1
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van Aalst EJ, Yekefallah M, A M van Beekveld R, Breukink E, Weingarth M, Wylie BJ. Coordination of bilayer properties by an inward-rectifier K + channel is a cooperative process driven by protein-lipid interaction. J Struct Biol X 2024; 9:100101. [PMID: 38883399 PMCID: PMC11176924 DOI: 10.1016/j.yjsbx.2024.100101] [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: 03/19/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
Physical properties of biological membranes directly or indirectly govern biological processes. Yet, the interplay between membrane and integral membrane proteins is difficult to assess due to reciprocal effects between membrane proteins, individual lipids, and membrane architecture. Using solid-state NMR (SSNMR) we previously showed that KirBac1.1, a bacterial Inward-Rectifier K+ channel, nucleates bilayer ordering and microdomain formation through tethering anionic lipids. Conversely, these lipids cooperatively bind cationic residues to activate the channel and initiate K+ flux. The mechanistic details governing the relationship between cooperative lipid loading and bilayer ordering are, however, unknown. To investigate, we generated KirBac1.1 samples with different concentrations of 13C-lableded phosphatidyl glycerol (PG) lipids and acquired a full suite of SSNMR 1D temperature series experiments using the ordered all-trans (AT) and disordered trans-gauche (TG) acyl conformations as markers of bilayer dynamics. We observed increased AT ordered signal, decreased TG disordered signal, and increased bilayer melting temperature with increased PG concentration. Further, we identified cooperativity between ordering and direct binding of PG lipids, indicating KirBac1.1-driven bilayer ordering and microdomain formation is a classically cooperative Hill-type process driven by and predicated upon direct binding of PG lipids. Our results provide unique mechanistic insight into how proteins and lipids in tandem contribute to supramolecular bilayer heterogeneity in the lipid membrane.
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Affiliation(s)
- Evan J van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Maryam Yekefallah
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Roy A M van Beekveld
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Markus Weingarth
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Benjamin J Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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2
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Yekefallah M, van Aalst EJ, van Beekveld RAM, Eason IR, Breukink E, Weingarth M, Wylie BJ. Cooperative Gating of a K + Channel by Unmodified Biological Anionic Lipids Viewed by Solid-State NMR Spectroscopy. J Am Chem Soc 2024; 146:4421-4432. [PMID: 38334076 PMCID: PMC10885140 DOI: 10.1021/jacs.3c09266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Lipids adhere to membrane proteins to stimulate or suppress molecular and ionic transport and signal transduction. Yet, the molecular details of lipid-protein interaction and their functional impact are poorly characterized. Here we combine NMR, coarse-grained molecular dynamics (CGMD), and functional assays to reveal classic cooperativity in the binding and subsequent activation of a bacterial inward rectifier potassium (Kir) channel by phosphatidylglycerol (PG), a common component of many membranes. Past studies of lipid activation of Kir channels focused primarily on phosphatidylinositol bisphosphate, a relatively rare signaling lipid that is tightly regulated in space and time. We use solid-state NMR to quantify the binding of unmodified 13C-PG to the K+ channel KirBac1.1 in liposomes. This specific lipid-protein interaction has a dissociation constant (Kd) of ∼7 mol percentage PG (ΧPG) with positive cooperativity (n = 3.8) and approaches saturation near 20% ΧPG. Liposomal flux assays show that K+ flux also increases with PG in a cooperative manner with an EC50 of ∼20% ΧPG, within the physiological range. Further quantitative fitting of these data reveals that PG acts as a partial (80%) agonist with fivefold K+ flux amplification. Comparisons of NMR chemical shift perturbation and CGMD simulations at different ΧPG confirm the direct interaction of PG with key residues, several of which would not be accessible to lipid headgroups in the closed state of the channel. Allosteric regulation by a common lipid is directly relevant to the activation mechanisms of several human ion channels. This study highlights the role of concentration-dependent lipid-protein interactions and tightly controlled protein allostery in the activation and regulation of ion channels.
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Affiliation(s)
- Maryam Yekefallah
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Evan J. van Aalst
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Roy A. M. van Beekveld
- Department
of Chemistry, Faculty of Science, Utrecht
University, Padualaan 8, Utrecht3584
CH, The Netherlands
| | - Isaac R. Eason
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Eefjan Breukink
- Membrane
Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584
CH, The Netherlands
| | - Markus Weingarth
- Department
of Chemistry, Faculty of Science, Utrecht
University, Padualaan 8, Utrecht3584
CH, The Netherlands
| | - Benjamin J. Wylie
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409, United States
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3
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Li D, Shi D, Wang L. Structural insights in the permeation mechanism of an activated GIRK2 channel. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184231. [PMID: 37739205 DOI: 10.1016/j.bbamem.2023.184231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/19/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023]
Abstract
G protein-gated inwardly rectifying potassium (GIRK) channels play a significant role in physiopathology by the regulation of cell excitability. This regulation depends on the K+ ion conduction induced by structural constrictions: the selectivity filters (SFs), helix bundle crossings (HBCs), and G-loop gates. To explore why no permeation occurred when the constrictions were kept in the open state, a 4-K+-related occupancy mechanism was proposed. Unfortunately, this hypothesis was neither assessed, nor was the energetic characteristics presented. To identify the permeation mechanism on an atomic level, all-atom molecular dynamic (MD) simulations and a coupled quantum mechanics and molecular mechanics (QM/MM) method were used for the GIRK2 mutant R201A. It was found that the R201A had a moderate conductive capability in the presence of PIP2. Furthermore, the 4-K+ group of ions was found to dominate the conduction through the activated HBC gate. This shielding-like mechanism was assessed by the potential energy barrier along the conduction pathway. Mutation studies did further support the assumption that E152 was responsible for the mechanism. Moreover, E152 was most probably facilitating the inflow of ions from the SF to the cavity. On the contrary, N184 had no remarkable effect on this mechanism, except for the conduction efficiency. These findings highlighted the necessity of a multi-ion distribution for the conduction to take place, and indicated that the K+ migration was not only determined by the channel conductive state in the GIRK channel. The here presented multi-ion permeation mechanism may help to provide an effective way to regulate the channelopathies.
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Affiliation(s)
- Dailin Li
- Key Laboratory of Environmental Biotechnology (XMUT), Fujian Province University, Xiamen University of Technology, Xiamen 361005, China.
| | - Dingyuan Shi
- Key Laboratory of Environmental Biotechnology (XMUT), Fujian Province University, Xiamen University of Technology, Xiamen 361005, China
| | - Lei Wang
- Key Laboratory of Environmental Biotechnology (XMUT), Fujian Province University, Xiamen University of Technology, Xiamen 361005, China
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4
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Hernandez CC, Gimenez LE, Dahir NS, Peisley A, Cone RD. The unique structural characteristics of the Kir 7.1 inward rectifier potassium channel: a novel player in energy homeostasis control. Am J Physiol Cell Physiol 2023; 324:C694-C706. [PMID: 36717105 PMCID: PMC10026989 DOI: 10.1152/ajpcell.00335.2022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 02/01/2023]
Abstract
The inward rectifier potassium channel Kir7.1, encoded by the KCNJ13 gene, is a tetramer composed of two-transmembrane domain-spanning monomers, closer in homology to Kir channels associated with potassium transport such as Kir1.1, 1.2, and 1.3. Compared with other channels, Kir7.1 exhibits small unitary conductance and low dependence on external potassium. Kir7.1 channels also show a phosphatidylinositol 4,5-bisphosphate (PIP2) dependence for opening. Accordingly, retinopathy-associated Kir7.1 mutations mapped at the binding site for PIP2 resulted in channel gating defects leading to channelopathies such as snowflake vitreoretinal degeneration and Leber congenital amaurosis in blind patients. Lately, this channel's role in energy homeostasis was reported due to the direct interaction with the melanocortin type 4 receptor (MC4R) in the hypothalamus. As this channel seems to play a multipronged role in potassium homeostasis and neuronal excitability, we will discuss what is predicted from a structural viewpoint and its possible implications for hunger control.
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Affiliation(s)
- Ciria C Hernandez
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Luis E Gimenez
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Naima S Dahir
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Alys Peisley
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Roger D Cone
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States
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5
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Bukiya AN, Rosenhouse-Dantsker A. From Crosstalk to Synergism: The Combined Effect of Cholesterol and PI(4,5)P 2 on Inwardly Rectifying Potassium Channels. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1422:169-191. [PMID: 36988881 DOI: 10.1007/978-3-031-21547-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Inwardly rectifying potassium (Kir) channels are integral membrane proteins that control the flux of potassium ions across cell membranes and regulate membrane permeability. All eukaryotic Kir channels require the membrane phospholipid phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) for activation. In recent years, it has become evident that the function of many members of this family of channels is also mediated by another essential lipid-cholesterol. Here, we focus on members of the Kir2 and Kir3 subfamilies and their modulation by these two key lipids. We discuss how PI(4,5)P2 and cholesterol bind to Kir2 and Kir3 channels and how they affect channel activity. We also discuss the accumulating evidence indicating that there is interplay between PI(4,5)P2 and cholesterol in the modulation of Kir2 and Kir3 channels. In particular, we review the crosstalk between PI(4,5)P2 and cholesterol in the modulation of the ubiquitously expressed Kir2.1 channel and the synergy between these two lipids in the modulation of the Kir3.4 channel, which is primarily expressed in the heart. Additionally, we demonstrate that there is also synergy in the modulation of Kir3.2 channels, which are expressed in the brain. These observations suggest that alterations in the relative levels PI(4,5)P2 and cholesterol may fine-tune Kir channel activity.
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Affiliation(s)
- Anna N Bukiya
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
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6
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Moseng MA, Su CC, Rios K, Cui M, Lyu M, Glaza P, Klenotic PA, Delpire E, Yu EW. Inhibition mechanism of NKCC1 involves the carboxyl terminus and long-range conformational coupling. SCIENCE ADVANCES 2022; 8:eabq0952. [PMID: 36306358 PMCID: PMC9616490 DOI: 10.1126/sciadv.abq0952] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
The Na-K-2Cl cotransporter-1 (NKCC1) is an electroneutral Na+-dependent transporter responsible for simultaneously translocating Na+, K+, and Cl- ions into cells. In human tissue, NKCC1 plays a critical role in regulating cytoplasmic volume, fluid intake, chloride homeostasis, and cell polarity. Here, we report four structures of human NKCC1 (hNKCC1), both in the absence and presence of loop diuretic (bumetanide or furosemide), using single-particle cryo-electron microscopy. These structures allow us to directly observe various novel conformations of the hNKCC1 dimer. They also reveal two drug-binding sites located at the transmembrane and cytosolic carboxyl-terminal domains, respectively. Together, our findings enable us to delineate an inhibition mechanism that involves a coupled movement between the cytosolic and transmembrane domains of hNKCC1.
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Affiliation(s)
- Mitchell A. Moseng
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kerri Rios
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Meng Cui
- Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Boston, MA 02115, USA
| | - Meinan Lyu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Przemyslaw Glaza
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Philip A. Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Eric Delpire
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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7
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Cao Y, Yang R, Wang W, Jiang S, Yang C, Wang Q, Liu N, Xue Y, Lee I, Meng X, Yuan Z. Effects of membrane lipids on phospholamban pentameric channel structure and ion transportation mechanisms. Int J Biol Macromol 2022; 224:766-775. [DOI: 10.1016/j.ijbiomac.2022.10.164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/10/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022]
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8
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Gazgalis D, Cantwell L, Xu Y, Thakur GA, Cui M, Guarnieri F, Logothetis DE. Use of a Molecular Switch Probe to Activate or Inhibit GIRK1 Heteromers In Silico Reveals a Novel Gating Mechanism. Int J Mol Sci 2022; 23:ijms231810820. [PMID: 36142730 PMCID: PMC9502415 DOI: 10.3390/ijms231810820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/16/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
G protein-gated inwardly rectifying K+ (GIRK) channels form highly active heterotetramers in the body, such as in neurons (GIRK1/GIRK2 or GIRK1/2) and heart (GIRK1/GIRK4 or GIRK1/4). Based on three-dimensional atomic resolution structures for GIRK2 homotetramers, we built heterotetrameric GIRK1/2 and GIRK1/4 models in a lipid bilayer environment. By employing a urea-based activator ML297 and its molecular switch, the inhibitor GAT1587, we captured channel gating transitions and K+ ion permeation in sub-microsecond molecular dynamics (MD) simulations. This allowed us to monitor the dynamics of the two channel gates (one transmembrane and one cytosolic) as well as their control by the required phosphatidylinositol bis 4-5-phosphate (PIP2). By comparing differences in the two trajectories, we identify three hydrophobic residues in the transmembrane domain 1 (TM1) of GIRK1, namely, F87, Y91, and W95, which form a hydrophobic wire induced by ML297 and de-induced by GAT1587 to orchestrate channel gating. This includes bending of the TM2 and alignment of a dipole of two acidic GIRK1 residues (E141 and D173) in the permeation pathway to facilitate K+ ion conduction. Moreover, the TM movements drive the movement of the Slide Helix relative to TM1 to adjust interactions of the CD-loop that controls the gating of the cytosolic gate. The simulations reveal that a key basic residue that coordinates PIP2 to stabilize the pre-open and open states of the transmembrane gate flips in the inhibited state to form a direct salt-bridge interaction with the cytosolic gate and destabilize its open state.
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Affiliation(s)
- Dimitrios Gazgalis
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Boston, MA 02115, USA
| | - Lucas Cantwell
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Boston, MA 02115, USA
| | - Yu Xu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Boston, MA 02115, USA
| | - Ganesh A. Thakur
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Boston, MA 02115, USA
| | - Meng Cui
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Boston, MA 02115, USA
- Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA
| | - Frank Guarnieri
- Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA
| | - Diomedes E. Logothetis
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Boston, MA 02115, USA
- Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA
- Department of Chemistry and Chemical Biology, College of Science, Boston, MA 02115, USA
- Roux Institute, Northeastern University, Portland, ME 04101, USA
- Correspondence:
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9
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Cui M, Xu K, Gada K, Shalomov B, Ban M, Eptaminitaki GC, Kawano T, Plant LD, Dascal N, Logothetis DE. A novel small molecule selective activator of homomeric GIRK4 channels. J Biol Chem 2022; 298:102009. [PMID: 35525275 PMCID: PMC9194863 DOI: 10.1016/j.jbc.2022.102009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 11/26/2022] Open
Abstract
G protein–sensitive inwardly rectifying potassium (GIRK) channels are important pharmaceutical targets for neuronal, cardiac, and endocrine diseases. Although a number of GIRK channel modulators have been discovered in recent years, most lack selectivity. GIRK channels function as either homomeric (i.e., GIRK2 and GIRK4) or heteromeric (e.g., GIRK1/2, GIRK1/4, and GIRK2/3) tetramers. Activators, such as ML297, ivermectin, and GAT1508, have been shown to activate heteromeric GIRK1/2 channels better than GIRK1/4 channels with varying degrees of selectivity but not homomeric GIRK2 and GIRK4 channels. In addition, VU0529331 was discovered as the first homomeric GIRK channel activator, but it shows weak selectivity for GIRK2 over GIRK4 (or G4) homomeric channels. Here, we report the first highly selective small-molecule activator targeting GIRK4 homomeric channels, 3hi2one-G4 (3-[2-(3,4-dimethoxyphenyl)-2-oxoethyl]-3-hydroxy-1-(1-naphthylmethyl)-1,3-dihydro-2H-indol-2-one). We show that 3hi2one-G4 does not activate GIRK2, GIRK1/2, or GIRK1/4 channels. Using molecular modeling, mutagenesis, and electrophysiology, we analyzed the binding site of 3hi2one-G4 formed by the transmembrane 1, transmembrane 2, and slide helix regions of the GIRK4 channel, near the phosphatidylinositol-4,5-bisphosphate binding site, and show that it causes channel activation by strengthening channel–phosphatidylinositol-4,5-bisphosphate interactions. We also identify slide helix residue L77 in GIRK4, corresponding to residue I82 in GIRK2, as a major determinant of isoform-specific selectivity. We propose that 3hi2one-G4 could serve as a useful pharmaceutical probe in studying GIRK4 channel function and may also be pursued in drug optimization studies to tackle GIRK4-related diseases such as primary aldosteronism and late-onset obesity.
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Affiliation(s)
- Meng Cui
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, 02115, USA; Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA.
| | - Keman Xu
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, 02115, USA
| | - Kirin Gada
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, 02115, USA
| | - Boris Shalomov
- Department of Physiology and Pharmacology and Sagol School of Neuroscience, School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Michelle Ban
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, 02115, USA
| | - Giasemi C Eptaminitaki
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, 02115, USA
| | - Takeharu Kawano
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, 02115, USA
| | - Leigh D Plant
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, 02115, USA; Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA
| | - Nathan Dascal
- Department of Physiology and Pharmacology and Sagol School of Neuroscience, School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Diomedes E Logothetis
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, 02115, USA; Chemistry and Chemical Biology, College of Science, Northeastern University, Boston, MA 02115, USA; Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA.
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10
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Abstract
Cholesterol is one of the main components found in plasma membranes and is involved in lipid-dependent signaling enabled by integral membrane proteins such as inwardly rectifying potassium (Kir) channels. Similar to other ion channels, most of the Kir channels are down-regulated by cholesterol. One of the very few notable exceptions is Kir3.4, which is up-regulated by this important lipid. Here, we discovered and characterized a molecular switch that controls the impact (up-regulation vs. down-regulation) of cholesterol on Kir3.4. Our results provide a detailed molecular mechanism of tunable cholesterol regulation of a potassium channel. Cholesterol decreases the activity of the majority of ion channels while increasing the activity of only a few, yet it remains unclear how. Here, we used the inwardly rectifying potassium channel Kir3.4, which is up-regulated by cholesterol, as a tool to address this question. Employing mutagenesis and electrophysiology, we discovered a molecular switch that controls the impact of cholesterol on the channel. Through a single point mutation at position 182 in the transmembrane domain of Kir3.4, we converted the cholesterol-driven up-regulation of the channel into down-regulation. Microseconds-long coarse-grained and atomistic molecular dynamics simulations revealed that the effect of the point mutation propagated toward the selectivity filter of the channel whose conformation controls the conductance of the channel. Planar lipid bilayer experiments validated these results, showing that although cholesterol up-regulated Kir3.4 by increasing its open probability, cholesterol down-regulated the mutant by decreasing its conductance. Further studies underscored the role of mutation-specific alterations of cholesterol distribution in proximity to the channel in cholesterol’s impact on channel activity, highlighting the role of subtle molecular differences in determining how cholesterol distributes around proteins and affects their function.
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11
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Nam YW, Cui M, Salem El-Sayed N, Orfali R, Nguyen M, Yang G, Rahman MA, Lee J, Zhang M. Subtype-selective positive modulation of K Ca 2 channels depends on the HA/HB helices. Br J Pharmacol 2022; 179:460-472. [PMID: 34458981 PMCID: PMC8799485 DOI: 10.1111/bph.15676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 06/29/2021] [Accepted: 07/29/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND AND PURPOSE In the activated state of small-conductance Ca2+ -activated potassium (KCa 2) channels, calmodulin interacts with the HA/HB helices and the S4-S5 linker. CyPPA potentiates KCa 2.2a and KCa 2.3 channel activity but not the KCa 2.1 and KCa 3.1 subtypes. EXPERIMENTAL APPROACH Site-directed mutagenesis, patch-clamp recordings and in silico modelling were utilised to explore the structural determinants for the subtype-selective modulation of KCa 2 channels by CyPPA. KEY RESULTS Mutating residues in the HA (V420) and HB (K467) helices of KCa 2.2a channels to their equivalent residues in KCa 3.1 channels diminished the potency of CyPPA. CyPPA elicited prominent responses on mutant KCa 3.1 channels with an arginine residue in the HB helix substituted for its equivalent lysine residue in the KCa 2.2a channels (R355K). KCa 2.1 channels harbouring a three-amino-acid insertion upstream of the cognate R438 residues in the HB helix showed no response to CyPPA, whereas the deletion mutant (KCa 2.1_ΔA434/Q435/K436) became sensitive to CyPPA. In molecular dynamics simulations, CyPPA docked between calmodulin C-lobe and the HA/HB helices widens the cytoplasmic gate of KCa 2.2a channels. CONCLUSION AND IMPLICATIONS Selectivity of CyPPA among KCa 2 and KCa 3.1 channel subtypes relies on the HA/HB helices.
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Affiliation(s)
- Young-Woo Nam
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, USA
| | - Meng Cui
- Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Boston, Massachusetts, 02115, USA
| | - Naglaa Salem El-Sayed
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, USA
| | - Razan Orfali
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, USA
| | - Misa Nguyen
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, USA
| | - Grace Yang
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, USA
| | - Mohammad Asikur Rahman
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, USA
| | - Judy Lee
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, USA
| | - Miao Zhang
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, USA
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12
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Fathizadeh A, Senning E, Elber R. Impact of the Protonation State of Phosphatidylinositol 4,5-Bisphosphate (PIP2) on the Binding Kinetics and Thermodynamics to Transient Receptor Potential Vanilloid (TRPV5): A Milestoning Study. J Phys Chem B 2021; 125:9547-9556. [PMID: 34396776 DOI: 10.1021/acs.jpcb.1c04052] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding of phosphatidylinositol 4,5-bisphosphate (PIP2) to the ion channel transient receptor potential vanilloid 5 (TRPV5) is critical for its function. We use atomically detailed simulations and the milestoning theory to compute the free energy profile and the kinetics of PIP2 binding to TRPV5. We estimate the rate of binding and the impact of the protonation state on the process. Several channel residues are identified as influential in the association event and will be interesting targets for mutation analysis. Our simulations reveal that PIP2 binds to TRPV5 in an unprotonated state and is protonated in the membrane. The switch between the protonation state of PIP2 is modeled as a diabatic transition and occurs about halfway through the reaction.
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13
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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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14
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Li DL, Hu L, Wang L, Chen CL. Permeation mechanisms through the selectivity filter and the open helix bundle crossing gate of GIRK2. Comput Struct Biotechnol J 2020; 18:3950-3958. [PMID: 33335691 PMCID: PMC7734222 DOI: 10.1016/j.csbj.2020.11.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 12/01/2022] Open
Abstract
G protein-gated inwardly rectifying potassium channels (GIRK) are essential for the regulation of cellular excitability, a physiological function that relies critically on the conduction of K+ ions, which is dependent on two molecular mechanisms, namely selectivity and gating. Molecular Dynamics (MD) studies have shown that K+ conduction remains inefficient even with open channel gates, therefore further detailed study on the permeation events is required. In this study, all-atom MD simulations were employed to investigate the permeation mechanism through the GIRK2 selectivity filter (SF) and its open helix bundle crossing (HBC) gate. Our results show that it is the SF rather than the HBC or the G-loop gate that determines the permeation efficiency upon activation of the channel. SF-permeation is accomplished by a water-K+ coupled mechanism and the entry to the S1 coordination site is likely affected by a SF tilt. Moreover, we show that a 4-K+ occupancy in the SF-HBC cavity is required for the permeation through an open HBC, where three K+ ions around E152 help to abolish the unfavorable cation-dipole interactions that function as an energy barrier, while the fourth K+ located near the HBC allows for the inward transport. These findings facilitate further understanding of the dynamic permeation mechanisms through GIRK2 and potentially provide an alternative regulatory approach for the Kir3 family given the overall high evolutionary residue conservation.
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Affiliation(s)
- Dai-Lin Li
- Key Laboratory of Environmental Biotechnology (XMUT), Fujian Province University, Xiamen University of Technology, Xiamen 361005, China
| | - Liang Hu
- School of Computer and Information Engineering, Xiamen University of Technology, Xiamen 361005, China
| | - Lei Wang
- Key Laboratory of Environmental Biotechnology (XMUT), Fujian Province University, Xiamen University of Technology, Xiamen 361005, China
| | - Chin-Ling Chen
- School of Computer and Information Engineering, Xiamen University of Technology, Xiamen 361005, China.,School of Information Engineering, Changchun Sci-Tech University, Changchun 130600, China.,Department of Computer Science and Information Engineering, Chaoyang University of Technology, Taichung 41349, Taiwan
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15
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New Structural insights into Kir channel gating from molecular simulations, HDX-MS and functional studies. Sci Rep 2020; 10:8392. [PMID: 32439887 PMCID: PMC7242327 DOI: 10.1038/s41598-020-65246-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
Inward rectifier potassium (Kir) channels play diverse and important roles in shaping action potentials in biological membranes. An increasing number of diseases are now known to be directly associated with abnormal Kir function. However, the gating of Kir still remains unknown. To increase our understanding of its gating mechanism, a dynamical view of the entire channel is essential. Here the gating activation was studied using a recent developped in silico method, MDeNM, which combines normal mode analysis and molecular dynamics simulations that showed for the very first time the importance of interrelated collective and localized conformational movements. In particular, we highlighted the role played by concerted movements of the different regions throughout the entire protein, such as the cytoplasmic and transmembrane domains and the slide helices. In addition, the HDX-MS analysis achieved in these studies provided a comprehensive and detailed view of the dynamics associated with open/closed transition of the Kir channel in coherence with the theoretical results. MDeNM gives access to the probability of the different opening states that are in agreement with our electrophysiological experiments. The investigations presented in this article are important to remedy dysfunctional channels and are of interest for designing new pharmacological compounds.
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16
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Van Aalst E, Yekefallah M, Mehta AK, Eason I, Wylie B. Codon Harmonization of a Kir3.1-KirBac1.3 Chimera for Structural Study Optimization. Biomolecules 2020; 10:biom10030430. [PMID: 32164257 PMCID: PMC7175280 DOI: 10.3390/biom10030430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/27/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
The expression of functional, folded, and isotopically enriched membrane proteins is an enduring bottleneck for nuclear magnetic resonance (NMR) studies. Indeed, historically, protein yield optimization has been insufficient to allow NMR analysis of many complex Eukaryotic membrane proteins. However, recent work has found that manipulation of plasmid codons improves the odds of successful NMR-friendly protein production. In the last decade, numerous studies showed that matching codon usage patterns in recombinant gene sequences to those in the native sequence is positively correlated with increased protein yield. This phenomenon, dubbed codon harmonization, may be a powerful tool in optimizing recombinant expression of difficult-to-produce membrane proteins for structural studies. Here, we apply this technique to an inward rectifier K+ Channel (Kir) 3.1-KirBac1.3 chimera. Kir3.1 falls within the G protein-coupled inward rectifier K+ (GIRK) channel family, thus NMR studies may inform on the nuances of GIRK gating action in the presence and absence of its G Protein, lipid, and small molecule ligands. In our hands, harmonized plasmids increase protein yield nearly two-fold compared to the traditional ‘fully codon optimized’ construct. We then employ a fluorescence-based functional assay and solid-state NMR correlation spectroscopy to show the final protein product is folded and functional.
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Affiliation(s)
- Evan Van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79423, USA; (E.V.A.); (M.Y.); (I.E.)
| | - Maryam Yekefallah
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79423, USA; (E.V.A.); (M.Y.); (I.E.)
| | - Anil K. Mehta
- National High Magnetic Field Laboratory and McKnight Brain Institute, University of Florida, Box 10015, Gainesville, FL 32610, USA;
| | - Isaac Eason
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79423, USA; (E.V.A.); (M.Y.); (I.E.)
| | - Benjamin Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79423, USA; (E.V.A.); (M.Y.); (I.E.)
- Correspondence:
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17
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Xu Y, Cantwell L, Molosh AI, Plant LD, Gazgalis D, Fitz SD, Dustrude ET, Yang Y, Kawano T, Garai S, Noujaim SF, Shekhar A, Logothetis DE, Thakur GA. The small molecule GAT1508 activates brain-specific GIRK1/2 channel heteromers and facilitates conditioned fear extinction in rodents. J Biol Chem 2020; 295:3614-3634. [PMID: 31953327 DOI: 10.1074/jbc.ra119.011527] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/09/2020] [Indexed: 01/31/2023] Open
Abstract
G-protein-gated inwardly-rectifying K+ (GIRK) channels are targets of Gi/o-protein-signaling systems that inhibit cell excitability. GIRK channels exist as homotetramers (GIRK2 and GIRK4) or heterotetramers with nonfunctional homomeric subunits (GIRK1 and GIRK3). Although they have been implicated in multiple conditions, the lack of selective GIRK drugs that discriminate among the different GIRK channel subtypes has hampered investigations into their precise physiological relevance and therapeutic potential. Here, we report on a highly-specific, potent, and efficacious activator of brain GIRK1/2 channels. Using a chemical screen and electrophysiological assays, we found that this activator, the bromothiophene-substituted small molecule GAT1508, is specific for brain-expressed GIRK1/2 channels rather than for cardiac GIRK1/4 channels. Computational models predicted a GAT1508-binding site validated by experimental mutagenesis experiments, providing insights into how urea-based compounds engage distant GIRK1 residues required for channel activation. Furthermore, we provide computational and experimental evidence that GAT1508 is an allosteric modulator of channel-phosphatidylinositol 4,5-bisphosphate interactions. Through brain-slice electrophysiology, we show that subthreshold GAT1508 concentrations directly stimulate GIRK currents in the basolateral amygdala (BLA) and potentiate baclofen-induced currents. Of note, GAT1508 effectively extinguished conditioned fear in rodents and lacked cardiac and behavioral side effects, suggesting its potential for use in pharmacotherapy for post-traumatic stress disorder. In summary, our findings indicate that the small molecule GAT1508 has high specificity for brain GIRK1/2 channel subunits, directly or allosterically activates GIRK1/2 channels in the BLA, and facilitates fear extinction in a rodent model.
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Affiliation(s)
- Yu Xu
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, and Center for Drug Discovery, Northeastern University, Boston, Massachusetts 02115
| | - Lucas Cantwell
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, and Center for Drug Discovery, Northeastern University, Boston, Massachusetts 02115
| | - Andrei I Molosh
- Department of Psychiatry, Paul and Carole Stark Neurosciences Research Institute, Indiana Clinical and Translational Sciences Institute, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Leigh D Plant
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, and Center for Drug Discovery, Northeastern University, Boston, Massachusetts 02115
| | - Dimitris Gazgalis
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, and Center for Drug Discovery, Northeastern University, Boston, Massachusetts 02115
| | - Stephanie D Fitz
- Department of Psychiatry, Paul and Carole Stark Neurosciences Research Institute, Indiana Clinical and Translational Sciences Institute, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Erik T Dustrude
- Department of Psychiatry, Paul and Carole Stark Neurosciences Research Institute, Indiana Clinical and Translational Sciences Institute, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Yuchen Yang
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, and Center for Drug Discovery, Northeastern University, Boston, Massachusetts 02115
| | - Takeharu Kawano
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, and Center for Drug Discovery, Northeastern University, Boston, Massachusetts 02115
| | - Sumanta Garai
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, and Center for Drug Discovery, Northeastern University, Boston, Massachusetts 02115
| | - Sami F Noujaim
- Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida 33612
| | - Anantha Shekhar
- Department of Psychiatry, Paul and Carole Stark Neurosciences Research Institute, Indiana Clinical and Translational Sciences Institute, Indiana University School of Medicine, Indianapolis, Indiana 46202.
| | - Diomedes E Logothetis
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, and Center for Drug Discovery, Northeastern University, Boston, Massachusetts 02115.
| | - Ganesh A Thakur
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, and Center for Drug Discovery, Northeastern University, Boston, Massachusetts 02115.
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18
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Li D, Jin T, Gazgalis D, Cui M, Logothetis DE. On the mechanism of GIRK2 channel gating by phosphatidylinositol bisphosphate, sodium, and the Gβγ dimer. J Biol Chem 2019; 294:18934-18948. [PMID: 31659119 DOI: 10.1074/jbc.ra119.010047] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/21/2019] [Indexed: 12/19/2022] Open
Abstract
G protein-gated inwardly rectifying K+ (GIRK) channels belong to the inward-rectifier K+ (Kir) family, are abundantly expressed in the heart and the brain, and require that phosphatidylinositol bisphosphate is present so that intracellular channel-gating regulators such as Gβγ and Na+ ions can maintain the channel-open state. However, despite high-resolution structures (GIRK2) and a large number of functional studies, we do not have a coherent picture of how Gβγ and Na+ ions control gating of GIRK2 channels. Here, we utilized computational modeling and all-atom microsecond-scale molecular dynamics simulations to determine which gates are controlled by Na+ and Gβγ and how each regulator uses the channel domain movements to control gate transitions. We found that Na+ ions control the cytosolic gate of the channel through an anti-clockwise rotation, whereas Gβγ stabilizes the transmembrane gate in the open state through a rocking movement of the cytosolic domain. Both effects alter the way in which the channel interacts with phosphatidylinositol bisphosphate and thereby stabilizes the open states of the respective gates. These studies of GIRK channel dynamics present for the first time a comprehensive structural model that is consistent with the great body of literature on GIRK channel function.
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Affiliation(s)
- Dailin Li
- Key Laboratory of Environmental Biotechnology, Fujian Province University, Xiamen University of Technology, Xiamen, 361024 China; Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Bouve College of Health Sciences, Boston, Massachusetts 02115.
| | - Taihao Jin
- Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Bouve College of Health Sciences, Boston, Massachusetts 02115
| | - Dimitris Gazgalis
- Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Bouve College of Health Sciences, Boston, Massachusetts 02115
| | - Meng Cui
- Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Bouve College of Health Sciences, Boston, Massachusetts 02115
| | - Diomedes E Logothetis
- Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Bouve College of Health Sciences, Boston, Massachusetts 02115.
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19
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Weise-Cross L, Resta TC, Jernigan NL. Redox Regulation of Ion Channels and Receptors in Pulmonary Hypertension. Antioxid Redox Signal 2019; 31:898-915. [PMID: 30569735 PMCID: PMC7061297 DOI: 10.1089/ars.2018.7699] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 12/11/2018] [Indexed: 02/06/2023]
Abstract
Significance: Pulmonary hypertension (PH) is characterized by elevated vascular resistance due to vasoconstriction and remodeling of the normally low-pressure pulmonary vasculature. Redox stress contributes to the pathophysiology of this disease by altering the regulation and activity of membrane receptors, K+ channels, and intracellular Ca2+ homeostasis. Recent Advances: Antioxidant therapies have had limited success in treating PH, leading to a growing appreciation that reductive stress, in addition to oxidative stress, plays a role in metabolic and cell signaling dysfunction in pulmonary vascular cells. Reactive oxygen species generation from mitochondria and NADPH oxidases has substantial effects on K+ conductance and membrane potential, and both receptor-operated and store-operated Ca2+ entry. Critical Issues: Some specific redox changes resulting from oxidation, S-nitrosylation, and S-glutathionylation are known to modulate membrane receptor and ion channel activity in PH. However, many sites of regulation that have been elucidated in nonpulmonary cell types have not been tested in the pulmonary vasculature, and context-specific molecular mechanisms are lacking. Future Directions: Here, we review what is known about redox regulation of membrane receptors and ion channels in PH. Further investigation of the mechanisms involved is needed to better understand the etiology of PH and develop better targeted treatment strategies.
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Affiliation(s)
- Laura Weise-Cross
- Vascular Physiology Group, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Thomas C. Resta
- Vascular Physiology Group, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Nikki L. Jernigan
- Vascular Physiology Group, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
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20
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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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21
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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22
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Kano H, Toyama Y, Imai S, Iwahashi Y, Mase Y, Yokogawa M, Osawa M, Shimada I. Structural mechanism underlying G protein family-specific regulation of G protein-gated inwardly rectifying potassium channel. Nat Commun 2019; 10:2008. [PMID: 31043612 PMCID: PMC6494913 DOI: 10.1038/s41467-019-10038-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/12/2019] [Indexed: 01/26/2023] Open
Abstract
G protein-gated inwardly rectifying potassium channel (GIRK) plays a key role in regulating neurotransmission. GIRK is opened by the direct binding of the G protein βγ subunit (Gβγ), which is released from the heterotrimeric G protein (Gαβγ) upon the activation of G protein-coupled receptors (GPCRs). GIRK contributes to precise cellular responses by specifically and efficiently responding to the Gi/o-coupled GPCRs. However, the detailed mechanisms underlying this family-specific and efficient activation are largely unknown. Here, we investigate the structural mechanism underlying the Gi/o family-specific activation of GIRK, by combining cell-based BRET experiments and NMR analyses in a reconstituted membrane environment. We show that the interaction formed by the αA helix of Gαi/o mediates the formation of the Gαi/oβγ-GIRK complex, which is responsible for the family-specific activation of GIRK. We also present a model structure of the Gαi/oβγ-GIRK complex, which provides the molecular basis underlying the specific and efficient regulation of GIRK.
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Affiliation(s)
- Hanaho Kano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuki Toyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shunsuke Imai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuta Iwahashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoko Mase
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mariko Yokogawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Faculty of Pharmacy, Keio University, Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Faculty of Pharmacy, Keio University, Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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23
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Bizzarri B, Botta L, Aversa D, Mercuri NB, Poli G, Barbieri A, Berretta N, Saladino R. L-DOPA-quinone Mediated Recovery from GIRK Channel Firing Inhibition in Dopaminergic Neurons. ACS Med Chem Lett 2019; 10:431-436. [PMID: 30996775 PMCID: PMC6466524 DOI: 10.1021/acsmedchemlett.8b00477] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/09/2019] [Indexed: 01/07/2023] Open
Abstract
The oxidative degeneration of dopamine-releasing (DAergic) neurons in the substantia nigra pars compacta (SNc) has attracted much interest in preclinical research, due to its involvement in Parkinson's disease manifestations. Evidence exists on the participation of quinone derivatives in mitochondrial dysfunction, alpha synuclein protein aggregation, and protein degradation. With the aim to investigate the role of L-DOPA-quinone in DAergic neuron functions, we synthesized L-DOPA-quinone by use of 2-iodoxybenzoic acid and measured its activity in recovery from dopamine-mediated firing inhibition of SNc neurons. Noteworthy, L-DOPA-quinone counteracts firing inhibition in SNc DAergic neurons caused by GIRK opening. A possible mechanism to explain the effect of L-DOPA-quinone on GIRK channel has been proposed by computational models. Overall, the study showed the possibility that L-DOPA-quinone stabilizes GIRK in a preopen conformation through formation of a covalent adduct with cysteine-65 on the GIRK2 subunit of the protein.
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Affiliation(s)
- Bruno
M. Bizzarri
- Dipartimento
di Scienze Ecologiche e Biologiche, Università
della Tuscia, Via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Lorenzo Botta
- Dipartimento
di Scienze Ecologiche e Biologiche, Università
della Tuscia, Via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Daniela Aversa
- IRCCS
Fondazione Santa Lucia, Via Ardeatina, 306/354, 00142 Rome, Italy
| | - Nicola B. Mercuri
- IRCCS
Fondazione Santa Lucia, Via Ardeatina, 306/354, 00142 Rome, Italy
- Dipartimento
di Medicina dei Sistemi, Università
di Roma Tor Vergata, Via Montpellier, 1, 00133 Rome, Italy
| | - Giulio Poli
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
degli studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Alessandro Barbieri
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
degli studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Nicola Berretta
- IRCCS
Fondazione Santa Lucia, Via Ardeatina, 306/354, 00142 Rome, Italy
| | - Raffaele Saladino
- Dipartimento
di Scienze Ecologiche e Biologiche, Università
della Tuscia, Via S. C. De Lellis 44, 01100 Viterbo, Italy
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24
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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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25
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Structural basis for the ethanol action on G-protein-activated inwardly rectifying potassium channel 1 revealed by NMR spectroscopy. Proc Natl Acad Sci U S A 2018; 115:3858-3863. [PMID: 29581303 DOI: 10.1073/pnas.1722257115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Ethanol consumption leads to a wide range of pharmacological effects by acting on the signaling proteins in the human nervous system, such as ion channels. Despite its familiarity and biological importance, very little is known about the molecular mechanisms underlying the ethanol action, due to extremely weak binding affinity and the dynamic nature of the ethanol interaction. In this research, we focused on the primary in vivo target of ethanol, G-protein-activated inwardly rectifying potassium channel (GIRK), which is responsible for the ethanol-induced analgesia. By utilizing solution NMR spectroscopy, we characterized the changes in the structure and dynamics of GIRK induced by ethanol binding. We demonstrated here that ethanol binds to GIRK with an apparent dissociation constant of 1.0 M and that the actual physiological binding site of ethanol is located on the cavity formed between the neighboring cytoplasmic regions of the GIRK tetramer. From the methyl-based NMR relaxation analyses, we revealed that ethanol activates GIRK by shifting the conformational equilibrium processes, which are responsible for the gating of GIRK, to stabilize an open conformation of the cytoplasmic ion gate. We suggest that the dynamic molecular mechanism of the ethanol-induced activation of GIRK represents a general model of the ethanol action on signaling proteins in the human nervous system.
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26
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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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27
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Synergistic activation of G protein-gated inwardly rectifying potassium channels by cholesterol and PI(4,5)P 2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1233-1241. [PMID: 28377218 DOI: 10.1016/j.bbamem.2017.03.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/16/2017] [Accepted: 03/31/2017] [Indexed: 11/23/2022]
Abstract
G-protein gated inwardly rectifying potassium (GIRK or Kir3) channels play a major role in the control of the heart rate, and require the membrane phospholipid phosphatidylinositol-bis-phosphate (PI(4,5)P2) for activation. Recently, we have shown that the activity of the heterotetrameric Kir3.1/Kir3.4 channel that underlies atrial KACh currents was enhanced by cholesterol. Similarly, the activities of both the Kir3.4 homomer and its active pore mutant Kir3.4* (Kir3.4_S143T) were also enhanced by cholesterol. Here we employ planar lipid bilayers to investigate the crosstalk between PI(4,5)P2 and cholesterol, and demonstrate that these two lipids act synergistically to activate Kir3.4* currents. Further studies using the Xenopus oocytes heterologous expression system suggest that PI(4,5)P2 and cholesterol act via distinct binding sites. Whereas PI(4,5)P2 binds to the cytosolic domain of the channel, the putative binding region of cholesterol is located at the center of the transmembrane domain overlapping the central glycine hinge region of the channel. Together, our data suggest that changes in the levels of two key membrane lipids - cholesterol and PI(4,5)P2 - could act in concert to provide fine-tuning of Kir3 channel function.
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28
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Competition of calcified calmodulin N lobe and PIP2 to an LQT mutation site in Kv7.1 channel. Proc Natl Acad Sci U S A 2017; 114:E869-E878. [PMID: 28096388 DOI: 10.1073/pnas.1612622114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Voltage-gated potassium 7.1 (Kv7.1) channel and KCNE1 protein coassembly forms the slow potassium current IKS that repolarizes the cardiac action potential. The physiological importance of the IKS channel is underscored by the existence of mutations in human Kv7.1 and KCNE1 genes, which cause cardiac arrhythmias, such as the long-QT syndrome (LQT) and atrial fibrillation. The proximal Kv7.1 C terminus (CT) binds calmodulin (CaM) and phosphatidylinositol-4,5-bisphosphate (PIP2), but the role of CaM in channel function is still unclear, and its possible interaction with PIP2 is unknown. Our recent crystallographic study showed that CaM embraces helices A and B with the apo C lobe and calcified N lobe, respectively. Here, we reveal the competition of PIP2 and the calcified CaM N lobe to a previously unidentified site in Kv7.1 helix B, also known to harbor an LQT mutation. Protein pulldown, molecular docking, molecular dynamics simulations, and patch-clamp recordings indicate that residues K526 and K527 in Kv7.1 helix B form a critical site where CaM competes with PIP2 to stabilize the channel open state. Data indicate that both PIP2 and Ca2+-CaM perform the same function on IKS channel gating by producing a left shift in the voltage dependence of activation. The LQT mutant K526E revealed a severely impaired channel function with a right shift in the voltage dependence of activation, a reduced current density, and insensitivity to gating modulation by Ca2+-CaM. The results suggest that, after receptor-mediated PIP2 depletion and increased cytosolic Ca2+, calcified CaM N lobe interacts with helix B in place of PIP2 to limit excessive IKS current inhibition.
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29
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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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30
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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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31
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Meng XY, Liu S, Cui M, Zhou R, Logothetis DE. The Molecular Mechanism of Opening the Helix Bundle Crossing (HBC) Gate of a Kir Channel. Sci Rep 2016; 6:29399. [PMID: 27439597 PMCID: PMC4954981 DOI: 10.1038/srep29399] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 06/20/2016] [Indexed: 11/19/2022] Open
Abstract
Inwardly rectifying K+ (Kir) channels, serving as natural molecular nanomachines, transport potassium ions across the plasma membrane of the cell. Along the ion permeation pathway, three relatively narrow regions (the selectivity filter (SF), the inner helix bundle crossing (HBC), and the cytosolic G loop) may serve as gates to control ion permeation. Our previous molecular dynamics simulations based on the crystal structure of a Kir3.1 chimera revealed the possible gating mechanism of the G loop gate. Here, we introduced a proline mutation in the inner helix and obtained a channel model of the open HBC gate. The open HBC gate reaches 0.6 nm in diameter, which allows partial hydrated K+ ions to pass through. During the gating process, both the transmembrane helices TM1 and TM2 cooperatively rotate in a counterclockwise direction (viewed from the extracellular side) with the aid of the phospholipid PIP2. Only when all the transmembrane helices adopt a counterclockwise rotation, the HBC gate can be stabilized in the open state. We estimate that introduction of the proline mutation decreases the energy required to open the HBC gate by about 1.4 kcal/mol (ΔΔG).
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Affiliation(s)
- Xuan-Yu Meng
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.,Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Shengtang Liu
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Meng Cui
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center 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
| | - Diomedes E Logothetis
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
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32
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Xue Q, Zheng QC, Zhang JL, Cui YL, Zhang HX. Exploring the mechanism how Marburg virus VP35 recognizes and binds dsRNA by molecular dynamics simulations and free energy calculations. Biopolymers 2016; 101:849-60. [PMID: 24459115 DOI: 10.1002/bip.22463] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/16/2014] [Accepted: 01/17/2014] [Indexed: 12/14/2022]
Abstract
Filoviruses often cause terrible infectious disease which has not been successfully dealt with pharmacologically. All filoviruses encode a unique protein termed VP35 which can mask doubled-stranded RNA to deactivate interferon. The interface of VP35-dsRNA would be a feasible target for structure-based antiviral agent design. To explore the essence of VP35-dsRNA interaction, molecular dynamics simulation combined with MM-GBSA calculations were performed on Marburg virus VP35-dsRNA complex and several mutational complexes. The energetic analysis indicates that nonpolar interactions provide the main driving force for the binding process. Although the intermolecular electrostatic interactions play important roles in VP35-dsRNA interaction, the whole polar interactions are unfavorable for binding which result in a low binding affinity. Compared with wild type VP35, the studied mutants F228A, R271A, and K298A have obviously reduced binding free energies with dsRNA reflecting in the reduction of polar or nonpolar interactions. The results also indicate that the loss of binding affinity for one dsRNA strand would abolish the total binding affinity. Three important residues Arg271, Arg294, and Lys298 which makes the largest contribution for binding in VP35 lose their binding affinity significantly in mutants. The uncovering of VP35-dsRNA recognition mechanism will provide some insights for development of antiviral drug.
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Affiliation(s)
- Qiao Xue
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, China
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Pöyry S, Vattulainen I. Role of charged lipids in membrane structures - Insight given by simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2322-2333. [PMID: 27003126 DOI: 10.1016/j.bbamem.2016.03.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/09/2016] [Accepted: 03/11/2016] [Indexed: 01/28/2023]
Abstract
Lipids and proteins are the main components of cell membranes. It is becoming increasingly clear that lipids, in addition to providing an environment for proteins to work in, are in many cases also able to modulate the structure and function of those proteins. Particularly charged lipids such as phosphatidylinositols and phosphatidylserines are involved in several examples of such effects. Molecular dynamics simulations have proved an invaluable tool in exploring these aspects. This so-called computational microscope can provide both complementing explanations for the experimental results and guide experiments to fruitful directions. In this paper, we review studies that have utilized molecular dynamics simulations to unravel the roles of charged lipids in membrane structures. We focus on lipids as active constituents of the membranes, affecting both general membrane properties as well as non-lipid membrane components, mainly proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sanja Pöyry
- Department of Physics, Tampere University of Technology, POB 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, POB 692, FI-33101 Tampere, Finland; MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark; Department of Physics, University of Helsinki, POB 64, FI-00014 Helsinki, Finland.
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34
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The ICl,swell inhibitor DCPIB blocks Kir channels that possess weak affinity for PIP2. Pflugers Arch 2016; 468:817-24. [PMID: 26837888 DOI: 10.1007/s00424-016-1794-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/17/2016] [Accepted: 01/20/2016] [Indexed: 12/15/2022]
Abstract
Inwardly rectifying K(+) (Kir) channels are important contributors to the resting membrane potential and regulate cellular excitability. The activity of Kir channels depends critically on the phospholipid PIP2. Several modulators of the activity of Kir channels alter the apparent affinity of the channel to PIP2. Channels with high apparent affinity to PIP2 may not respond to a given modulator, but mutations that decrease such affinity can render the channel susceptible to modulation. Here, we identify a known inhibitor of the swelling-activated Cl(-) current, DCPIB, as an effective inhibitor of a number of Kir channels both in native cardiac cells and in heterologous expression systems. We show that the apparent affinity to PIP2 determines whether DCPIB will serve as an efficient blocker of Kir channels. These effects are consistent with a model in which DCPIB competes with PIP2 for a common binding site.
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Abstract
UNLABELLED Inwardly rectifying potassium channels enforce tight control of resting membrane potential in excitable cells. The Kir3.2 channel, a member of the Kir3 subfamily of G-protein-activated potassium channels (GIRKs), plays several roles in the nervous system, including key responsibility in the GABAB pathway of inhibition, in pain perception pathways via opioid receptors, and is also involved in alcoholism. PKC phosphorylation acts on the channel to reduce activity, yet the mechanism is incompletely understood. Using the heterologous Xenopus oocyte system combined with molecular dynamics simulations, we show that PKC modulation of channel activity is dependent on Ser-196 in Kir3.2 such that, when this site is phosphorylated, the channel is less sensitive to PKC inhibition. This reduced inhibition is dependent on an interaction between phospho-Ser (SEP)-196 and Arg-201, reducing Arg-201 interaction with the sodium-binding site Asp-228. Neutralization of either SEP-196 or Arg-201 leads to a channel with reduced activity and increased sensitivity to PKC inhibition. This study clarifies the role of Ser-196 as an allosteric modulator of PKC inhibition and suggests that the SEP-196/Arg-201 interaction is critical for maintaining maximal channel activity. SIGNIFICANCE STATEMENT The inwardly rectifying potassium 3.2 (Kir3.2) channel is found principally in neurons that regulate diverse brain functions, including pain perception, alcoholism, and substance addiction. Activation or inhibition of this channel leads to changes in neuronal firing and chemical message transmission. The Kir3.2 channel is subject to regulation by intracellular signals including sodium, G-proteins, ethanol, the phospholipid phosphatidylinositol bis-phosphate, and phosphorylation by protein kinases. Here, we take advantage of the recently published structure of Kir3.2 to provide an in-depth molecular view of how phosphorylation of a specific residue previously thought to be the target of PKC promotes channel gating and acts as an allosteric modulator of PKC-mediated inhibition.
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36
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Hatcher-Solis C, Fribourg M, Spyridaki K, Younkin J, Ellaithy A, Xiang G, Liapakis G, Gonzalez-Maeso J, Zhang H, Cui M, Logothetis DE. G protein-coupled receptor signaling to Kir channels in Xenopus oocytes. Curr Pharm Biotechnol 2015; 15:987-95. [PMID: 25374032 DOI: 10.2174/1389201015666141031111916] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/04/2014] [Accepted: 10/06/2014] [Indexed: 01/30/2023]
Abstract
Kir3 (or GIRK) channels have been known for nearly three decades to be activated by direct interactions with the βγ subunits of heterotrimeric G (Gαβγ) proteins in a membrane-delimited manner. Gα also interacts with GIRK channels and since PTX-sensitive Gα subunits show higher affinity of interaction they confer signaling specificity to G Protein- Coupled Receptors (GPCRs) that normally couple to these G protein subunits. In heterologous systems, overexpression of non PTX-sensitive Gα subunits scavenges the available Gβγ and biases GIRK activation through GPCRs that couple to these Gα subunits. Moreover, all Kir channels rely on their direct interactions with the phospholipid PIP2 to maintain their activity. Thus, signals that activate phospholipase C (e.g. through Gq signaling) to hydrolyze PIP2 result in inhibition of Kir channel activity. In this review, we illustrate with experiments performed in Xenopus oocytes that Kir channels can be used efficiently as reporters of GPCR function through Gi, Gs or Gq signaling. The membrane-delimited nature of this expression system makes it highly efficient for constructing dose-response curves yielding highly reproducible apparent affinities of different ligands for each GPCR tested.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Diomedes E Logothetis
- Department of Physiology and Biophysics, Medical College of Virginia Campus, Sanger Hall 3-038a, Virginia Commonwealth University, School of Medicine, 1101 E. Marshall Street, Richmond, VA 23298-0551, USA.
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37
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Logothetis DE, Mahajan R, Adney SK, Ha J, Kawano T, Meng XY, Cui M. Unifying Mechanism of Controlling Kir3 Channel Activity by G Proteins and Phosphoinositides. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 123:1-26. [PMID: 26422981 DOI: 10.1016/bs.irn.2015.05.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The question that started with the pioneering work of Otto Loewi in the 1920s, to identify how stimulation of the vagus nerve decreased heart rate, is approaching its 100th year anniversary. In the meantime, we have learned that the neurotransmitter acetylcholine acting through muscarinic M2 receptors activates cardiac potassium (Kir3) channels via the βγ subunits of G proteins, an important effect that contributes to slowing atrial pacemaker activity. Concurrent stimulation of M1 or M3 receptors hydrolyzes PIP2, a signaling phospholipid essential to maintaining Kir3 channel activity, thus causing desensitization of channel activity and protecting the heart from overinhibition of pacemaker activity. Four mammalian members of the Kir3 subfamily, expressed in heart, brain, endocrine organs, etc., are modulated by a plethora of stimuli to regulate cellular excitability. With the recent great advances in ion channel structural biology, three-dimensional structures of Kir3 channels with PIP2 and the Gβγ subunits are now available. Mechanistic insights have emerged that explain how modulatory control of activity feeds into a core mechanism of channel-PIP2 interactions to regulate the conformation of channel gates. This complex but beautiful system continues to surprise us for almost 100 years with an apparent wisdom in its intricate design.
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Affiliation(s)
- Diomedes E Logothetis
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA.
| | - Rahul Mahajan
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Scott K Adney
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Junghoon Ha
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Takeharu Kawano
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Xuan-Yu Meng
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Meng Cui
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
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38
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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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Zhang M, Meng XY, Zhang JF, Cui M, Logothetis DE. Molecular overlap in the regulation of SK channels by small molecules and phosphoinositides. SCIENCE ADVANCES 2015; 1:e1500008. [PMID: 26366439 PMCID: PMC4563807 DOI: 10.1126/sciadv.1500008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 05/29/2015] [Indexed: 06/05/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PIP2) directly interacts with the small-conductance Ca2+-activated K+ 2-a (SK2-a) channel/calmodulin complex, serving as a critical element in the regulation of channel activity. We report that changes of protein conformation in close proximity to the PIP2 binding site induced by a small-molecule SK channel modulator, NS309, can effectively enhance the interaction between the protein and PIP2 to potentiate channel activity. This novel modulation of PIP2 sensitivity by small-molecule drugs is likely not to be limited in its application to SK channels, representing an intriguing strategy to develop drugs controlling the activity of the large number of PIP2-dependent proteins.
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Affiliation(s)
- Miao Zhang
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, 1101 East Marshall Street, Richmond, VA 23298, USA
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, 9401 Jeronimo Road, Irvine, CA 92618, USA
| | - Xuan-Yu Meng
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, 1101 East Marshall Street, Richmond, VA 23298, USA
| | - Ji-fang Zhang
- Department of Molecular Physiology and Biophysics, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
- Farber Institute for Neurosciences and Graduate Program in Neuroscience, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Meng Cui
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, 1101 East Marshall Street, Richmond, VA 23298, USA
| | - Diomedes E. Logothetis
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, 1101 East Marshall Street, Richmond, VA 23298, USA
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40
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Tang QY, Larry T, Hendra K, Yamamoto E, Bell J, Cui M, Logothetis DE, Boland LM. Mutations in Nature Conferred a High Affinity Phosphatidylinositol 4,5-Bisphosphate-binding Site in Vertebrate Inwardly Rectifying Potassium Channels. J Biol Chem 2015; 290:16517-29. [PMID: 25957411 DOI: 10.1074/jbc.m115.640409] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/06/2022] Open
Abstract
All vertebrate inwardly rectifying potassium (Kir) channels are activated by phosphatidylinositol 4,5-bisphosphate (PIP2) (Logothetis, D. E., Petrou, V. I., Zhang, M., Mahajan, R., Meng, X. Y., Adney, S. K., Cui, M., and Baki, L. (2015) Annu. Rev. Physiol. 77, 81-104; Fürst, O., Mondou, B., and D'Avanzo, N. (2014) Front. Physiol. 4, 404-404). Structural components of a PIP2-binding site are conserved in vertebrate Kir channels but not in distantly related animals such as sponges and sea anemones. To expand our understanding of the structure-function relationships of PIP2 regulation of Kir channels, we studied AqKir, which was cloned from the marine sponge Amphimedon queenslandica, an animal that represents the phylogenetically oldest metazoans. A requirement for PIP2 in the maintenance of AqKir activity was examined in intact oocytes by activation of a co-expressed voltage-sensing phosphatase, application of wortmannin (at micromolar concentrations), and activation of a co-expressed muscarinic acetylcholine receptor. All three mechanisms to reduce the availability of PIP2 resulted in inhibition of AqKir current. However, time-dependent rundown of AqKir currents in inside-out patches could not be re-activated by direct application to the inside membrane surface of water-soluble dioctanoyl PIP2, and the current was incompletely re-activated by the more hydrophobic arachidonyl stearyl PIP2. When we introduced mutations to AqKir to restore two positive charges within the vertebrate PIP2-binding site, both forms of PIP2 strongly re-activated the mutant sponge channels in inside-out patches. Molecular dynamics simulations validate the additional hydrogen bonding potential of the sponge channel mutants. Thus, nature's mutations conferred a high affinity activation of vertebrate Kir channels by PIP2, and this is a more recent evolutionary development than the structures that explain ion channel selectivity and inward rectification.
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Affiliation(s)
- Qiong-Yao Tang
- From the Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298, the Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, XuZhou Medical College, Xuzhou, 221004 Jiangsu Province, China
| | - Trevor Larry
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
| | - Kalen Hendra
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
| | - Erica Yamamoto
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
| | - Jessica Bell
- the Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, and
| | - Meng Cui
- From the Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298
| | - Diomedes E Logothetis
- From the Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298
| | - Linda M Boland
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
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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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42
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Fowler PW, Bollepalli MK, Rapedius M, Nematian-Ardestani E, Shang L, Sansom MS, Tucker SJ, Baukrowitz T. Insights into the structural nature of the transition state in the Kir channel gating pathway. Channels (Austin) 2014; 8:551-5. [PMID: 25483285 PMCID: PMC4594414 DOI: 10.4161/19336950.2014.962371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In a previous study we identified an extensive gating network within the inwardly rectifying Kir1.1 (ROMK) channel by combining systematic scanning mutagenesis and functional analysis with structural models of the channel in the closed, pre-open and open states. This extensive network appeared to stabilize the open and pre-open states, but the network fragmented upon channel closure. In this study we have analyzed the gating kinetics of different mutations within key parts of this gating network. These results suggest that the structure of the transition state (TS), which connects the pre-open and closed states of the channel, more closely resembles the structure of the pre-open state. Furthermore, the G-loop, which occurs at the center of this extensive gating network, appears to become unstructured in the TS because mutations within this region have a ‘catalytic’ effect upon the channel gating kinetics.
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Affiliation(s)
- Philip W Fowler
- a Department of Biochemistry ; University of Oxford , Oxford , UK
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43
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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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44
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Zhang M, Meng XY, Cui M, Pascal JM, Logothetis DE, Zhang JF. Selective phosphorylation modulates the PIP2 sensitivity of the CaM-SK channel complex. Nat Chem Biol 2014; 10:753-9. [PMID: 25108821 DOI: 10.1038/nchembio.1592] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 06/19/2014] [Indexed: 11/09/2022]
Abstract
Phosphatidylinositol bisphosphate (PIP2) regulates the activities of many membrane proteins, including ion channels, through direct interactions. However, the affinity of PIP2 is so high for some channel proteins that its physiological role as a modulator has been questioned. Here we show that PIP2 is a key cofactor for activation of small conductance Ca2+-activated potassium channels (SKs) by Ca(2+)-bound calmodulin (CaM). Removal of the endogenous PIP2 inhibits SKs. The PIP2-binding site resides at the interface of CaM and the SK C terminus. We further demonstrate that the affinity of PIP2 for its target proteins can be regulated by cellular signaling. Phosphorylation of CaM T79, located adjacent to the PIP2-binding site, by casein kinase 2 reduces the affinity of PIP2 for the CaM-SK channel complex by altering the dynamic interactions among amino acid residues surrounding the PIP2-binding site. This effect of CaM phosphorylation promotes greater channel inhibition by G protein-mediated hydrolysis of PIP2.
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Affiliation(s)
- Miao Zhang
- 1] Department of Molecular Physiology and Biophysics, Thomas Jefferson University, Philadelphia, Pennsylvania, USA. [2] Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Xuan-Yu Meng
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Meng Cui
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - John M Pascal
- Department of Biochemistry &Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Diomedes E Logothetis
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Ji-Fang Zhang
- 1] Department of Molecular Physiology and Biophysics, Thomas Jefferson University, Philadelphia, Pennsylvania, USA. [2] Farber Institute for Neurosciences, Thomas Jefferson University, Philadelphia, Pennsylvania, USA. [3] Graduate Program in Neuroscience, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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45
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Inanobe A, Nakagawa A, Kurachi Y. Conformational changes underlying pore dilation in the cytoplasmic domain of mammalian inward rectifier K+ channels. PLoS One 2013; 8:e79844. [PMID: 24244570 PMCID: PMC3823594 DOI: 10.1371/journal.pone.0079844] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 09/25/2013] [Indexed: 11/18/2022] Open
Abstract
The cytoplasmic domain of inward rectifier K+ (Kir) channels associates with cytoplasmic ligands and undergoes conformational change to control the gate present in its transmembrane domain. Ligand-operated activation appears to cause dilation of the pore at the cytoplasmic domain. However, it is still unclear how the cytoplasmic domain supports pore dilation and how alterations to this domain affect channel activity. In the present study, we focused on 2 spatially adjacent residues, i.e., Glu236 and Met313, of the G protein-gated Kir channel subunit Kir3.2. In the closed state, these pore-facing residues are present on adjacent βD and βH strands, respectively. We mutated both residues, expressed them with the m2-muscarinic receptor in Xenopus oocytes, and measured the acetylcholine-dependent K+ currents. The dose-response curves of the Glu236 mutants tended to be shifted to the right. In comparison, the slopes of the concentration-dependent curves were reduced and the single-channel properties were altered in the Met313 mutants. The introduction of arginine at position 236 conferred constitutive activity and caused a leftward shift in the conductance-voltage relationship. The crystal structure of the cytoplasmic domain of the mutant showed that the arginine contacts the main chains of the βH and βI strands of the adjacent subunit. Because the βH strand forms a β sheet with the βI and βD strands, the immobilization of the pore-forming β sheet appears to confer unique properties to the mutant. These results suggest that the G protein association triggers pore dilation at the cytoplasmic domain in functional channels, and the pore-constituting structural elements contribute differently to these conformational changes.
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Affiliation(s)
- Atsushi Inanobe
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Center for Advanced Medical Engineering and Informatics, Osaka University, Suita, Osaka, Japan
- * E-mail: (AI); (YK)
| | - Atsushi Nakagawa
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Yoshihisa Kurachi
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Center for Advanced Medical Engineering and Informatics, Osaka University, Suita, Osaka, Japan
- * E-mail: (AI); (YK)
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Rosenhouse-Dantsker A, Noskov S, Durdagi S, Logothetis DE, Levitan I. Identification of novel cholesterol-binding regions in Kir2 channels. J Biol Chem 2013; 288:31154-64. [PMID: 24019518 DOI: 10.1074/jbc.m113.496117] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inwardly rectifying potassium (Kir) channels play an important role in setting the resting membrane potential and modulating membrane excitability. We have recently shown that cholesterol regulates representative members of the Kir family and that in the majority of the cases, cholesterol suppresses channel function. Furthermore, recent data indicate that cholesterol regulates Kir channels by specific sterol-protein interactions, yet the location of the cholesterol binding site in Kir channels is unknown. Using a combined computational-experimental approach, we show that cholesterol may bind to two nonanular hydrophobic regions in the transmembrane domain of Kir2.1 located between adjacent subunits of the channel. The location of the binding regions suggests that cholesterol modulates channel function by affecting the hinging motion at the center of the pore-lining transmembrane helix that underlies channel gating either directly or through the interface between the N and C termini of the channel.
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Affiliation(s)
- Avia Rosenhouse-Dantsker
- From the Department of Medicine, Pulmonary Section, University of Illinois, Chicago, Illinois 60612
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47
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Membrane channels as integrators of G-protein-mediated signaling. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:521-31. [PMID: 24028827 DOI: 10.1016/j.bbamem.2013.08.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/14/2013] [Accepted: 08/21/2013] [Indexed: 01/03/2023]
Abstract
A variety of extracellular stimuli regulate cellular responses via membrane receptors. A well-known group of seven-transmembrane domain-containing proteins referred to as G protein-coupled receptors, directly couple with the intracellular GTP-binding proteins (G proteins) across cell membranes and trigger various cellular responses by regulating the activity of several enzymes as well as ion channels. Many specific populations of ion channels are directly controlled by G proteins; however, indirect modulation of some channels by G protein-dependent phosphorylation events and lipid metabolism is also observed. G protein-mediated diverse modifications affect the ion channel activities and spatio-temporally regulate membrane potentials as well as of intracellular Ca(2+) concentrations in both excitatory and non-excitatory cells. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. Guest Editor: Jean Claude Hervé.
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48
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Mahajan R, Ha J, Zhang M, Kawano T, Kozasa T, Logothetis DE. A computational model predicts that Gβγ acts at a cleft between channel subunits to activate GIRK1 channels. Sci Signal 2013; 6:ra69. [PMID: 23943609 DOI: 10.1126/scisignal.2004075] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The atrial G protein (heterotrimeric guanine nucleotide-binding protein)-regulated inwardly rectifying K(+) (GIRK1 and GIRK4) heterotetrameric channels underlie the acetylcholine-induced K(+) current responsible for vagal inhibition of heart rate and are activated by the G protein βγ subunits (Gβγ). We used a multistage protein-protein docking approach with data from published structures of GIRK1 and Gβγ to generate an experimentally testable interaction model of Gβγ docked onto the cytosolic domains of the GIRK1 homotetramer. The model suggested a mechanism by which Gβγ promotes the open state of a specific cytosolic gate in the channel, the G loop gate. The predicted structure showed that the Gβ subunit interacts with the channel near the site of action for ethanol and stabilizes an intersubunit cleft formed by two loops (LM and DE) of adjacent channel subunits. Using a heterologous expression system, we disrupted the predicted GIRK1- and Gβγ-interacting residues by mutation of one protein and then rescued the regulatory activity by mutating reciprocal residues in the other protein. Disulfide cross-linking of channels and Gβγ with cysteine mutations at the predicted interacting residues yielded activated channels. The mechanism of Gβγ-induced activation of GIRK4 was distinct from GIRK1 homotetramers. However, GIRK1-GIRK4 heterotetrameric channels activated by Gβγ displayed responses indicating that the GIRK1 subunit dominated the response pattern. This work demonstrated that combining computational with experimental approaches is an effective method for elucidating interactions within protein complexes that otherwise might be challenging to decipher.
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Affiliation(s)
- Rahul Mahajan
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
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49
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Rosenhouse-Dantsker A, Noskov S, Logothetis DE, Levitan I. Cholesterol sensitivity of KIR2.1 depends on functional inter-links between the N and C termini. Channels (Austin) 2013; 7:303-12. [PMID: 23807091 DOI: 10.4161/chan.25437] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In recent years, cholesterol has been emerging as a major regulator of ion channel function. We have previously shown that cholesterol suppresses Kir2 channels, a subfamily of constitutively active strongly rectifying K (+) channels. Furthermore, our earlier studies have shown that cholesterol sensitivity of Kir2 channels depends on a group of residues that form a belt-like structure around the cytosolic pore of the channel in proximity to the transmembrane domain. In this study, we focus on the contributions of different structural domains of Kir2 channels in the regulation of their cholesterol sensitivity. Focusing on the mildest mutation in the sensitivity belt, L222I, we show that the sensitivity of the channel to cholesterol can be restored by crosstalk between three distinct cytosolic regions: the C-terminal CD loop, the EF and GA loops of the C-terminus, and the βA sheet of the N-terminus. Thus, in addition to the importance of residues that affect the cytosolic G-loop gate in the sensitivity of Kir2 channels to cholesterol, our data suggest an important role to the interactions at the interface between the channel's N- and C- termini that couple the intracellular domains of its four subunits during gating.
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50
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Bushman JD, Zhou Q, Shyng SL. A Kir6.2 pore mutation causes inactivation of ATP-sensitive potassium channels by disrupting PIP2-dependent gating. PLoS One 2013; 8:e63733. [PMID: 23700433 PMCID: PMC3659044 DOI: 10.1371/journal.pone.0063733] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/05/2013] [Indexed: 11/18/2022] Open
Abstract
In the absence of intracellular nucleotides, ATP-sensitive potassium (KATP) channels exhibit spontaneous activity via a phosphatidylinositol-4,5-bisphosphate (PIP2)-dependent gating process. Previous studies show that stability of this activity requires subunit-subunit interactions in the cytoplasmic domain of Kir6.2; selective mutagenesis and disease mutations at the subunit interface result in time-dependent channel inactivation. Here, we report that mutation of the central glycine in the pore-lining second transmembrane segment (TM2) to proline in Kir6.2 causes KATP channel inactivation. Unlike C-type inactivation, a consequence of selectivity filter closure, in many K(+) channels, the rate of inactivation in G156P channels was insensitive to changes in extracellular ion concentrations or ion species fluxing through the pore. Instead, the rate of G156P inactivation decreased with exogenous application of PIP2 and increased when PIP2-channel interaction was inhibited with neomycin or poly-L-lysine. These findings indicate the G156P mutation reduces the ability of PIP2 to stabilize the open state of KATP channels, similar to mutations in the cytoplasmic domain that produce inactivation. Consistent with this notion, when PIP2-dependent open state stability was substantially increased by addition of a second gain-of-function mutation, G156P inactivation was abolished. Importantly, bath application and removal of Mg(2+)-free ATP or a nonhydrolyzable analog of ATP, which binds to the cytoplasmic domain of Kir6.2 and causes channel closure, recover G156P channel from inactivation, indicating crosstalk between cytoplasmic and transmembrane domains. The G156P mutation provides mechanistic insight into the structural and functional interactions between the pore and cytoplasmic domains of Kir6.2 during gating.
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Affiliation(s)
- Jeremy D. Bushman
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Qing Zhou
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Show-Ling Shyng
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, United States of America
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