | - Yuan Ji
- Department of Medical Physiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marien J C Houtman
- Department of Medical Physiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marlieke Veldhuis
- Department of Medical Physiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
| | - Fee Romunde
- Department of Medical Physiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
| | - Bart Kok
- Department of Medical Physiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marcel A G van der Heyden
- Department of Medical Physiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
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27
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Liu Y, LoCaste CE, Liu W, Poltash ML, Russell DH, Laganowsky A. Selective binding of a toxin and phosphatidylinositides to a mammalian potassium channel. Nat Commun 2019; 10:1352. [PMID: 30902995 PMCID: PMC6430785 DOI: 10.1038/s41467-019-09333-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 03/05/2019] [Indexed: 02/05/2023] Open
Abstract
G-protein-gated inward rectifying potassium channels (GIRKs) require Gβγ subunits and phosphorylated phosphatidylinositides (PIPs) for gating. Although studies have provided insight into these interactions, the mechanism of how these events are modulated by Gβγ and the binding affinity between PIPs and GIRKs remains poorly understood. Here, native ion mobility mass spectrometry is employed to directly monitor small molecule binding events to mouse GIRK2. GIRK2 binds the toxin tertiapin Q and PIPs selectively and with significantly higher affinity than other phospholipids. A mutation in GIRK2 that causes a rotation in the cytoplasmic domain, similarly to Gβγ-binding to the wild-type channel, revealed differences in the selectivity towards PIPs. More specifically, PIP isoforms known to weakly activate GIRKs have decreased binding affinity. Taken together, our results reveal selective small molecule binding and uncover a mechanism by which rotation of the cytoplasmic domain can modulate GIRK•PIP interactions.
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Affiliation(s)
- Yang Liu
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, 77030, USA
| | - Catherine E LoCaste
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
| | - Wen Liu
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, 77030, USA
| | - Michael L Poltash
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA.
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28
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Chung HW, Petersen EN, Cabanos C, Murphy KR, Pavel MA, Hansen AS, Ja WW, Hansen SB. A Molecular Target for an Alcohol Chain-Length Cutoff. J Mol Biol 2019; 431:196-209. [PMID: 30529033 PMCID: PMC6360937 DOI: 10.1016/j.jmb.2018.11.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 11/23/2022]
Abstract
Despite the widespread consumption of ethanol, mechanisms underlying its anesthetic effects remain uncertain. n-Alcohols induce anesthesia up to a specific chain length and then lose potency-an observation known as the "chain-length cutoff effect." This cutoff effect is thought to be mediated by alcohol binding sites on proteins such as ion channels, but where these sites are for long-chain alcohols and how they mediate a cutoff remain poorly defined. In animals, the enzyme phospholipase D (PLD) has been shown to generate alcohol metabolites (e.g., phosphatidylethanol) with a cutoff, but no phenotype has been shown connecting PLD to an anesthetic effect. Here we show loss of PLD blocks ethanol-mediated hyperactivity in Drosophila melanogaster (fruit fly), demonstrating that PLD mediates behavioral responses to alcohol in vivo. Furthermore, the metabolite phosphatidylethanol directly competes for the endogenous PLD product phosphatidic acid at lipid-binding sites within potassium channels [e.g., TWIK-related K+ channel type 1 (K2P2.1, TREK-1)]. This gives rise to a PLD-dependent cutoff in TREK-1. We propose an alcohol pathway where PLD produces lipid-alcohol metabolites that bind to and regulate downstream effector molecules including lipid-regulated potassium channels.
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Affiliation(s)
- Hae-Won Chung
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - E Nicholas Petersen
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Cerrone Cabanos
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Keith R Murphy
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA; Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA; Program in Integrative Biology and Neuroscience, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Mahmud Arif Pavel
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Andrew S Hansen
- HBBiotech, BioInnovations Gateway, Salt Lake City, UT 84115, USA
| | - William W Ja
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA; Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Scott B Hansen
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA.
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29
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Coyote-Maestas W, He Y, Myers CL, Schmidt D. Domain insertion permissibility-guided engineering of allostery in ion channels. Nat Commun 2019; 10:290. [PMID: 30655517 PMCID: PMC6336875 DOI: 10.1038/s41467-018-08171-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/17/2018] [Indexed: 01/01/2023] Open
Abstract
Allostery is a fundamental principle of protein regulation that remains hard to engineer, particularly in membrane proteins such as ion channels. Here we use human Inward Rectifier K+ Channel Kir2.1 to map site-specific permissibility to the insertion of domains with different biophysical properties. We find that permissibility is best explained by dynamic protein properties, such as conformational flexibility. Several regions in Kir2.1 that are equivalent to those regulated in homologs, such as G-protein-gated inward rectifier K+ channels (GIRK), have differential permissibility; that is, for these sites permissibility depends on the structural properties of the inserted domain. Our data and the well-established link between protein dynamics and allostery led us to propose that differential permissibility is a metric of latent allosteric capacity in Kir2.1. In support of this notion, inserting light-switchable domains into sites with predicted latent allosteric capacity renders Kir2.1 activity sensitive to light. Allostery is a fundamental principle of protein regulation that remains challenging to engineer. Here authors screen human Inward Rectifier K + Channel Kir2.1 for permissibility to domain insertions and propose that differential permissibility is a metric of latent allosteric capacity in Kir2.1.
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Affiliation(s)
- Willow Coyote-Maestas
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, 55455, MN, USA
| | - Yungui He
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, 55455, MN, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, 55455, MN, USA
| | - Daniel Schmidt
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, 55455, MN, USA.
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30
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Meng XY, Kang SG, Zhou R. Molecular mechanism of phosphoinositides' specificity for the inwardly rectifying potassium channel Kir2.2. Chem Sci 2018; 9:8352-8362. [PMID: 30542582 PMCID: PMC6247517 DOI: 10.1039/c8sc01284a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/04/2018] [Indexed: 12/04/2022] Open
Abstract
We investigated the binding mechanism of PI(4,5)P2 and variants on the inwardly rectifying potassium channel, Kir2.2. Our results not only demonstrated the molecular origin for their binding specificity, but also revealed the major driving forces.
Phosphoinositides are essential signaling lipids that play a critical role in regulating ion channels, and their dysregulation often results in fatal diseases including cardiac arrhythmia and paralysis. Despite decades of intensive research, the underlying molecular mechanism of lipid agonism and specificity remains largely unknown. Here, we present a systematic study of the binding mechanism and specificity of a native agonist, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and two of its variants, PI(3,4)P2 and PI(3,4,5)P3, on inwardly rectifying potassium channel Kir2.2, using molecular dynamics simulations and free energy perturbations (FEPs). Our results demonstrate that the major driving force for the PI(4,5)P2 specificity on Kir2.2 comes from the highly organized salt-bridge network formed between the charged inositol head and phosphodiester linker of PI(4,5)P2. The unsaturated arachidonic chain is also shown to contribute to the stable binding through hydrophobic interactions with nearby Kir2.2 hydrophobic residues. Consistent with previous experimental findings, our FEP results confirmed that non-native ligands, PI(3,4)P2 and PI(3,4,5)P3, show significant loss in binding affinity as a result of the substantial shift from the native binding mode and unfavorable local solvation environment. However, surprisingly, the underlying molecular pictures for the unfavorable binding of both ligands are quite distinctive: for PI(3,4)P2, it is due to a direct destabilization in the bound state, whereas for PI(3,4,5)P3, it is due to a relative stabilization in its free state. Our findings not only provide a theoretical basis for the ligand specificity, but also generate new insights into the allosteric modulation of ligand-gated ion channels.
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Affiliation(s)
- Xuan-Yu Meng
- State Key Laboratory of Radiation Medicine and Protection , School for Radiological and Interdisciplinary Sciences (RAD-X) , Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Seung-Gu Kang
- IBM Thomas J. Watson Research Center , Yorktown Heights , NY 10598 , USA .
| | - Ruhong Zhou
- State Key Laboratory of Radiation Medicine and Protection , School for Radiological and Interdisciplinary Sciences (RAD-X) , Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China.,IBM Thomas J. Watson Research Center , Yorktown Heights , NY 10598 , USA . .,Department of Chemistry , Columbia University , New York , NY 10027 , USA
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31
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Cabanos C, Wang M, Han X, Hansen SB. A Soluble Fluorescent Binding Assay Reveals PIP 2 Antagonism of TREK-1 Channels. Cell Rep 2018; 20:1287-1294. [PMID: 28793254 PMCID: PMC5586213 DOI: 10.1016/j.celrep.2017.07.034] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/12/2017] [Accepted: 07/13/2017] [Indexed: 12/19/2022] Open
Abstract
Lipid regulation of ion channels by low-abundance signaling lipids phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidic acid (PA) has emerged as a central cellular mechanism for controlling ion channels and the excitability of nerves. A lack of robust assays suitable for facile detection of a lipid bound to a channel has hampered the probing of the lipid binding sites and measuring the pharmacology of putative lipid agonists for ion channels. Here, we show a fluorescent PIP2 competition assay for detergent-purified potassium channels, including TWIK-1-related K+-channel (TREK-1). Anionic lipids PA and phosphatidylglycerol (PG) bind dose dependently (9.1 and 96 mM, respectively) and agonize the channel. Our assay shows PIP2 binds with high affinity (0.87 mM) but surprisingly can directly antagonize TREK-1 in liposomes. We propose a model for TREK-1 lipid regulation where PIP2 can compete with PA and PG agonism based on the affinity of the lipid for a site within the channel.
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Affiliation(s)
- Cerrone Cabanos
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Miao Wang
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA
| | - Xianlin Han
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA
| | - Scott B Hansen
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA.
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32
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Duncan AL, Reddy T, Koldsø H, Hélie J, Fowler PW, Chavent M, Sansom MSP. Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes. Sci Rep 2017; 7:16647. [PMID: 29192147 PMCID: PMC5709381 DOI: 10.1038/s41598-017-16865-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/15/2017] [Indexed: 01/07/2023] Open
Abstract
Cell membranes are crowded and complex environments. To investigate the effect of protein-lipid interactions on dynamic organization in mammalian cell membranes, we have performed coarse-grained molecular dynamics simulations containing >100 copies of an inwardly rectifying potassium (Kir) channel which forms specific interactions with the regulatory lipid phosphatidylinositol 4,5-bisphosphate (PIP2). The tendency of protein molecules to cluster has the effect of organizing the membrane into dynamic compartments. At the same time, the diversity of lipids present has a marked effect on the clustering behavior of ion channels. Sub-diffusion of proteins and lipids is observed. Protein crowding alters the sub-diffusive behavior of proteins and lipids such as PIP2 which interact tightly with Kir channels. Protein crowding also affects bilayer properties, such as membrane undulations and bending rigidity, in a PIP2-dependent manner. This interplay between the diffusion and the dynamic organization of Kir channels may have important implications for channel function.
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Affiliation(s)
- Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Tyler Reddy
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- T-6, MS K710, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- D. E. Shaw Research, 120 W 45th St., New York, NY, 10036, USA
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Semmle, Blue Boar Court, 9 Alfred St, Oxford, OX1 4EH, UK
| | - Philip W Fowler
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- IPBS-CNRS, Toulouse, Midi-Pyrénées, France
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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33
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Smrt ST, Draney AW, Singaram I, Lorieau JL. Structure and Dynamics of Membrane Proteins and Membrane Associated Proteins with Native Bicelles from Eukaryotic Tissues. Biochemistry 2017; 56:5318-5327. [PMID: 28915027 DOI: 10.1021/acs.biochem.7b00575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Sean T. Smrt
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Adrian W. Draney
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Indira Singaram
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Justin L. Lorieau
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
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34
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Lacin E, Aryal P, Glaaser IW, Bodhinathan K, Tsai E, Marsh N, Tucker SJ, Sansom MSP, Slesinger PA. Dynamic role of the tether helix in PIP 2-dependent gating of a G protein-gated potassium channel. J Gen Physiol 2017; 149:799-811. [PMID: 28720589 PMCID: PMC5560777 DOI: 10.1085/jgp.201711801] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/06/2017] [Accepted: 06/21/2017] [Indexed: 01/21/2023] Open
Abstract
G protein–gated inwardly rectifying potassium (GIRK) channels are activated by the phospholipid phosphatidylinositol 4,5 bisphosphate (PIP2). Using functional and computational experiments, Lacin et al. reveal that PIP2 interacts with the tether helix of the neuronal GIRK channel in a dynamic way. G protein–gated inwardly rectifying potassium (GIRK) channels control neuronal excitability in the brain and are implicated in several different neurological diseases. The anionic phospholipid phosphatidylinositol 4,5 bisphosphate (PIP2) is an essential cofactor for GIRK channel gating, but the precise mechanism by which PIP2 opens GIRK channels remains poorly understood. Previous structural studies have revealed several highly conserved, positively charged residues in the “tether helix” (C-linker) that interact with the negatively charged PIP2. However, these crystal structures of neuronal GIRK channels in complex with PIP2 provide only snapshots of PIP2’s interaction with the channel and thus lack details about the gating transitions triggered by PIP2 binding. Here, our functional studies reveal that one of these conserved basic residues in GIRK2, Lys200 (6′K), supports a complex and dynamic interaction with PIP2. When Lys200 is mutated to an uncharged amino acid, it activates the channel by enhancing the interaction with PIP2. Atomistic molecular dynamic simulations of neuronal GIRK2 with the same 6′ substitution reveal an open GIRK2 channel with PIP2 molecules adopting novel positions. This dynamic interaction with PIP2 may explain the intrinsic low open probability of GIRK channels and the mechanism underlying activation by G protein Gβγ subunits and ethanol.
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Affiliation(s)
- Emre Lacin
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Prafulla Aryal
- Department of Biochemistry, University of Oxford, Oxford, England, UK.,OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, England, UK
| | - Ian W Glaaser
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Eric Tsai
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nidaa Marsh
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Stephen J Tucker
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, England, UK.,Department of Physics, University of Oxford, Oxford, England, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, England, UK.,OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, England, UK
| | - Paul A Slesinger
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY
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35
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Principalli MA, Lemel L, Rongier A, Godet AC, Langer K, Revilloud J, Darré L, Domene C, Vivaudou M, Moreau CJ. Functional mapping of the N-terminal arginine cluster and C-terminal acidic residues of Kir6.2 channel fused to a G protein-coupled receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2144-2153. [PMID: 28757124 DOI: 10.1016/j.bbamem.2017.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/06/2017] [Accepted: 07/26/2017] [Indexed: 10/19/2022]
Abstract
Ion channel-coupled receptors (ICCRs) are original man-made ligand-gated ion channels created by fusion of G protein-coupled receptors (GPCRs) to the inward-rectifier potassium channel Kir6.2. GPCR conformational changes induced by ligand binding are transduced into electrical current by the ion channel. This functional coupling is closely related to the length of the linker region formed by the GPCR C-terminus (C-ter) and Kir6.2N-terminus (N-ter). Manipulating the GPCR C-ter length allows to finely tune the channel regulation, both in amplitude and sign (opening or closing Kir6.2). In this work, we demonstrate that the primary sequence of the channel N-terminal domain is an additional parameter for the functional coupling with GPCRs. As for all Kir channels, a cluster of basic residues is present in the N-terminal domain of Kir6.2 and is composed of 5 arginines which are proximal to the GPCR C-ter in the fusion proteins. Using a functional mapping approach, we demonstrate the role of specific arginines (R27 and R32) for the function of ICCRs, indicating that the position and not the cluster of positively-charged arginines is critical for the channel regulation by the GPCR. Following observations provided by molecular dynamics simulation, we explore the hypothesis of interaction of these arginines with acidic residues, and using site-directed mutagenesis, we identified aspartate D307 and glutamate E308 residues as critical for the function of ICCRs. These results demonstrate the critical role of the N-terminal and C-terminal charged residues of Kir6.2 for its allosteric regulation by the fused GPCR.
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Affiliation(s)
- Maria A Principalli
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Laura Lemel
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Anaëlle Rongier
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Anne-Claire Godet
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Karla Langer
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Jean Revilloud
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Leonardo Darré
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Carmen Domene
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Michel Vivaudou
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Christophe J Moreau
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France.
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36
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Borschel WF, Wang S, Lee S, Nichols CG. Control of Kir channel gating by cytoplasmic domain interface interactions. J Gen Physiol 2017; 149:561-576. [PMID: 28389584 PMCID: PMC5412532 DOI: 10.1085/jgp.201611719] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/29/2016] [Accepted: 03/01/2017] [Indexed: 12/19/2022] Open
Abstract
The pore-forming unit of ATP-sensitive K channels is composed of four Kir6.2 subunits. Borschel et al. show that salt bridges between the cytoplasmic domain of adjacent Kir6.2 subunits determine the degree to which channels inactivate after removal of ATP. Inward rectifier potassium (Kir) channels are expressed in almost all mammalian tissues and play critical roles in the control of excitability. Pancreatic ATP-sensitive K (KATP) channels are key regulators of insulin secretion and comprise Kir6.2 subunits coupled to sulfonylurea receptors. Because these channels are reversibly inhibited by cytoplasmic ATP, they link cellular metabolism with membrane excitability. Loss-of-function mutations in the pore-forming Kir6.2 subunit cause congenital hyperinsulinism as a result of diminished channel activity. Here, we show that several disease mutations, which disrupt intersubunit salt bridges at the interface of the cytoplasmic domains (CD-I) of adjacent subunits, induce loss of channel activity via a novel channel behavior: after ATP removal, channels open but then rapidly inactivate. Re-exposure to inhibitory ATP causes recovery from this inactivation. Inactivation can be abolished by application of phosphatidylinositol-4,5-bisphosphate (PIP2) to the cytoplasmic face of the membrane, an effect that can be explained by a simple kinetic model in which PIP2 binding competes with the inactivation process. Kir2.1 channels contain homologous salt bridges, and we find that mutations that disrupt CD-I interactions in Kir2.1 also reduce channel activity and PIP2 sensitivity. Kir2.1 channels also contain an additional CD-I salt bridge that is not present in Kir6.2 channels. Introduction of this salt bridge into Kir6.2 partially rescues inactivating mutants from the phenotype. These results indicate that the stability of the intersubunit CD-I is a major determinant of the inactivation process in Kir6.2 and may control gating in other Kir channels.
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Affiliation(s)
- William F Borschel
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Shizhen Wang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Sunjoo Lee
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Colin G Nichols
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 .,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
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37
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Enhancing biopharmaceutical attributes of phospholipid complex-loaded nanostructured lipidic carriers of mangiferin: Systematic development, characterization and evaluation. Int J Pharm 2017; 518:289-306. [DOI: 10.1016/j.ijpharm.2016.12.044] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/14/2016] [Accepted: 12/17/2016] [Indexed: 12/12/2022]
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38
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Grandi E, Sanguinetti MC, Bartos DC, Bers DM, Chen-Izu Y, Chiamvimonvat N, Colecraft HM, Delisle BP, Heijman J, Navedo MF, Noskov S, Proenza C, Vandenberg JI, Yarov-Yarovoy V. Potassium channels in the heart: structure, function and regulation. J Physiol 2016; 595:2209-2228. [PMID: 27861921 DOI: 10.1113/jp272864] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 07/18/2016] [Indexed: 12/22/2022] Open
Abstract
This paper is the outcome of the fourth UC Davis Systems Approach to Understanding Cardiac Excitation-Contraction Coupling and Arrhythmias Symposium, a biannual event that aims to bring together leading experts in subfields of cardiovascular biomedicine to focus on topics of importance to the field. The theme of the 2016 symposium was 'K+ Channels and Regulation'. Experts in the field contributed their experimental and mathematical modelling perspectives and discussed emerging questions, controversies and challenges on the topic of cardiac K+ channels. This paper summarizes the topics of formal presentations and informal discussions from the symposium on the structural basis of voltage-gated K+ channel function, as well as the mechanisms involved in regulation of K+ channel gating, expression and membrane localization. Given the critical role for K+ channels in determining the rate of cardiac repolarization, it is hardly surprising that essentially every aspect of K+ channel function is exquisitely regulated in cardiac myocytes. This regulation is complex and highly interrelated to other aspects of myocardial function. K+ channel regulatory mechanisms alter, and are altered by, physiological challenges, pathophysiological conditions, and pharmacological agents. An accompanying paper focuses on the integrative role of K+ channels in cardiac electrophysiology, i.e. how K+ currents shape the cardiac action potential, and how their dysfunction can lead to arrhythmias, and discusses K+ channel-based therapeutics. A fundamental understanding of K+ channel regulatory mechanisms and disease processes is fundamental to reveal new targets for human therapy.
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Affiliation(s)
- Eleonora Grandi
- Department of Pharmacology, University of California, Davis, Davis, CA, 95616, USA
| | - Michael C Sanguinetti
- Department of Internal Medicine, University of Utah, Nora Eccles Harrison Cardiovascular Research and Training Institute, Salt Lake City, UT, 84112, USA
| | - Daniel C Bartos
- Department of Pharmacology, University of California, Davis, Davis, CA, 95616, USA
| | - Donald M Bers
- Department of Pharmacology, University of California, Davis, Davis, CA, 95616, USA
| | - Ye Chen-Izu
- Department of Pharmacology, University of California, Davis, Davis, CA, 95616, USA.,Department of Internal Medicine, Division of Cardiology, University of California, Davis, CA, 95616, USA
| | - Nipavan Chiamvimonvat
- Department of Internal Medicine, Division of Cardiology, University of California, Davis, CA, 95616, USA
| | - Henry M Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Brian P Delisle
- Department of Physiology, University of Kentucky, Lexington, KY, 40536, USA
| | - Jordi Heijman
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Faculty of Health, Medicine, and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Manuel F Navedo
- Department of Pharmacology, University of California, Davis, Davis, CA, 95616, USA
| | - Sergei Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Catherine Proenza
- Department of Physiology and Biophysics, University of Colorado - Anschutz Medical Campus, Denver, CO, 80045, USA
| | - Jamie I Vandenberg
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, CA, 95616, USA
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39
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Structural Basis for Differences in Dynamics Induced by Leu Versus Ile Residues in the CD Loop of Kir Channels. Mol Neurobiol 2016; 53:5948-5961. [PMID: 26520451 PMCID: PMC5085999 DOI: 10.1007/s12035-015-9466-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 09/28/2015] [Indexed: 12/22/2022]
Abstract
The effect of the conserved Leu/Ile site in the CD loop on the gating dynamics of Kir channels and corresponding micro-structural mechanism remains unclear. Molecular dynamics simulations were performed to investigate the structural mechanism of chicken Kir2.2. Compared to WT, the I223L mutant channel bound to PIP2 more strongly, was activated more rapidly, and maintained the activation state more stably after PIP2 dissociation. Cellular electrophysiology assays of mouse Kir2.1 and human Kir2.2 indicated that, consistent with simulations, the Leu residue increased the channel responses to PIP2 through increased binding affinity and faster activation kinetics, and the deactivation kinetics decreased upon PIP2 inhibition. The Ile residue induced the opposite responses. This difference was attributed to the distinct hydrophobic side chain symmetries of Leu and Ile; switching between these residues caused the interaction network to redistribute and offered effective conformation transduction in the Leu systems, which had more rigid and independent subunits.
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40
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Li J, Xiao S, Xie X, Zhou H, Pang C, Li S, Zhang H, Logothetis DE, Zhan Y, An H. Three pairs of weak interactions precisely regulate the G-loop gate of Kir2.1 channel. Proteins 2016; 84:1929-1937. [PMID: 27699887 DOI: 10.1002/prot.25176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 06/30/2016] [Accepted: 09/19/2016] [Indexed: 11/08/2022]
Abstract
Kir2.1 (also known as IRK1) plays key roles in regulation of resting membrane potential and cell excitability. To achieve its physiological roles, Kir2.1 performs a series of conformational transition, named as gating. However, the structural basis of gating is still obscure. Here, we combined site-directed mutation, two-electrode voltage clamp with molecular dynamics simulations and determined that H221 regulates the gating process of Kir2.1 by involving a weak interaction network. Our data show that the H221R mutant accelerates the rundown kinetics and decelerates the reactivation kinetics of Kir2.1. Compared with the WT channel, the H221R mutation strengthens the interaction between the CD- and G-loops (E303-R221) which stabilizes the close state of the G-loop gate and weakens the interactions between C-linker and CD-loop (R221-R189) and the adjacent G-loops (E303-R312) which destabilizes the open state of G-loop gate. Our data indicate that the three pairs of interactions (E303-H221, H221-R189 and E303-R312) precisely regulate the G-loop gate by controlling the conformation of G-loop. Proteins 2016; 84:1929-1937. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Junwei Li
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, 300401, China.,Department of Electrical Engineering and Computer Science, Hebei University of Technology, Langfang, 065000, China
| | - Shaoying Xiao
- Department of Urban Planning, School of Architecture and Art Design, Hebei University of Technology, Tianjin, 300401, China
| | - Xiaoxiao Xie
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, 300401, China
| | - Hui Zhou
- Department of Mathematics and Physics, North China Electric Power University, Baoding, 071003, China
| | - Chunli Pang
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, 300401, China
| | - Shanshan Li
- Department of Mechatronics Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Hailin Zhang
- Key Laboratory of Neural and Vascular Biology, Ministry of Education, The Key Laboratory of Pharmacology and Toxicology for New Drug, Hebei Province, Department of Pharmacology, Hebei Medical University, Shijiazhuang, 050017, China
| | - Diomedes E Logothetis
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, 23298
| | - Yong Zhan
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, 300401, China
| | - Hailong An
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, 300401, China
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41
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Kurata HT. Emerging complexities of lipid regulation of potassium channels. J Gen Physiol 2016; 148:201-5. [PMID: 27574290 PMCID: PMC5004341 DOI: 10.1085/jgp.201611671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 08/04/2016] [Indexed: 02/04/2023] Open
Affiliation(s)
- Harley T Kurata
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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42
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Lee SJ, Ren F, Zangerl-Plessl EM, Heyman S, Stary-Weinzinger A, Yuan P, Nichols CG. Structural basis of control of inward rectifier Kir2 channel gating by bulk anionic phospholipids. J Gen Physiol 2016; 148:227-37. [PMID: 27527100 PMCID: PMC5004336 DOI: 10.1085/jgp.201611616] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/12/2016] [Indexed: 01/11/2023] Open
Abstract
Phospholipids are required to bind to two distinct sites on the inward rectifier potassium channel for maximal efficacy. Lee et al. show that a membrane-associating tryptophan residue in the second site can mimic the effect of phospholipid binding and cause a conformational change to reveal the primary binding site. Inward rectifier potassium (Kir) channel activity is controlled by plasma membrane lipids. Phosphatidylinositol-4,5-bisphosphate (PIP2) binding to a primary site is required for opening of classic inward rectifier Kir2.1 and Kir2.2 channels, but interaction of bulk anionic phospholipid (PL−) with a distinct second site is required for high PIP2 sensitivity. Here we show that introduction of a lipid-partitioning tryptophan at the second site (K62W) generates high PIP2 sensitivity, even in the absence of PL−. Furthermore, high-resolution x-ray crystal structures of Kir2.2[K62W], with or without added PIP2 (2.8- and 2.0-Å resolution, respectively), reveal tight tethering of the C-terminal domain (CTD) to the transmembrane domain (TMD) in each condition. Our results suggest a refined model for phospholipid gating in which PL− binding at the second site pulls the CTD toward the membrane, inducing the formation of the high-affinity primary PIP2 site and explaining the positive allostery between PL− binding and PIP2 sensitivity.
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Affiliation(s)
- Sun-Joo Lee
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Feifei Ren
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | | | - Sarah Heyman
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Anna Stary-Weinzinger
- Department of Pharmacology and Toxicology, University of Vienna, A-1090 Vienna, Austria
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Colin G Nichols
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
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43
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Hresko RC, Kraft TE, Quigley A, Carpenter EP, Hruz PW. Mammalian Glucose Transporter Activity Is Dependent upon Anionic and Conical Phospholipids. J Biol Chem 2016; 291:17271-82. [PMID: 27302065 PMCID: PMC5016126 DOI: 10.1074/jbc.m116.730168] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 01/05/2023] Open
Abstract
The regulated movement of glucose across mammalian cell membranes is mediated by facilitative glucose transporters (GLUTs) embedded in lipid bilayers. Despite the known importance of phospholipids in regulating protein structure and activity, the lipid-induced effects on the GLUTs remain poorly understood. We systematically examined the effects of physiologically relevant phospholipids on glucose transport in liposomes containing purified GLUT4 and GLUT3. The anionic phospholipids, phosphatidic acid, phosphatidylserine, phosphatidylglycerol, and phosphatidylinositol, were found to be essential for transporter function by activating it and stabilizing its structure. Conical lipids, phosphatidylethanolamine and diacylglycerol, enhanced transporter activity up to 3-fold in the presence of anionic phospholipids but did not stabilize protein structure. Kinetic analyses revealed that both lipids increase the kcat of transport without changing the Km values. These results allowed us to elucidate the activation of GLUT by plasma membrane phospholipids and to extend the field of membrane protein-lipid interactions to the family of structurally and functionally related human solute carriers.
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Affiliation(s)
| | | | - Andrew Quigley
- the Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Elisabeth P Carpenter
- the Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Paul W Hruz
- From the Departments of Pediatrics and Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110 and
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44
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Wang S, Vafabakhsh R, Borschel WF, Ha T, Nichols CG. Structural dynamics of potassium-channel gating revealed by single-molecule FRET. Nat Struct Mol Biol 2015; 23:31-36. [PMID: 26641713 PMCID: PMC4833211 DOI: 10.1038/nsmb.3138] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/06/2015] [Indexed: 01/06/2023]
Abstract
Crystallography has provided invaluable insights to ion channel selectivity and gating, but to advance understanding to a new level, dynamic views of channel structures within membranes are essential. We labeled tetrameric KirBac1.1 potassium channels with single donor and acceptor fluorophores at different sites, and examined structural dynamics within lipid membranes by single molecule FRET. We found that the extracellular region is structurally rigid in both closed and open states, whereas the N-terminal slide helix undergoes marked conformational fluctuations. The cytoplasmic C-terminal domain fluctuates between two major structural states both of which become less dynamic and move away from the pore axis and away from the membrane in closed channels. Our results reveal mobile and rigid conformations of functionally relevant KirBac1.1 channel motifs, implying similar dynamics for similar motifs in eukaryotic Kir channels and for cation channels in general.
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Affiliation(s)
- Shizhen Wang
- Center for Investigation of Membrane Excitability Diseases, Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis MO
| | - Reza Vafabakhsh
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL
| | - William F Borschel
- Center for Investigation of Membrane Excitability Diseases, Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis MO
| | - Taekjip Ha
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL.,Howard Hughes Medical Institute, Baltimore, MD.,Department of Biophysics and Biophysical Chemistry, Department of Biophysics, Department of Biomedical Engineering, Baltimore, MD
| | - Colin G Nichols
- Center for Investigation of Membrane Excitability Diseases, Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis MO
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45
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Zubcevic L, Wang S, Bavro VN, Lee SJ, Nichols CG, Tucker SJ. Modular Design of the Selectivity Filter Pore Loop in a Novel Family of Prokaryotic 'Inward Rectifier' (NirBac) channels. Sci Rep 2015; 5:15305. [PMID: 26470642 PMCID: PMC4607889 DOI: 10.1038/srep15305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/11/2015] [Indexed: 11/09/2022] Open
Abstract
Potassium channels exhibit a modular design with distinct structural and functional domains; in particular, a highly conserved pore-loop sequence that determines their ionic selectivity. We now report the functional characterisation of a novel group of functionally non-selective members of the prokaryotic 'inward rectifier' subfamily of K(+) channels. These channels share all the key structural domains of eukaryotic and prokaryotic Kir/KirBac channels, but instead possess unique pore-loop selectivity filter sequences unrelated to any other known ionic selectivity filter. The strikingly unusual architecture of these 'NirBac' channels defines a new family of functionally non-selective ion channels, and also provides important insights into the modular design of ion channels, as well as the evolution of ionic selectivity within this superfamily of tetrameric cation channels.
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Affiliation(s)
- Lejla Zubcevic
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Shizhen Wang
- Washington University St. Louis, School Of Medicine, Centre for the Investigation of Membrane Excitability Diseases (CIMED), St. Louis, MO, USA
| | - Vassiliy N. Bavro
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Sun-Joo Lee
- Washington University St. Louis, School Of Medicine, Centre for the Investigation of Membrane Excitability Diseases (CIMED), St. Louis, MO, USA
| | - Colin G. Nichols
- Washington University St. Louis, School Of Medicine, Centre for the Investigation of Membrane Excitability Diseases (CIMED), St. Louis, MO, USA
| | - Stephen J. Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, United Kingdom
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46
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Rohacs T. Phosphoinositide regulation of TRPV1 revisited. Pflugers Arch 2015; 467:1851-69. [PMID: 25754030 PMCID: PMC4537841 DOI: 10.1007/s00424-015-1695-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/12/2015] [Accepted: 02/16/2015] [Indexed: 01/22/2023]
Abstract
The heat- and capsaicin-sensitive transient receptor potential vanilloid 1 ion channel (TRPV1) is regulated by plasma membrane phosphoinositides. The effects of these lipids on this channel have been controversial. Recent articles re-ignited the debate and also offered resolution to place some of the data in a coherent picture. This review summarizes the literature on this topic and provides a detailed and critical discussion on the experimental evidence for the various effects of phosphatidylinositol 4,5-bisphosphayte [PI(4,5)P2 or PIP2] on TRPV1. We conclude that PI(4,5)P2 and potentially its precursor PI(4)P are positive cofactors for TRPV1, acting via direct interaction with the channel, and their depletion by Ca(2+)-induced activation of phospholipase Cδ isoforms (PLCδ) limits channel activity during capsaicin-induced desensitization. Other negatively charged lipids at higher concentrations can also support channel activity, which may explain some controversies in the literature. PI(4,5)P2 also partially inhibits channel activity in some experimental settings, and relief from this inhibition upon PLCβ activation may contribute to sensitization. The negative effect of PI(4,5)P2 is more controversial and its mechanism is less well understood. Other TRP channels from the TRPV and TRPC families may also undergo similar dual regulation by phosphoinositides, thus the complexity of TRPV1 regulation is not unique to this channel.
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Affiliation(s)
- Tibor Rohacs
- Department of Pharmacology and Physiology Rutgers, New Jersey Medical School, 185 South Orange Ave, Newark, NJ, USA,
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47
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Identification of the Conformational transition pathway in PIP2 Opening Kir Channels. Sci Rep 2015; 5:11289. [PMID: 26063437 PMCID: PMC4462750 DOI: 10.1038/srep11289] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/29/2015] [Indexed: 11/08/2022] Open
Abstract
The gating of Kir channels depends critically on phosphatidylinositol 4,5-bisphosphate (PIP2), but the detailed mechanism by which PIP2 regulates Kir channels remains obscure. Here, we performed a series of Targeted molecular dynamics simulations on the full-length Kir2.1 channel and, for the first time, were able to achieve the transition from the closed to the open state. Our data show that with the upward motion of the cytoplasmic domain (CTD) the structure of the C-Linker changes from a loop to a helix. The twisting of the C-linker triggers the rotation of the CTD, which induces a small downward movement of the CTD and an upward motion of the slide helix toward the membrane that pulls the inner helix gate open. At the same time, the rotation of the CTD breaks the interaction between the CD- and G-loops thus releasing the G-loop. The G-loop then bounces away from the CD-loop, which leads to the opening of the G-loop gate and the full opening of the pore. We identified a series of interaction networks, between the N-terminus, CD loop, C linker and G loop one by one, which exquisitely regulates the global conformational changes during the opening of Kir channels by PIP2.
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48
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Hansen SB. Lipid agonism: The PIP2 paradigm of ligand-gated ion channels. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1851:620-8. [PMID: 25633344 PMCID: PMC4540326 DOI: 10.1016/j.bbalip.2015.01.011] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/05/2015] [Accepted: 01/17/2015] [Indexed: 01/08/2023]
Abstract
The past decade, membrane signaling lipids emerged as major regulators of ion channel function. However, the molecular nature of lipid binding to ion channels remained poorly described due to a lack of structural information and assays to quantify and measure lipid binding in a membrane. How does a lipid-ligand bind to a membrane protein in the plasma membrane, and what does it mean for a lipid to activate or regulate an ion channel? How does lipid binding compare to activation by soluble neurotransmitter? And how does the cell control lipid agonism? This review focuses on lipids and their interactions with membrane proteins, in particular, ion channels. I discuss the intersection of membrane lipid biology and ion channel biophysics. A picture emerges of membrane lipids as bona fide agonists of ligand-gated ion channels. These freely diffusing signals reside in the plasma membrane, bind to the transmembrane domain of protein, and cause a conformational change that allosterically gates an ion channel. The system employs a catalog of diverse signaling lipids ultimately controlled by lipid enzymes and raft localization. I draw upon pharmacology, recent protein structure, and electrophysiological data to understand lipid regulation and define inward rectifying potassium channels (Kir) as a new class of PIP2 lipid-gated ion channels.
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Affiliation(s)
- Scott B Hansen
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter FL 33458, USA; Department of Neuroscience, The Scripps Research Institute, Jupiter FL 33458, USA.
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49
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Linder T, Wang S, Zangerl-Plessl EM, Nichols CG, Stary-Weinzinger A. Molecular Dynamics Simulations of KirBac1.1 Mutants Reveal Global Gating Changes of Kir Channels. J Chem Inf Model 2015; 55:814-22. [PMID: 25794351 PMCID: PMC4415035 DOI: 10.1021/acs.jcim.5b00010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 12/12/2022]
Abstract
Prokaryotic inwardly rectifying (KirBac) potassium channels are homologous to mammalian Kir channels. Their activity is controlled by dynamical conformational changes that regulate ion flow through a central pore. Understanding the dynamical rearrangements of Kir channels during gating requires high-resolution structure information from channels crystallized in different conformations and insight into the transition steps, which are difficult to access experimentally. In this study, we use MD simulations on wild type KirBac1.1 and an activatory mutant to investigate activation gating of KirBac channels. Full atomistic MD simulations revealed that introducing glutamate in position 143 causes significant widening at the helix bundle crossing gate, enabling water flux into the cavity. Further, global rearrangements including a twisting motion as well as local rearrangements at the subunit interface in the cytoplasmic domain were observed. These structural rearrangements are similar to recently reported KirBac3.1 crystal structures in closed and open conformation, suggesting that our simulations capture major conformational changes during KirBac1.1 opening. In addition, an important role of protein-lipid interactions during gating was observed. Slide-helix and C-linker interactions with lipids were strengthened during activation gating.
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Affiliation(s)
- Tobias Linder
- Department
of Pharmacology and Toxicology, University
of Vienna, 1090 Vienna, Austria
| | - Shizhen Wang
- Center
for Investigation of Membrane Excitability Diseases, Department of
Cell Biology and Physiology, Washington
University School of Medicine, St. Louis, Missouri 63110, United States
| | | | - Colin G. Nichols
- Center
for Investigation of Membrane Excitability Diseases, Department of
Cell Biology and Physiology, Washington
University School of Medicine, St. Louis, Missouri 63110, United States
| | - Anna Stary-Weinzinger
- Department
of Pharmacology and Toxicology, University
of Vienna, 1090 Vienna, Austria
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50
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Logothetis DE, Petrou VI, Zhang M, Mahajan R, Meng XY, Adney SK, Cui M, Baki L. Phosphoinositide control of membrane protein function: a frontier led by studies on ion channels. Annu Rev Physiol 2014; 77:81-104. [PMID: 25293526 DOI: 10.1146/annurev-physiol-021113-170358] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Anionic phospholipids are critical constituents of the inner leaflet of the plasma membrane, ensuring appropriate membrane topology of transmembrane proteins. Additionally, in eukaryotes, the negatively charged phosphoinositides serve as key signals not only through their hydrolysis products but also through direct control of transmembrane protein function. Direct phosphoinositide control of the activity of ion channels and transporters has been the most convincing case of the critical importance of phospholipid-protein interactions in the functional control of membrane proteins. Furthermore, second messengers, such as [Ca(2+)]i, or posttranslational modifications, such as phosphorylation, can directly or allosterically fine-tune phospholipid-protein interactions and modulate activity. Recent advances in structure determination of membrane proteins have allowed investigators to obtain complexes of ion channels with phosphoinositides and to use computational and experimental approaches to probe the dynamic mechanisms by which lipid-protein interactions control active and inactive protein states.
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Affiliation(s)
- Diomedes E Logothetis
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298-0551;
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