1
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Liu Z, Wang F, Yuan H, Tian F, Yang C, Hu F, Liu Y, Tang M, Ping M, Kang C, Luo T, Yang G, Hu M, Gao Z, Li P. An LQT2-related mutation in the voltage-sensing domain is involved in switching the gating polarity of hERG. BMC Biol 2024; 22:29. [PMID: 38317233 PMCID: PMC11380439 DOI: 10.1186/s12915-024-01833-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 01/23/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Cyclic Nucleotide-Binding Domain (CNBD)-family channels display distinct voltage-sensing properties despite sharing sequence and structural similarity. For example, the human Ether-a-go-go Related Gene (hERG) channel and the Hyperpolarization-activated Cyclic Nucleotide-gated (HCN) channel share high amino acid sequence similarity and identical domain structures. hERG conducts outward current and is activated by positive membrane potentials (depolarization), whereas HCN conducts inward current and is activated by negative membrane potentials (hyperpolarization). The structural basis for the "opposite" voltage-sensing properties of hERG and HCN remains unknown. RESULTS We found the voltage-sensing domain (VSD) involves in modulating the gating polarity of hERG. We identified that a long-QT syndrome type 2-related mutation within the VSD, K525N, mediated an inwardly rectifying non-deactivating current, perturbing the channel closure, but sparing the open state and inactivated state. K525N rescued the current of a non-functional mutation in the pore helix region (F627Y) of hERG. K525N&F627Y switched hERG into a hyperpolarization-activated channel. The reactivated inward current induced by hyperpolarization mediated by K525N&F627Y can be inhibited by E-4031 and dofetilide quite well. Moreover, we report an extracellular interaction between the S1 helix and the S5-P region is crucial for modulating the gating polarity. The alanine substitution of several residues in this region (F431A, C566A, I607A, and Y611A) impaired the inward current of K525N&F627Y. CONCLUSIONS Our data provide evidence that a potential cooperation mechanism in the extracellular vestibule of the VSD and the PD would determine the gating polarity in hERG.
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Affiliation(s)
- Zhipei Liu
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Feng Wang
- School of Pharmacy, Zunyi Medical University, Zunyi, 563000, China
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
| | - Hui Yuan
- School of Pharmacy, Zunyi Medical University, Zunyi, 563000, China
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
| | - Fuyun Tian
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chuanyan Yang
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Fei Hu
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yiyao Liu
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
| | - Meiqin Tang
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Meixuan Ping
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunlan Kang
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ting Luo
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, China
| | - Guimei Yang
- School of Pharmacy, Zunyi Medical University, Zunyi, 563000, China
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
| | - Mei Hu
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China
- Pharmacology Laboratory, Zhongshan Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Zhongshan, 528401, China
| | - Zhaobing Gao
- School of Pharmacy, Zunyi Medical University, Zunyi, 563000, China.
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China.
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ping Li
- School of Pharmacy, Zunyi Medical University, Zunyi, 563000, China.
- Zhongshan Institute for Drug Discovery, Zhongshan, 528400, China.
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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Fan C, Flood E, Sukomon N, Agarwal S, Allen TW, Nimigean CM. Calcium-gated potassium channel blockade via membrane-facing fenestrations. Nat Chem Biol 2024; 20:52-61. [PMID: 37653172 PMCID: PMC10847966 DOI: 10.1038/s41589-023-01406-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
Quaternary ammonium blockers were previously shown to bind in the pore to block both open and closed conformations of large-conductance calcium-activated potassium (BK and MthK) channels. Because blocker entry was assumed through the intracellular entryway (bundle crossing), closed-pore access suggested that the gate was not at the bundle crossing. Structures of closed MthK, a Methanobacterium thermoautotrophicum homolog of BK channels, revealed a tightly constricted intracellular gate, leading us to investigate the membrane-facing fenestrations as alternative pathways for blocker access directly from the membrane. Atomistic free energy simulations showed that intracellular blockers indeed access the pore through the fenestrations, and a mutant channel with narrower fenestrations displayed no closed-state TPeA block at concentrations that blocked the wild-type channel. Apo BK channels display similar fenestrations, suggesting that blockers may use them as access paths into closed channels. Thus, membrane fenestrations represent a non-canonical pathway for selective targeting of specific channel conformations, opening novel ways to selectively drug BK channels.
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Affiliation(s)
- Chen Fan
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria, Australia
- Schrödinger, Inc., New York, NY, USA
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Shubhangi Agarwal
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Victoria, Australia.
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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3
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Nordquist E, Zhang G, Barethiya S, Ji N, White KM, Han L, Jia Z, Shi J, Cui J, Chen J. Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels. PLoS Comput Biol 2023; 19:e1011460. [PMID: 37713443 PMCID: PMC10529646 DOI: 10.1371/journal.pcbi.1011460] [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: 06/24/2023] [Revised: 09/27/2023] [Accepted: 08/24/2023] [Indexed: 09/17/2023] Open
Abstract
Machine learning has played transformative roles in numerous chemical and biophysical problems such as protein folding where large amount of data exists. Nonetheless, many important problems remain challenging for data-driven machine learning approaches due to the limitation of data scarcity. One approach to overcome data scarcity is to incorporate physical principles such as through molecular modeling and simulation. Here, we focus on the big potassium (BK) channels that play important roles in cardiovascular and neural systems. Many mutants of BK channel are associated with various neurological and cardiovascular diseases, but the molecular effects are unknown. The voltage gating properties of BK channels have been characterized for 473 site-specific mutations experimentally over the last three decades; yet, these functional data by themselves remain far too sparse to derive a predictive model of BK channel voltage gating. Using physics-based modeling, we quantify the energetic effects of all single mutations on both open and closed states of the channel. Together with dynamic properties derived from atomistic simulations, these physical descriptors allow the training of random forest models that could reproduce unseen experimentally measured shifts in gating voltage, ∆V1/2, with a RMSE ~ 32 mV and correlation coefficient of R ~ 0.7. Importantly, the model appears capable of uncovering nontrivial physical principles underlying the gating of the channel, including a central role of hydrophobic gating. The model was further evaluated using four novel mutations of L235 and V236 on the S5 helix, mutations of which are predicted to have opposing effects on V1/2 and suggest a key role of S5 in mediating voltage sensor-pore coupling. The measured ∆V1/2 agree quantitatively with prediction for all four mutations, with a high correlation of R = 0.92 and RMSE = 18 mV. Therefore, the model can capture nontrivial voltage gating properties in regions where few mutations are known. The success of predictive modeling of BK voltage gating demonstrates the potential of combining physics and statistical learning for overcoming data scarcity in nontrivial protein function prediction.
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Affiliation(s)
- Erik Nordquist
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Guohui Zhang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Shrishti Barethiya
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Nathan Ji
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Kelli M. White
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Lu Han
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Zhiguang Jia
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Jingyi Shi
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
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4
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Nordquist E, Zhang G, Barethiya S, Ji N, White KM, Han L, Jia Z, Shi J, Cui J, Chen J. Incorporating physics to overcome data scarcity in predictive modeling of protein function: a case study of BK channels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.24.546384. [PMID: 37425916 PMCID: PMC10327070 DOI: 10.1101/2023.06.24.546384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Machine learning has played transformative roles in numerous chemical and biophysical problems such as protein folding where large amount of data exists. Nonetheless, many important problems remain challenging for data-driven machine learning approaches due to the limitation of data scarcity. One approach to overcome data scarcity is to incorporate physical principles such as through molecular modeling and simulation. Here, we focus on the big potassium (BK) channels that play important roles in cardiovascular and neural systems. Many mutants of BK channel are associated with various neurological and cardiovascular diseases, but the molecular effects are unknown. The voltage gating properties of BK channels have been characterized for 473 site-specific mutations experimentally over the last three decades; yet, these functional data by themselves remain far too sparse to derive a predictive model of BK channel voltage gating. Using physics-based modeling, we quantify the energetic effects of all single mutations on both open and closed states of the channel. Together with dynamic properties derived from atomistic simulations, these physical descriptors allow the training of random forest models that could reproduce unseen experimentally measured shifts in gating voltage, ΔV 1/2 , with a RMSE ∼ 32 mV and correlation coefficient of R ∼ 0.7. Importantly, the model appears capable of uncovering nontrivial physical principles underlying the gating of the channel, including a central role of hydrophobic gating. The model was further evaluated using four novel mutations of L235 and V236 on the S5 helix, mutations of which are predicted to have opposing effects on V 1/2 and suggest a key role of S5 in mediating voltage sensor-pore coupling. The measured ΔV 1/2 agree quantitatively with prediction for all four mutations, with a high correlation of R = 0.92 and RMSE = 18 mV. Therefore, the model can capture nontrivial voltage gating properties in regions where few mutations are known. The success of predictive modeling of BK voltage gating demonstrates the potential of combining physics and statistical learning for overcoming data scarcity in nontrivial protein function prediction. Author Summary Deep machine learning has brought many exciting breakthroughs in chemistry, physics and biology. These models require large amount of training data and struggle when the data is scarce. The latter is true for predictive modeling of the function of complex proteins such as ion channels, where only hundreds of mutational data may be available. Using the big potassium (BK) channel as a biologically important model system, we demonstrate that a reliable predictive model of its voltage gating property could be derived from only 473 mutational data by incorporating physics-derived features, which include dynamic properties from molecular dynamics simulations and energetic quantities from Rosetta mutation calculations. We show that the final random forest model captures key trends and hotspots in mutational effects of BK voltage gating, such as the important role of pore hydrophobicity. A particularly curious prediction is that mutations of two adjacent residues on the S5 helix would always have opposite effects on the gating voltage, which was confirmed by experimental characterization of four novel mutations. The current work demonstrates the importance and effectiveness of incorporating physics in predictive modeling of protein function with scarce data.
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Affiliation(s)
- Erik Nordquist
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Guohui Zhang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shrishti Barethiya
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Nathan Ji
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA
| | - Kelli M. White
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lu Han
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Zhiguang Jia
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Jingyi Shi
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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5
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Kurauskas V, Tonelli M, Henzler-Wildman K. Full opening of helix bundle crossing does not lead to NaK channel activation. J Gen Physiol 2022; 154:213659. [PMID: 36326620 PMCID: PMC9640265 DOI: 10.1085/jgp.202213196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/11/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022] Open
Abstract
A critical part of ion channel function is the ability to open and close in response to stimuli and thus conduct ions in a regulated fashion. While x-ray diffraction studies of ion channels suggested a general steric gating mechanism located at the helix bundle crossing (HBC), recent functional studies on several channels indicate that the helix bundle crossing is wide-open even in functionally nonconductive channels. Two NaK channel variants were crystallized in very different open and closed conformations, which served as important models of the HBC gating hypothesis. However, neither of these NaK variants is conductive in liposomes unless phenylalanine 92 is mutated to alanine (F92A). Here, we use NMR to probe distances at near-atomic resolution of the two NaK variants in lipid bicelles. We demonstrate that in contrast to the crystal structures, both NaK variants are in a fully open conformation, akin to Ca2+-bound MthK channel structure where the HBC is widely open. While we were not able to determine what a conductive NaK structure is like, our further inquiry into the gating mechanism suggests that the selectivity filter and pore helix are coupled to the M2 helix below and undergo changes in the structure when F92 is mutated. Overall, our data show that NaK exhibits coupling between the selectivity filter and HBC, similar to K+ channels, and has a more complex gating mechanism than previously thought, where the full opening of HBC does not lead to channel activation.
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Affiliation(s)
- Vilius Kurauskas
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin—Madison, Madison, WI
| | - Katherine Henzler-Wildman
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI
- National Magnetic Resonance Facility at Madison, University of Wisconsin—Madison, Madison, WI
- Correspondence to Katherine Henzler-Wildman:
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6
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Gabriel TS, Hansen UP, Urban M, Drexler N, Winterstein T, Rauh O, Thiel G, Kast SM, Schroeder I. Asymmetric Interplay Between K + and Blocker and Atomistic Parameters From Physiological Experiments Quantify K + Channel Blocker Release. Front Physiol 2021; 12:737834. [PMID: 34777005 PMCID: PMC8586521 DOI: 10.3389/fphys.2021.737834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022] Open
Abstract
Modulating the activity of ion channels by blockers yields information on both the mode of drug action and on the biophysics of ion transport. Here we investigate the interplay between ions in the selectivity filter (SF) of K+ channels and the release kinetics of the blocker tetrapropylammonium in the model channel KcvNTS. A quantitative expression calculates blocker release rate constants directly from voltage-dependent ion occupation probabilities in the SF. The latter are obtained by a kinetic model of single-channel currents recorded in the absence of the blocker. The resulting model contains only two adjustable parameters of ion-blocker interaction and holds for both symmetric and asymmetric ionic conditions. This data-derived model is corroborated by 3D reference interaction site model (3D RISM) calculations on several model systems, which show that the K+ occupation probability is unaffected by the blocker, a direct consequence of the strength of the ion-carbonyl attraction in the SF, independent of the specific protein background. Hence, KcvNTS channel blocker release kinetics can be reduced to a small number of system-specific parameters. The pore-independent asymmetric interplay between K+ and blocker ions potentially allows for generalizing these results to similar potassium channels.
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Affiliation(s)
- Tobias S Gabriel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Ulf-Peter Hansen
- Department of Structural Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Martin Urban
- Physikalische Chemie III, Technische Universita̋t Dortmund, Dortmund, Germany
| | - Nils Drexler
- Institute of Physiology II, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Tobias Winterstein
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Oliver Rauh
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universita̋t Dortmund, Dortmund, Germany
| | - Indra Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany.,Institute of Physiology II, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
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7
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Suma A, Granata D, Thomson AS, Carnevale V, Rothberg BS. Polyamine blockade and binding energetics in the MthK potassium channel. J Gen Physiol 2021; 152:151703. [PMID: 32342093 PMCID: PMC7335011 DOI: 10.1085/jgp.201912527] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/24/2020] [Indexed: 11/20/2022] Open
Abstract
Polyamines such as spermidine and spermine are found in nearly all cells, at concentrations ranging up to 0.5 mM. These cations are endogenous regulators of cellular K+ efflux, binding tightly in the pores of inwardly rectifying K+ (Kir) channels in a voltage-dependent manner. Although the voltage dependence of Kir channel polyamine blockade is thought to arise at least partially from the energetically coupled movements of polyamine and K+ ions through the pore, the nature of physical interactions between these molecules is unclear. Here we analyze the polyamine-blocking mechanism in the model K+ channel MthK, using a combination of electrophysiology and computation. Spermidine (SPD3+) and spermine (SPM4+) each blocked current through MthK channels in a voltage-dependent manner, and blockade by these polyamines was described by a three-state kinetic scheme over a wide range of polyamine concentrations. In the context of the scheme, both SPD3+ and SPM4+ access a blocking site with similar effective gating valences (0.84 ± 0.03 e0 for SPD3+ and 0.99 ± 0.04 e0 for SPM4+), whereas SPM4+ binds in the blocked state with an ∼20-fold higher affinity than SPD3+ (Kd = 28.1 ± 3.1 µM for SPD3+ and 1.28 ± 0.20 µM for SPM4+), consistent with a free energy difference of 1.8 kcal/mol. Molecular simulations of the MthK pore in complex with either SPD3+ or SPM4+ are consistent with the leading amine interacting with the hydroxyl groups of T59, at the selectivity filter threshold, with access to this site governed by outward movement of K+ ions. These coupled movements can account for a large fraction of the voltage dependence of blockade. In contrast, differences in binding energetics between SPD3+ and SPM4+ may arise from distinct electrostatic interactions between the polyamines and carboxylate oxygens on the side chains of E92 and E96, located in the pore-lining helix.
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Affiliation(s)
- Antonio Suma
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA
| | - Daniele Granata
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA
| | - Andrew S Thomson
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA
| | - Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA
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8
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Vouga AG, Rockman ME, Yan J, Jacobson MA, Rothberg BS. State-dependent inhibition of BK channels by the opioid agonist loperamide. J Gen Physiol 2021; 153:212539. [PMID: 34357374 PMCID: PMC8352719 DOI: 10.1085/jgp.202012834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/19/2021] [Accepted: 07/08/2021] [Indexed: 12/20/2022] Open
Abstract
Large-conductance Ca2+-activated K+ (BK) channels control a range of physiological functions, and their dysfunction is linked to human disease. We have found that the widely used drug loperamide (LOP) can inhibit activity of BK channels composed of either α-subunits (BKα channels) or α-subunits plus the auxiliary γ1-subunit (BKα/γ1 channels), and here we analyze the molecular mechanism of LOP action. LOP applied at the cytosolic side of the membrane rapidly and reversibly inhibited BK current, an effect that appeared as a decay in voltage-activated BK currents. The apparent affinity for LOP decreased with hyperpolarization in a manner consistent with LOP behaving as an inhibitor of open, activated channels. Increasing LOP concentration reduced the half-maximal activation voltage, consistent with relative stabilization of the LOP-inhibited open state. Single-channel recordings revealed that LOP did not reduce unitary BK channel current, but instead decreased BK channel open probability and mean open times. LOP elicited use-dependent inhibition, in which trains of brief depolarizing steps lead to accumulated reduction of BK current, whereas single brief depolarizing steps do not. The principal effects of LOP on BK channel gating are described by a mechanism in which LOP acts as a state-dependent pore blocker. Our results suggest that therapeutic doses of LOP may act in part by inhibiting K+ efflux through intestinal BK channels.
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Affiliation(s)
- Alexandre G Vouga
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA
| | - Michael E Rockman
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA
| | - Jiusheng Yan
- Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marlene A Jacobson
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia PA
| | - Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA
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9
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Proks P, Schewe M, Conrad LJ, Rao S, Rathje K, Rödström KEJ, Carpenter EP, Baukrowitz T, Tucker SJ. Norfluoxetine inhibits TREK-2 K2P channels by multiple mechanisms including state-independent effects on the selectivity filter gate. J Gen Physiol 2021; 153:212184. [PMID: 34032848 PMCID: PMC8155809 DOI: 10.1085/jgp.202012812] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 05/06/2021] [Indexed: 12/25/2022] Open
Abstract
The TREK subfamily of two-pore domain K+ (K2P) channels are inhibited by fluoxetine and its metabolite, norfluoxetine (NFx). Although not the principal targets of this antidepressant, TREK channel inhibition by NFx has provided important insights into the conformational changes associated with channel gating and highlighted the role of the selectivity filter in this process. However, despite the availability of TREK-2 crystal structures with NFx bound, the precise mechanisms underlying NFx inhibition remain elusive. NFx has previously been proposed to be a state-dependent inhibitor, but its binding site suggests many possible ways in which this positively charged drug might inhibit channel activity. Here we show that NFx exerts multiple effects on single-channel behavior that influence both the open and closed states of the channel and that the channel can become highly activated by 2-APB while remaining in the down conformation. We also show that the inhibitory effects of NFx are unrelated to its positive charge but can be influenced by agonists which alter filter stability, such as ML335, as well as by an intrinsic voltage-dependent gating process within the filter. NFx therefore not only inhibits channel activity by altering the equilibrium between up and down conformations but also can directly influence filter gating. These results provide further insight into the complex allosteric mechanisms that modulate filter gating in TREK K2P channels and highlight the different ways in which filter gating can be regulated to permit polymodal regulation.
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Affiliation(s)
- Peter Proks
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.,OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK
| | - Marcus Schewe
- Department of Physiology, University of Kiel, Kiel, Germany
| | - Linus J Conrad
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.,OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Kristin Rathje
- Department of Physiology, University of Kiel, Kiel, Germany
| | | | - Elisabeth P Carpenter
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK.,Centre for Medicines Discovery, University of Oxford, UK
| | | | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.,OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK
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10
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Mironenko A, Zachariae U, de Groot BL, Kopec W. The Persistent Question of Potassium Channel Permeation Mechanisms. J Mol Biol 2021; 433:167002. [PMID: 33891905 DOI: 10.1016/j.jmb.2021.167002] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 02/09/2023]
Abstract
Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K+ ions in and out of a cell, by employing a carefully designed selectivity filter, evolutionarily conserved from viruses to mammals. The structure of the selectivity filter was determined at atomic resolution by x-ray crystallography, showing a tight coordination of desolvated K+ ions by the channel. However, the molecular mechanism of K+ ions permeation through potassium channels remains unclear, with structural, functional and computational studies often providing conflicting data and interpretations. In this review, we will present the proposed mechanisms, discuss their origins, and will critically assess them against all available data. General properties shared by all potassium channels are introduced first, followed by the introduction of two main mechanisms of ion permeation: soft and direct knock-on. Then, we will discuss critical computational and experimental studies that shaped the field. We will especially focus on molecular dynamics (MD) simulations, that provided mechanistic and energetic aspects of K+ permeation, but at the same time created long-standing controversies. Further challenges and possible solutions are presented as well.
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Affiliation(s)
- Andrei Mironenko
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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11
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Schmidt M, Schroeder I, Bauer D, Thiel G, Hamacher K. Inferring functional units in ion channel pores via relative entropy. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:37-57. [PMID: 33523249 PMCID: PMC7872957 DOI: 10.1007/s00249-020-01480-7] [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] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 10/11/2020] [Accepted: 11/09/2020] [Indexed: 11/25/2022]
Abstract
Coarse-grained protein models approximate the first-principle physical potentials. Among those modeling approaches, the relative entropy framework yields promising and physically sound results, in which a mapping from the target protein structure and dynamics to a model is defined and subsequently adjusted by an entropy minimization of the model parameters. Minimization of the relative entropy is equivalent to maximization of the likelihood of reproduction of (configurational ensemble) observations by the model. In this study, we extend the relative entropy minimization procedure beyond parameter fitting by a second optimization level, which identifies the optimal mapping to a (dimension-reduced) topology. We consider anisotropic network models of a diverse set of ion channels and assess our findings by comparison to experimental results.
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Affiliation(s)
- Michael Schmidt
- Department of Physics, TU Darmstadt, Karolinenpl. 5, 64289 Darmstadt, Germany
| | - Indra Schroeder
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Daniel Bauer
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Gerhard Thiel
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Kay Hamacher
- Department of Physics, Department of Biology, Department of Computer Science, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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12
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Jiang Y, Idikuda V, Chowdhury S, Chanda B. Activation of the archaeal ion channel MthK is exquisitely regulated by temperature. eLife 2020; 9:e59055. [PMID: 33274718 PMCID: PMC7717905 DOI: 10.7554/elife.59055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/17/2020] [Indexed: 11/13/2022] Open
Abstract
Physiological response to thermal stimuli in mammals is mediated by a structurally diverse class of ion channels, many of which exhibit polymodal behavior. To probe the diversity of biophysical mechanisms of temperature-sensitivity, we characterized the temperature-dependent activation of MthK, a two transmembrane calcium-activated potassium channel from thermophilic archaebacteria. Our functional complementation studies show that these channels are more efficient at rescuing K+ transport at 37°C than at 24°C. Electrophysiological activity of the purified MthK is extremely sensitive (Q10 >100) to heating particularly at low-calcium concentrations whereas channels lacking the calcium-sensing RCK domain are practically insensitive. By analyzing single-channel activities at limiting calcium concentrations, we find that temperature alters the coupling between the cytoplasmic RCK domains and the pore domain. These findings reveal a hitherto unexplored mechanism of temperature-dependent regulation of ion channel gating and shed light on ancient origins of temperature-sensitivity.
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Affiliation(s)
- Yihao Jiang
- Department of Anesthesiology, Washington University School of MedicineSt. LouisUnited States
- Center for the Investigation of Membrane Excitability Diseases (CIMED)St. LouisUnited States
| | - Vinay Idikuda
- Department of Anesthesiology, Washington University School of MedicineSt. LouisUnited States
- Center for the Investigation of Membrane Excitability Diseases (CIMED)St. LouisUnited States
| | - Sandipan Chowdhury
- Department of Anesthesiology, Washington University School of MedicineSt. LouisUnited States
- Center for the Investigation of Membrane Excitability Diseases (CIMED)St. LouisUnited States
| | - Baron Chanda
- Department of Anesthesiology, Washington University School of MedicineSt. LouisUnited States
- Center for the Investigation of Membrane Excitability Diseases (CIMED)St. LouisUnited States
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13
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Selectivity filter ion binding affinity determines inactivation in a potassium channel. Proc Natl Acad Sci U S A 2020; 117:29968-29978. [PMID: 33154158 DOI: 10.1073/pnas.2009624117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Potassium channels can become nonconducting via inactivation at a gate inside the highly conserved selectivity filter (SF) region near the extracellular side of the membrane. In certain ligand-gated channels, such as BK channels and MthK, a Ca2+-activated K+ channel from Methanobacterium thermoautotrophicum, the SF has been proposed to play a role in opening and closing rather than inactivation, although the underlying conformational changes are unknown. Using X-ray crystallography, identical conductive MthK structures were obtained in wide-ranging K+ concentrations (6 to 150 mM), unlike KcsA, whose SF collapses at low permeant ion concentrations. Surprisingly, three of the SF's four binding sites remained almost fully occupied throughout this range, indicating high affinities (likely submillimolar), while only the central S2 site titrated, losing its ion at 6 mM, indicating low K+ affinity (∼50 mM). Molecular simulations showed that the MthK SF can also collapse in the absence of K+, similar to KcsA, but that even a single K+ binding at any of the SF sites, except S4, can rescue the conductive state. The uneven titration across binding sites differs from KcsA, where SF sites display a uniform decrease in occupancy with K+ concentration, in the low millimolar range, leading to SF collapse. We found that ions were disfavored in MthK's S2 site due to weaker coordination by carbonyl groups, arising from different interactions with the pore helix and water behind the SF. We conclude that these differences in interactions endow the seemingly identical SFs of KcsA and MthK with strikingly different inactivating phenotypes.
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14
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Nimigean CM. Polyamine block of MthK potassium channels. J Gen Physiol 2020; 152:151820. [PMID: 32459330 PMCID: PMC7335008 DOI: 10.1085/jgp.202012614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Crina M. Nimigean
- Departments of Anesthesiology, and Physiology and Biophysics, Weill Cornell Medical College, New York, NY
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15
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A constricted opening in Kir channels does not impede potassium conduction. Nat Commun 2020; 11:3024. [PMID: 32541684 PMCID: PMC7295778 DOI: 10.1038/s41467-020-16842-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/28/2020] [Indexed: 01/07/2023] Open
Abstract
The canonical mechanistic model explaining potassium channel gating is of a conformational change that alternately dilates and constricts a collar-like intracellular entrance to the pore. It is based on the premise that K+ ions maintain a complete hydration shell while passing between the transmembrane cavity and cytosol, which must be accommodated. To put the canonical model to the test, we locked the conformation of a Kir K+ channel to prevent widening of the narrow collar. Unexpectedly, conduction was unimpaired in the locked channels. In parallel, we employed all-atom molecular dynamics to simulate K+ ions moving along the conduction pathway between the lower cavity and cytosol. During simulations, the constriction did not significantly widen. Instead, transient loss of some water molecules facilitated K+ permeation through the collar. The low free energy barrier to partial dehydration in the absence of conformational change indicates Kir channels are not gated by the canonical mechanism.
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16
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Gu RX, de Groot BL. Lipid-protein interactions modulate the conformational equilibrium of a potassium channel. Nat Commun 2020; 11:2162. [PMID: 32358584 PMCID: PMC7195391 DOI: 10.1038/s41467-020-15741-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/18/2020] [Indexed: 01/17/2023] Open
Abstract
Cell membranes actively participate in the regulation of protein structure and function. In this work, we conduct molecular dynamics simulations to investigate how different membrane environments affect protein structure and function in the case of MthK, a potassium channel. We observe different ion permeation rates of MthK in membranes with different properties, and ascribe them to a shift of the conformational equilibrium between two states of the channel that differ according to whether a transmembrane helix has a kink. Further investigations indicate that two key residues in the kink region mediate a crosstalk between two gates at the selectivity filter and the central cavity, respectively. Opening of one gate eventually leads to closure of the other. Our simulations provide an atomistic model of how lipid-protein interactions affect the conformational equilibrium of a membrane protein. The gating mechanism revealed for MthK may also apply to other potassium channels.
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Affiliation(s)
- Ruo-Xu Gu
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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17
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Fan C, Sukomon N, Flood E, Rheinberger J, Allen TW, Nimigean CM. Ball-and-chain inactivation in a calcium-gated potassium channel. Nature 2020; 580:288-293. [PMID: 32269335 PMCID: PMC7153497 DOI: 10.1038/s41586-020-2116-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/15/2020] [Indexed: 01/21/2023]
Abstract
Inactivation is the process by which ion channels terminate ion flux through their pores while the opening stimulus is still present1. In neurons, inactivation of both sodium and potassium channels is crucial for the generation of action potentials and regulation of firing frequency1,2. A cytoplasmic domain of either the channel or an accessory subunit is thought to plug the open pore to inactivate the channel via a 'ball-and-chain' mechanism3-7. Here we use cryo-electron microscopy to identify the molecular gating mechanism in calcium-activated potassium channels by obtaining structures of the MthK channel from Methanobacterium thermoautotrophicum-a purely calcium-gated and inactivating channel-in a lipid environment. In the absence of Ca2+, we obtained a single structure in a closed state, which was shown by atomistic simulations to be highly flexible in lipid bilayers at ambient temperature, with large rocking motions of the gating ring and bending of pore-lining helices. In Ca2+-bound conditions, we obtained several structures, including multiple open-inactivated conformations, further indication of a highly dynamic protein. These different channel conformations are distinguished by rocking of the gating rings with respect to the transmembrane region, indicating symmetry breakage across the channel. Furthermore, in all conformations displaying open channel pores, the N terminus of one subunit of the channel tetramer sticks into the pore and plugs it, with free energy simulations showing that this is a strong interaction. Deletion of this N terminus leads to functionally non-inactivating channels and structures of open states without a pore plug, indicating that this previously unresolved N-terminal peptide is responsible for a ball-and-chain inactivation mechanism.
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Affiliation(s)
- Chen Fan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
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18
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Schrecker M, Wunnicke D, Hänelt I. How RCK domains regulate gating of K+ channels. Biol Chem 2020; 400:1303-1322. [PMID: 31361596 DOI: 10.1515/hsz-2019-0153] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/02/2019] [Indexed: 11/15/2022]
Abstract
Potassium channels play a crucial role in the physiology of all living organisms. They maintain the membrane potential and are involved in electrical signaling, pH homeostasis, cell-cell communication and survival under osmotic stress. Many prokaryotic potassium channels and members of the eukaryotic Slo channels are regulated by tethered cytoplasmic domains or associated soluble proteins, which belong to the family of regulator of potassium conductance (RCK). RCK domains and subunits form octameric rings, which control ion gating. For years, a common regulatory mechanism was suggested: ligand-induced conformational changes in the octameric ring would pull open a gate in the pore via flexible linkers. Consistently, ligand-dependent conformational changes were described for various RCK gating rings. Yet, recent structural and functional data of complete ion channels uncovered that the following signal transduction to the pore domains is divers. The different RCK-regulated ion channels show remarkably heterogeneous mechanisms with neither the connection from the RCK domain to the pore nor the gate being conserved. Some channels even lack the flexible linkers, while in others the gate cannot easily be assigned. In this review we compare available structures of RCK-gated potassium channels, highlight the similarities and differences of channel gating, and delineate existing inconsistencies.
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Affiliation(s)
- Marina Schrecker
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt Main, Germany
| | - Dorith Wunnicke
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt Main, Germany
| | - Inga Hänelt
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt Main, Germany
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19
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Kopec W, Rothberg BS, de Groot BL. Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. Nat Commun 2019; 10:5366. [PMID: 31772184 PMCID: PMC6879586 DOI: 10.1038/s41467-019-13227-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/24/2019] [Indexed: 01/08/2023] Open
Abstract
Potassium channels are presumed to have two allosterically coupled gates, the activation gate and the selectivity filter gate, that control channel opening, closing, and inactivation. However, the molecular mechanism of how these gates regulate K+ ion flow through the channel remains poorly understood. An activation process, occurring at the selectivity filter, has been recently proposed for several potassium channels. Here, we use X-ray crystallography and extensive molecular dynamics simulations, to study ion permeation through a potassium channel MthK, for various opening levels of both gates. We find that the channel conductance is controlled at the selectivity filter, whose conformation depends on the activation gate. The crosstalk between the gates is mediated through a collective motion of channel helices, involving hydrophobic contacts between an isoleucine and a conserved threonine in the selectivity filter. We propose a gating model of selectivity filter-activated potassium channels, including pharmacologically relevant two-pore domain (K2P) and big potassium (BK) channels.
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Affiliation(s)
- Wojciech Kopec
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
| | - Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Bert L de Groot
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
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20
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Black KA, Jin R, He S, Gulbis JM. Changing perspectives on how the permeation pathway through potassium channels is regulated. J Physiol 2019; 599:1961-1976. [PMID: 31612997 DOI: 10.1113/jp278682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/25/2019] [Indexed: 11/08/2022] Open
Abstract
The primary means by which ion permeation through potassium channels is controlled, and the key to selective intervention in a range of pathophysiological conditions, is the process by which channels switch between non-conducting and conducting states. Conventionally, this has been explained by a steric mechanism in which the pore alternates between two conformations: a 'closed' state in which the conduction pathway is occluded and an 'open' state in which the pathway is sufficiently wide to accommodate fully hydrated ions. Recently, however, 'non-canonical' mechanisms have been proposed for some classes of K+ channels. The purpose of this review is to illuminate structural and dynamic relationships underpinning permeation control in K+ channels, indicating where additional data might resolve some of the remaining issues.
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Affiliation(s)
- Katrina A Black
- Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Ruitao Jin
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Sitong He
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Jacqueline M Gulbis
- Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3052, Australia
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21
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Gating modules of the AMPA receptor pore domain revealed by unnatural amino acid mutagenesis. Proc Natl Acad Sci U S A 2019; 116:13358-13367. [PMID: 31213549 DOI: 10.1073/pnas.1818845116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ionotropic glutamate receptors (iGluRs) are responsible for fast synaptic transmission throughout the vertebrate nervous system. Conformational changes of the transmembrane domain (TMD) underlying ion channel activation and desensitization remain poorly understood. Here, we explored the dynamics of the TMD of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type iGluRs using genetically encoded unnatural amino acid (UAA) photocross-linkers, p-benzoyl-l-phenylalanine (BzF) and p-azido-l-phenylalanine (AzF). We introduced these UAAs at sites throughout the TMD of the GluA2 receptor and characterized the mutants in patch-clamp recordings, exposing them to glutamate and ultraviolet (UV) light. This approach revealed a range of optical effects on the activity of mutant receptors. We found evidence for an interaction between the Pre-M1 and the M4 TMD helix during desensitization. Photoactivation at F579AzF, a residue behind the selectivity filter in the M2 segment, had extraordinarily broad effects on gating and desensitization. This observation suggests coupling to other parts of the receptor and like in other tetrameric ion channels, selectivity filter gating.
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22
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Rheinberger J, Gao X, Schmidpeter PA, Nimigean CM. Ligand discrimination and gating in cyclic nucleotide-gated ion channels from apo and partial agonist-bound cryo-EM structures. eLife 2018; 7:39775. [PMID: 30028291 PMCID: PMC6093708 DOI: 10.7554/elife.39775] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/19/2018] [Indexed: 12/11/2022] Open
Abstract
Cyclic nucleotide-modulated channels have important roles in visual signal transduction and pacemaking. Binding of cyclic nucleotides (cAMP/cGMP) elicits diverse functional responses in different channels within the family despite their high sequence and structure homology. The molecular mechanisms responsible for ligand discrimination and gating are unknown due to lack of correspondence between structural information and functional states. Using single particle cryo-electron microscopy and single-channel recording, we assigned functional states to high-resolution structures of SthK, a prokaryotic cyclic nucleotide-gated channel. The structures for apo, cAMP-bound, and cGMP-bound SthK in lipid nanodiscs, correspond to no, moderate, and low single-channel activity, respectively, consistent with the observation that all structures are in resting, closed states. The similarity between apo and ligand-bound structures indicates that ligand-binding domains are strongly coupled to pore and SthK gates in an allosteric, concerted fashion. The different orientations of cAMP and cGMP in the ‘resting’ and ‘activated’ structures suggest a mechanism for ligand discrimination. Ion channels are essential for transmitting signals in the nervous system and brain. One large group of ion channels includes members that are activated by cyclic nucleotides, small molecules used to transmit signals within cells. These cyclic nucleotide-gated channels play an important role in regulating our ability to see and smell. The activity of these ion channels has been studied for years, but scientists have only recently been able to look into their structure. Since structural biology methods require purified, well-behaved proteins, the members of this ion channel family selected for structural studies do not necessarily match those whose activity has been well established. There is a need for a good model that would allow both the structure and activity of a cyclic nucleotide-gated ion channel to be characterized. The cyclic nucleotide-gated ion channel, SthK, from bacteria called Spirochaeta thermophila, was identified as such model because both its activity and its structure are accessible. Rheinberger et al. have used cryo electron microscopy to solve several high-resolution structures of SthK channels. In two of the structures, SthK was bound to either one of two types of activating cyclic nucleotides – cAMP or cGMP – and in another structure, no cyclic nucleotides were bound. Separately recording the activity of individual channels allowed the activity states likely to be represented by these structures to be identified. Combining the results of the experiments revealed no activity from channels in an unbound state, low levels of activity for channels bound to cGMP, and moderate activity for channels bound to cAMP. Rheinberger et al. show that the channel, under the conditions experienced in cryo electron microscopy, is closed in all of the states studied. Unexpectedly, the binding of cyclic nucleotides produced no structural change even in the cyclic nucleotide-binding pocket of the channel, a region that was previously observed to undergo such changes when this region alone was crystallized. Rheinberger et al. deduce from this that the four subunits that make up the channel likely undergo the conformational change towards an open state all at once, rather than one by one. The structures and the basic functional characterization of SthK channels provide a strong starting point for future research into determining the entire opening and closing cycle for a cyclic nucleotide-gated channel. Human equivalents of the channel are likely to work in similar ways. The results presented by Rheinberger et al. could therefore be built upon to help address diseases that result from deficiencies in cyclic nucleotide-gated channels, such as loss of vision due to retinal degradation (retinitis pigmentosa or progressive cone dystrophy) and achromatopsia.
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Affiliation(s)
- Jan Rheinberger
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States
| | - Xiaolong Gao
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States
| | | | - Crina M Nimigean
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Department of Biochemistry, Weill Cornell Medical College, New York, United States
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23
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Rauh O, Hansen UP, Scheub DD, Thiel G, Schroeder I. Site-specific ion occupation in the selectivity filter causes voltage-dependent gating in a viral K + channel. Sci Rep 2018; 8:10406. [PMID: 29991721 PMCID: PMC6039446 DOI: 10.1038/s41598-018-28751-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/28/2018] [Indexed: 12/24/2022] Open
Abstract
Many potassium channels show voltage-dependent gating without a dedicated voltage sensor domain. This is not fully understood yet, but often explained by voltage-induced changes of ion occupation in the five distinct K+ binding sites in the selectivity filter. To better understand this mechanism of filter gating we measured the single-channel current and the rate constant of sub-millisecond channel closure of the viral K+ channel KcvNTS for a wide range of voltages and symmetric and asymmetric K+ concentrations in planar lipid membranes. A model-based analysis employed a global fit of all experimental data, i.e., using a common set of parameters for current and channel closure under all conditions. Three different established models of ion permeation and various relationships between ion occupation and gating were tested. Only one of the models described the data adequately. It revealed that the most extracellular binding site (S0) in the selectivity filter functions as the voltage sensor for the rate constant of channel closure. The ion occupation outside of S0 modulates its dependence on K+ concentration. The analysis uncovers an important role of changes in protein flexibility in mediating the effect from the sensor to the gate.
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Affiliation(s)
- O Rauh
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - U P Hansen
- Department of Structural Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - D D Scheub
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - G Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - I Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany.
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24
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Gielen M, Corringer P. The dual-gate model for pentameric ligand-gated ion channels activation and desensitization. J Physiol 2018; 596:1873-1902. [PMID: 29484660 PMCID: PMC5978336 DOI: 10.1113/jp275100] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/17/2018] [Accepted: 01/17/2018] [Indexed: 12/15/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate fast neurotransmission in the nervous system. Their dysfunction is associated with psychiatric, neurological and neurodegenerative disorders such as schizophrenia, epilepsy and Alzheimer's disease. Understanding their biophysical and pharmacological properties, at both the functional and the structural level, thus holds many therapeutic promises. In addition to their agonist-elicited activation, most pLGICs display another key allosteric property, namely desensitization, in which they enter a shut state refractory to activation upon sustained agonist binding. While the activation mechanisms of several pLGICs have been revealed at near-atomic resolution, the structural foundation of desensitization has long remained elusive. Recent structural and functional data now suggest that the activation and desensitization gates are distinct, and are located at both sides of the ion channel. Such a 'dual gate mechanism' accounts for the marked allosteric effects of channel blockers, a feature illustrated herein by theoretical kinetics simulations. Comparison with other classes of ligand- and voltage-gated ion channels shows that this dual gate mechanism emerges as a common theme for the desensitization and inactivation properties of structurally unrelated ion channels.
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Affiliation(s)
- Marc Gielen
- Channel Receptors UnitInstitut PasteurCNRS UMR 3571ParisFrance
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25
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Nanazashvili M, Sánchez-Rodríguez JE, Fosque B, Bezanilla F, Sackin H. LRET Determination of Molecular Distances during pH Gating of the Mammalian Inward Rectifier Kir1.1b. Biophys J 2018; 114:88-97. [PMID: 29320699 PMCID: PMC5773755 DOI: 10.1016/j.bpj.2017.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/23/2017] [Accepted: 10/19/2017] [Indexed: 01/31/2023] Open
Abstract
Gating of the mammalian inward rectifier Kir1.1 at the helix bundle crossing (HBC) by intracellular pH is believed to be mediated by conformational changes in the C-terminal domain (CTD). However, the exact motion of the CTD during Kir gating remains controversial. Crystal structures and single-molecule fluorescence resonance energy transfer of KirBac channels have implied a rigid body rotation and/or a contraction of the CTD as possible triggers for opening of the HBC gate. In our study, we used lanthanide-based resonance energy transfer on single-Cys dimeric constructs of the mammalian renal inward rectifier, Kir1.1b, incorporated into anionic liposomes plus PIP2, to determine unambiguous, state-dependent distances between paired Cys residues on diagonally opposite subunits. Functionality and pH dependence of our proteoliposome channels were verified in separate electrophysiological experiments. The lanthanide-based resonance energy transfer distances measured in closed (pH 6) and open (pH 8) conditions indicated neither expansion nor contraction of the CTD during gating, whereas the HBC gate widened by 8.8 ± 4 Å, from 6.3 ± 2 to 15.1 ± 6 Å, during opening. These results are consistent with a Kir gating model in which rigid body rotation of the large CTD around the permeation axis is correlated with opening of the HBC hydrophobic gate, allowing permeation of a 7 Å hydrated K ion.
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Affiliation(s)
- Mikheil Nanazashvili
- Department of Physiology and Biophysics, The Chicago Medical School, Rosalind Franklin University, North Chicago, Illinois
| | - Jorge E Sánchez-Rodríguez
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois; Departamento de Física, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Ben Fosque
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Henry Sackin
- Department of Physiology and Biophysics, The Chicago Medical School, Rosalind Franklin University, North Chicago, Illinois.
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26
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Howard RJ, Carnevale V, Delemotte L, Hellmich UA, Rothberg BS. Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:927-942. [PMID: 29258839 DOI: 10.1016/j.bbamem.2017.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/08/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022]
Abstract
Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
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Affiliation(s)
- Rebecca J Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden.
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 17121 Solna, Sweden.
| | - Ute A Hellmich
- Johannes Gutenberg University Mainz, Institute for Pharmacy and Biochemistry, Johann-Joachim-Becherweg 30, 55128 Mainz, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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27
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Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:909-926. [PMID: 29113819 DOI: 10.1016/j.bbamem.2017.10.033] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/24/2017] [Accepted: 10/28/2017] [Indexed: 11/22/2022]
Abstract
The expansion of computational power, better parameterization of force fields, and the development of novel algorithms to enhance the sampling of the free energy landscapes of proteins have allowed molecular dynamics (MD) simulations to become an indispensable tool to understand the function of biomolecules. The temporal and spatial resolution of MD simulations allows for the study of a vast number of processes of interest. Here, we review the computational efforts to uncover the conformational free energy landscapes of a subset of membrane proteins: ion channels, transporters and G-protein coupled receptors. We focus on the various enhanced sampling techniques used to study these questions, how the conclusions come together to build a coherent picture, and the relationship between simulation outcomes and experimental observables.
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28
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Zhou Y, Yang H, Cui J, Lingle CJ. Threading the biophysics of mammalian Slo1 channels onto structures of an invertebrate Slo1 channel. J Gen Physiol 2017; 149:985-1007. [PMID: 29025867 PMCID: PMC5677106 DOI: 10.1085/jgp.201711845] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/20/2017] [Indexed: 11/24/2022] Open
Abstract
Zhou et al. consider the biophysics of large-conductance Ca2+-activated Slo1 channels in the context of Aplysia Slo1 structures. For those interested in the machinery of ion channel gating, the Ca2+ and voltage-activated BK K+ channel provides a compelling topic for investigation, by virtue of its dual allosteric regulation by both voltage and intracellular Ca2+ and because its large-single channel conductance facilitates detailed kinetic analysis. Over the years, biophysical analyses have illuminated details of the allosteric regulation of BK channels and revealed insights into the mechanism of BK gating, e.g., inner cavity size and accessibility and voltage sensor-pore coupling. Now the publication of two structures of an Aplysia californica BK channel—one liganded and one metal free—promises to reinvigorate functional studies and interpretation of biophysical results. The new structures confirm some of the previous functional inferences but also suggest new perspectives regarding cooperativity between Ca2+-binding sites and the relationship between voltage- and Ca2+-dependent gating. Here we consider the extent to which the two structures explain previous functional data on pore-domain properties, voltage-sensor motions, and divalent cation binding and activation of the channel.
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Affiliation(s)
- Yu Zhou
- Department of Anesthesiology, Washington University School of Medicine, St. Louis MO
| | - Huanghe Yang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC
| | - Jianmin Cui
- Department of Biomedical Engineering, Washington University, St. Louis, MO
| | - Christopher J Lingle
- Department of Anesthesiology, Washington University School of Medicine, St. Louis MO
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29
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Heer FT, Posson DJ, Wojtas-Niziurski W, Nimigean CM, Bernèche S. Mechanism of activation at the selectivity filter of the KcsA K + channel. eLife 2017; 6:25844. [PMID: 28994652 PMCID: PMC5669632 DOI: 10.7554/elife.25844] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 10/05/2017] [Indexed: 12/26/2022] Open
Abstract
Potassium channels are opened by ligands and/or membrane potential. In voltage-gated K+ channels and the prokaryotic KcsA channel, conduction is believed to result from opening of an intracellular constriction that prevents ion entry into the pore. On the other hand, numerous ligand-gated K+ channels lack such gate, suggesting that they may be activated by a change within the selectivity filter, a narrow region at the extracellular side of the pore. Using molecular dynamics simulations and electrophysiology measurements, we show that ligand-induced conformational changes in the KcsA channel removes steric restraints at the selectivity filter, thus resulting in structural fluctuations, reduced K+ affinity, and increased ion permeation. Such activation of the selectivity filter may be a universal gating mechanism within K+ channels. The occlusion of the pore at the level of the intracellular gate appears to be secondary. Potassium channels are proteins found in almost all living organisms and are vital for many different biological processes. These proteins contain a pore that allows potassium ions to flow through cell membranes, but only when the channel is open. Most channels have a narrowing at the inward side of the pore, which was proposed to form a gate that controls the flow of ions. This gate only opens when the channel activates. Nearer the outward side of the pore is another narrow region called the selectivity filter. This region interacts selectively with potassium ions as they pass through the channel. Not all channels form a tight constriction at the inward end of their pore, yet they still only allow potassium ions to flow through when activated. This suggested that these channels might instead use the selectivity filter as a gate. It would also mean that whilst different potassium channels have similar structures, they do not share a common gating mechanism that controls the flow of ions. Heer et al. studied the bacterial channel called KcsA, which was thought to control the flow of potassium ions via a traditional inward gate. Computer simulations based on this protein’s structure, and experiments with purified KcsA in artificial membranes, showed that the selectivity filter was also involved when KcsA was activated. When the activated channel changed shape, the selectivity filter – which had been constrained by regions forming the pore – could now move and allow potassium ions to flow through the pore. Heer et al. confirmed using a mutant KcsA that the motion of the inward side of the pore upon activation affected the movement of the selectivity filter gate as predicted by the simulation. These findings show that the KcsA channel opens and closes at the selectivity filter. The changes at the inward side of the pore, previously believed to be the gate, firstly enable the selectivity filter to serve as a gate while also forming a secondary gate. Heer et al. propose that most if not all potassium channels may also use this mechanism. These findings illustrate that molecular simulations can be powerful for predicting how changes in the structure of a protein will affect its behavior. This and future studies of other potassium channels will help scientists to better understand the subtle differences between the diverse range of channels found across different organisms.
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Affiliation(s)
- Florian T Heer
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland.,Biozentrum, University of Basel, Basel, Switzerland
| | - David J Posson
- Department of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States
| | - Wojciech Wojtas-Niziurski
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland.,Biozentrum, University of Basel, Basel, Switzerland
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Department of Biochemistry, Weill Cornell Medical College, New York, United States
| | - Simon Bernèche
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland.,Biozentrum, University of Basel, Basel, Switzerland
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30
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Latorre R, Castillo K, Carrasquel-Ursulaez W, Sepulveda RV, Gonzalez-Nilo F, Gonzalez C, Alvarez O. Molecular Determinants of BK Channel Functional Diversity and Functioning. Physiol Rev 2017; 97:39-87. [DOI: 10.1152/physrev.00001.2016] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Large-conductance Ca2+- and voltage-activated K+ (BK) channels play many physiological roles ranging from the maintenance of smooth muscle tone to hearing and neurosecretion. BK channels are tetramers in which the pore-forming α subunit is coded by a single gene ( Slowpoke, KCNMA1). In this review, we first highlight the physiological importance of this ubiquitous channel, emphasizing the role that BK channels play in different channelopathies. We next discuss the modular nature of BK channel-forming protein, in which the different modules (the voltage sensor and the Ca2+ binding sites) communicate with the pore gates allosterically. In this regard, we review in detail the allosteric models proposed to explain channel activation and how the models are related to channel structure. Considering their extremely large conductance and unique selectivity to K+, we also offer an account of how these two apparently paradoxical characteristics can be understood consistently in unison, and what we have learned about the conduction system and the activation gates using ions, blockers, and toxins. Attention is paid here to the molecular nature of the voltage sensor and the Ca2+ binding sites that are located in a gating ring of known crystal structure and constituted by four COOH termini. Despite the fact that BK channels are coded by a single gene, diversity is obtained by means of alternative splicing and modulatory β and γ subunits. We finish this review by describing how the association of the α subunit with β or with γ subunits can change the BK channel phenotype and pharmacology.
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Affiliation(s)
- Ramon Latorre
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile; Universidad Andres Bello, Facultad de Ciencias Biologicas, Center for Bioinformatics and Integrative Biology, Avenida Republica 239, Santiago, Chile and Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Karen Castillo
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile; Universidad Andres Bello, Facultad de Ciencias Biologicas, Center for Bioinformatics and Integrative Biology, Avenida Republica 239, Santiago, Chile and Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Willy Carrasquel-Ursulaez
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile; Universidad Andres Bello, Facultad de Ciencias Biologicas, Center for Bioinformatics and Integrative Biology, Avenida Republica 239, Santiago, Chile and Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Romina V. Sepulveda
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile; Universidad Andres Bello, Facultad de Ciencias Biologicas, Center for Bioinformatics and Integrative Biology, Avenida Republica 239, Santiago, Chile and Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Fernando Gonzalez-Nilo
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile; Universidad Andres Bello, Facultad de Ciencias Biologicas, Center for Bioinformatics and Integrative Biology, Avenida Republica 239, Santiago, Chile and Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Carlos Gonzalez
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile; Universidad Andres Bello, Facultad de Ciencias Biologicas, Center for Bioinformatics and Integrative Biology, Avenida Republica 239, Santiago, Chile and Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Osvaldo Alvarez
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile; Universidad Andres Bello, Facultad de Ciencias Biologicas, Center for Bioinformatics and Integrative Biology, Avenida Republica 239, Santiago, Chile and Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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31
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Giese MH, Gardner A, Hansen A, Sanguinetti MC. Molecular mechanisms of Slo2 K + channel closure. J Physiol 2016; 595:2321-2336. [PMID: 27682982 DOI: 10.1113/jp273225] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/20/2016] [Indexed: 01/02/2023] Open
Abstract
KEY POINTS Intracellular Na+ -activated Slo2 potassium channels are in a closed state under normal physiological conditions, although their mechanisms of ion permeation gating are not well understood. A cryo-electron microscopy structure of Slo2.2 suggests that the ion permeation pathway of these channels is closed by a single constriction of the inner pore formed by the criss-crossing of the cytoplasmic ends of the S6 segments (the S6 bundle crossing) at a conserved Met residue. Functional characterization of mutant Slo2 channels suggests that hydrophobic interactions between Leu residues in the upper region of the S6 segments contribute to stabilizing the inner pore in a non-conducting state. Mutation of the conserved Met residues in the S6 segments to the negatively-charged Glu did not induce constitutive opening of Slo2.1 or Slo2.2, suggesting that ion permeation of Slo2 channels is not predominantly gated by the S6 bundle crossing. ABSTRACT Large conductance K+ -selective Slo2 channels are in a closed state unless activated by elevated [Na+ ]i . Our previous studies suggested that the pore helix/selectivity filter serves as the activation gate in Slo2 channels. In the present study, we evaluated two other potential mechanisms for stabilization of Slo2 channels in a closed state: (1) dewetting and collapse of the inner pore (hydrophobic gating) and (2) constriction of the inner pore by tight criss-crossing of the cytoplasmic ends of the S6 α-helical segments. Slo2 channels contain two conserved Leu residues in each of the four S6 segments that line the inner pore region nearest the bottom of the selectivity filter. To evaluate the potential role of these residues in hydrophobic gating, Leu267 and Leu270 in human Slo2.1 were each replaced by 15 different residues. The relative conductance of mutant channels was highly dependent on hydrophilicity and volume of the amino acid substituted for Leu267 and was maximal with L267H. Consistent with their combined role in hydrophobic gating, replacement of both Leu residues with the isosteric but polar residue Asn (L267N/L270N) stabilized channels in a fully open state. In a recent cryo-electron microscopy structure of chicken Slo2.2, the ion permeation pathway of the channel is closed by a constriction of the inner pore formed by criss-crossing of the S6 segments at a conserved Met. Inconsistent with the S6 segment crossing forming the activation gate, replacement of the homologous Met residues in human Slo2.1 or Slo2.2 with the negatively-charged Glu did not induce constitutive channel opening.
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Affiliation(s)
- M Hunter Giese
- Nora Eccles Harrison Cardiovascular Research & Training Institute
| | - Alison Gardner
- Nora Eccles Harrison Cardiovascular Research & Training Institute
| | - Angela Hansen
- Nora Eccles Harrison Cardiovascular Research & Training Institute
| | - Michael C Sanguinetti
- Nora Eccles Harrison Cardiovascular Research & Training Institute.,Department of Internal Medicine, Division of Cardiovascular Medicine, University of Utah, Salt Lake City, UT, USA
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32
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Unambiguous observation of blocked states reveals altered, blocker-induced, cardiac ryanodine receptor gating. Sci Rep 2016; 6:34452. [PMID: 27703263 PMCID: PMC5050499 DOI: 10.1038/srep34452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/12/2016] [Indexed: 11/08/2022] Open
Abstract
The flow of ions through membrane channels is precisely regulated by gates. The architecture and function of these elements have been studied extensively, shedding light on the mechanisms underlying gating. Recent investigations have focused on ion occupancy of the channel’s selectivity filter and its ability to alter gating, with most studies involving prokaryotic K+ channels. Some studies used large quaternary ammonium blocker molecules to examine the effects of altered ionic flux on gating. However, the absence of blocking events that are visibly distinct from closing events in K+ channels makes unambiguous interpretation of data from single channel recordings difficult. In this study, the large K+ conductance of the RyR2 channel permits direct observation of blocking events as distinct subconductance states and for the first time demonstrates the differential effects of blocker molecules on channel gating. This experimental platform provides valuable insights into mechanisms of blocker-induced modulation of ion channel gating.
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33
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Naranjo D, Moldenhauer H, Pincuntureo M, Díaz-Franulic I. Pore size matters for potassium channel conductance. J Gen Physiol 2016; 148:277-91. [PMID: 27619418 PMCID: PMC5037345 DOI: 10.1085/jgp.201611625] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/10/2016] [Indexed: 01/31/2023] Open
Abstract
Ion channels are membrane proteins that mediate efficient ion transport across the hydrophobic core of cell membranes, an unlikely process in their absence. K+ channels discriminate K+ over cations with similar radii with extraordinary selectivity and display a wide diversity of ion transport rates, covering differences of two orders of magnitude in unitary conductance. The pore domains of large- and small-conductance K+ channels share a general architectural design comprising a conserved narrow selectivity filter, which forms intimate interactions with permeant ions, flanked by two wider vestibules toward the internal and external openings. In large-conductance K+ channels, the inner vestibule is wide, whereas in small-conductance channels it is narrow. Here we raise the idea that the physical dimensions of the hydrophobic internal vestibule limit ion transport in K+ channels, accounting for their diversity in unitary conductance.
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Affiliation(s)
- David Naranjo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Playa Ancha, Valparaíso 2360103, Chile
| | - Hans Moldenhauer
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Playa Ancha, Valparaíso 2360103, Chile
| | - Matías Pincuntureo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Playa Ancha, Valparaíso 2360103, Chile Programa de Doctorado en Ciencias, mención Biofísica y Biología Computacional, Universidad de Valparaíso, Valparaíso 2360103, Chile
| | - Ignacio Díaz-Franulic
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Playa Ancha, Valparaíso 2360103, Chile Center for Bioinformatics and Integrative Biology, Universidad Andrés Bello, Santiago 8370146, Chile Fraunhofer Chile Research, Las Condes 7550296, Chile
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34
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Fineberg JD, Szanto TG, Panyi G, Covarrubias M. Closed-state inactivation involving an internal gate in Kv4.1 channels modulates pore blockade by intracellular quaternary ammonium ions. Sci Rep 2016; 6:31131. [PMID: 27502553 PMCID: PMC4977472 DOI: 10.1038/srep31131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 07/15/2016] [Indexed: 11/09/2022] Open
Abstract
Voltage-gated K(+) (Kv) channel activation depends on interactions between voltage sensors and an intracellular activation gate that controls access to a central pore cavity. Here, we hypothesize that this gate is additionally responsible for closed-state inactivation (CSI) in Kv4.x channels. These Kv channels undergo CSI by a mechanism that is still poorly understood. To test the hypothesis, we deduced the state of the Kv4.1 channel intracellular gate by exploiting the trap-door paradigm of pore blockade by internally applied quaternary ammonium (QA) ions exhibiting slow blocking kinetics and high-affinity for a blocking site. We found that inactivation gating seemingly traps benzyl-tributylammonium (bTBuA) when it enters the central pore cavity in the open state. However, bTBuA fails to block inactivated Kv4.1 channels, suggesting gated access involving an internal gate. In contrast, bTBuA blockade of a Shaker Kv channel that undergoes open-state P/C-type inactivation exhibits fast onset and recovery inconsistent with bTBuA trapping. Furthermore, the inactivated Shaker Kv channel is readily blocked by bTBuA. We conclude that Kv4.1 closed-state inactivation modulates pore blockade by QA ions in a manner that depends on the state of the internal activation gate.
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Affiliation(s)
- Jeffrey D Fineberg
- Department of Neuroscience, Vickie and Jack Farber Institute for Neuroscience at Thomas Jefferson University, Philadelphia, PA, USA.,Graduate Program in Molecular Physiology &Biophysics, Sidney Kimmel Medical College and College of Biomedical Sciences at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Tibor G Szanto
- Department of Biophysics &Cell Biology, Faculty of Medicine University of Debrecen, 4032 Debrecen, Hungary
| | - Gyorgy Panyi
- Department of Biophysics &Cell Biology, Faculty of Medicine University of Debrecen, 4032 Debrecen, Hungary.,MTA-DE-NAP B Ion Channel Structure-Function Research Group, RCMM University of Debrecen, 4032 Debrecen, Hungary
| | - Manuel Covarrubias
- Department of Neuroscience, Vickie and Jack Farber Institute for Neuroscience at Thomas Jefferson University, Philadelphia, PA, USA.,Graduate Program in Molecular Physiology &Biophysics, Sidney Kimmel Medical College and College of Biomedical Sciences at Thomas Jefferson University, Philadelphia, PA 19107, USA.,Vickie and Jack Farber Institute for Neuroscience at Thomas Jefferson University,Philadelphia, PA, USA
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35
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β1-subunit-induced structural rearrangements of the Ca2+- and voltage-activated K+ (BK) channel. Proc Natl Acad Sci U S A 2016; 113:E3231-9. [PMID: 27217576 DOI: 10.1073/pnas.1606381113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Large-conductance Ca(2+)- and voltage-activated K(+) (BK) channels are involved in a large variety of physiological processes. Regulatory β-subunits are one of the mechanisms responsible for creating BK channel diversity fundamental to the adequate function of many tissues. However, little is known about the structure of its voltage sensor domain. Here, we present the external architectural details of BK channels using lanthanide-based resonance energy transfer (LRET). We used a genetically encoded lanthanide-binding tag (LBT) to bind terbium as a LRET donor and a fluorophore-labeled iberiotoxin as the LRET acceptor for measurements of distances within the BK channel structure in a living cell. By introducing LBTs in the extracellular region of the α- or β1-subunit, we determined (i) a basic extracellular map of the BK channel, (ii) β1-subunit-induced rearrangements of the voltage sensor in α-subunits, and (iii) the relative position of the β1-subunit within the α/β1-subunit complex.
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Kim DM, Nimigean CM. Voltage-Gated Potassium Channels: A Structural Examination of Selectivity and Gating. Cold Spring Harb Perspect Biol 2016; 8:a029231. [PMID: 27141052 PMCID: PMC4852806 DOI: 10.1101/cshperspect.a029231] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Voltage-gated potassium channels play a fundamental role in the generation and propagation of the action potential. The discovery of these channels began with predictions made by early pioneers, and has culminated in their extensive functional and structural characterization by electrophysiological, spectroscopic, and crystallographic studies. With the aid of a variety of crystal structures of these channels, a highly detailed picture emerges of how the voltage-sensing domain reports changes in the membrane electric field and couples this to conformational changes in the activation gate. In addition, high-resolution structural and functional studies of K(+) channel pores, such as KcsA and MthK, offer a comprehensive picture on how selectivity is achieved in K(+) channels. Here, we illustrate the remarkable features of voltage-gated potassium channels and explain the mechanisms used by these machines with experimental data.
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Affiliation(s)
- Dorothy M Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York 10065
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York 10065
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37
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Moldenhauer H, Díaz-Franulic I, González-Nilo F, Naranjo D. Effective pore size and radius of capture for K(+) ions in K-channels. Sci Rep 2016; 6:19893. [PMID: 26831782 PMCID: PMC4735802 DOI: 10.1038/srep19893] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/21/2015] [Indexed: 11/09/2022] Open
Abstract
Reconciling protein functional data with crystal structure is arduous because rare conformations or crystallization artifacts occur. Here we present a tool to validate the dimensions of open pore structures of potassium-selective ion channels. We used freely available algorithms to calculate the molecular contour of the pore to determine the effective internal pore radius (rE) in several K-channel crystal structures. rE was operationally defined as the radius of the biggest sphere able to enter the pore from the cytosolic side. We obtained consistent rE estimates for MthK and Kv1.2/2.1 structures, with rE = 5.3–5.9 Å and rE = 4.5–5.2 Å, respectively. We compared these structural estimates with functional assessments of the internal mouth radii of capture (rC) for two electrophysiological counterparts, the large conductance calcium activated K-channel (rC = 2.2 Å) and the Shaker Kv-channel (rC = 0.8 Å), for MthK and Kv1.2/2.1 structures, respectively. Calculating the difference between rE and rC, produced consistent size radii of 3.1–3.7 Å and 3.6–4.4 Å for hydrated K+ ions. These hydrated K+ estimates harmonize with others obtained with diverse experimental and theoretical methods. Thus, these findings validate MthK and the Kv1.2/2.1 structures as templates for open BK and Kv-channels, respectively.
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Affiliation(s)
- Hans Moldenhauer
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Playa Ancha Valparaíso, Chile
| | - Ignacio Díaz-Franulic
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Playa Ancha Valparaíso, Chile.,Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Santiago, Chile and Fundación Fraunhofer-Chile, Las Condes, Chile
| | - Fernando González-Nilo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Playa Ancha Valparaíso, Chile.,Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Santiago, Chile and Fundación Fraunhofer-Chile, Las Condes, Chile
| | - David Naranjo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Playa Ancha Valparaíso, Chile
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38
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Kowal J, Chami M, Baumgartner P, Arheit M, Chiu PL, Rangl M, Scheuring S, Schröder GF, Nimigean CM, Stahlberg H. Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nat Commun 2015; 5:3106. [PMID: 24469021 PMCID: PMC4086158 DOI: 10.1038/ncomms4106] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/13/2013] [Indexed: 12/25/2022] Open
Abstract
Cyclic nucleotide-modulated ion channels are important for signal transduction and pacemaking in eukaryotes. The molecular determinants of ligand gating in these channels are still unknown, mainly because of a lack of direct structural information. Here we report ligand-induced conformational changes in full-length MloK1, a cyclic nucleotide-modulated potassium channel from the bacterium Mesorhizobium loti, analysed by electron crystallography and atomic force microscopy. Upon cAMP binding, the cyclic nucleotide-binding domains move vertically towards the membrane, and directly contact the S1–S4 voltage sensor domains. This is accompanied by a significant shift and tilt of the voltage sensor domain helices. In both states, the inner pore-lining helices are in an ‘open’ conformation. We propose a mechanism in which ligand binding can favour pore opening via a direct interaction between the cyclic nucleotide-binding domains and voltage sensors. This offers a simple mechanistic hypothesis for the coupling between ligand gating and voltage sensing in eukaryotic HCN channels. The molecular determinants underlying ligand gating of cyclic nucleotide-modulated ion channels remain unclear. Kowal et al. determine the conformational changes underlying cAMP binding to the bacterial channel MloK1, and propose a mechanism for coupling of ligand gating and voltage sensing in eukaryotic HCN channels.
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Affiliation(s)
- Julia Kowal
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Paul Baumgartner
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Marcel Arheit
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | | | - Martina Rangl
- U1006 INSERM, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13009 Marseille, France
| | - Simon Scheuring
- U1006 INSERM, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13009 Marseille, France
| | - Gunnar F Schröder
- 1] Forschungszentrum Jülich, Institute of Complex Systems, ICS-6: Structural Biochemistry, 52425 Jülich, Germany [2] Department of Physics, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Crina M Nimigean
- Departments of Anesthesiology, Physiology and Biophysics, and Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, New York 10065, USA
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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Posson DJ, Rusinova R, Andersen OS, Nimigean CM. Calcium ions open a selectivity filter gate during activation of the MthK potassium channel. Nat Commun 2015; 6:8342. [PMID: 26395539 PMCID: PMC4580985 DOI: 10.1038/ncomms9342] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 08/11/2015] [Indexed: 12/25/2022] Open
Abstract
Ion channel opening and closing are fundamental to cellular signalling and homeostasis. Gates that control K+ channel activity were found both at an intracellular pore constriction and within the selectivity filter near the extracellular side but the specific location of the gate that opens Ca2+-activated K+ channels has remained elusive. Using the Methanobacterium thermoautotrophicum homologue (MthK) and a stopped-flow fluorometric assay for fast channel activation, we show that intracellular quaternary ammonium blockers bind to closed MthK channels. Since the blockers are known to bind inside a central channel cavity, past the intracellular entryway, the gate must be within the selectivity filter. Furthermore, the blockers access the closed channel slower than the open channel, suggesting that the intracellular entryway narrows upon pore closure, without preventing access of either the blockers or the smaller K+. Thus, Ca2+-dependent gating in MthK occurs at the selectivity filter with coupled movement of the intracellular helices. Ion channels open and close to allow the regulated passage of ions through the membrane. Here the authors use selective ion channel blockers to analyse this regulation in a potassium channel and show that the gate is in the selectivity filter, past the entrance to the channel.
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Affiliation(s)
- David J Posson
- Department of Anesthesiology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
| | - Radda Rusinova
- Department of Anesthesiology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
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40
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Carrasquel-Ursulaez W, Contreras GF, Sepúlveda RV, Aguayo D, González-Nilo F, González C, Latorre R. Hydrophobic interaction between contiguous residues in the S6 transmembrane segment acts as a stimuli integration node in the BK channel. ACTA ACUST UNITED AC 2015; 145:61-74. [PMID: 25548136 PMCID: PMC4278184 DOI: 10.1085/jgp.201411194] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Phenylalanine 380 and leucine 377 in the BK channel S6 transmembrane helix of contiguous subunits participate in a hydrophobic interaction in both the closed and open state; this interaction is important in the allosteric coupling between the Ca2+ and voltage sensors and pore domain. Large-conductance Ca2+- and voltage-activated K+ channel (BK) open probability is enhanced by depolarization, increasing Ca2+ concentration, or both. These stimuli activate modular voltage and Ca2+ sensors that are allosterically coupled to channel gating. Here, we report a point mutation of a phenylalanine (F380A) in the S6 transmembrane helix that, in the absence of internal Ca2+, profoundly hinders channel opening while showing only minor effects on the voltage sensor active–resting equilibrium. Interpretation of these results using an allosteric model suggests that the F380A mutation greatly increases the free energy difference between open and closed states and uncouples Ca2+ binding from voltage sensor activation and voltage sensor activation from channel opening. However, the presence of a bulky and more hydrophobic amino acid in the F380 position (F380W) increases the intrinsic open–closed equilibrium, weakening the coupling between both sensors with the pore domain. Based on these functional experiments and molecular dynamics simulations, we propose that F380 interacts with another S6 hydrophobic residue (L377) in contiguous subunits. This pair forms a hydrophobic ring important in determining the open–closed equilibrium and, like an integration node, participates in the communication between sensors and between the sensors and pore. Moreover, because of its effects on open probabilities, the F380A mutant can be used for detailed voltage sensor experiments in the presence of permeant cations.
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Affiliation(s)
- Willy Carrasquel-Ursulaez
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
| | - Gustavo F Contreras
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
| | - Romina V Sepúlveda
- Centro de Bioinformática y Biología Integrativa and Doctorado en Biotecnología, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago 8370146, Chile Centro de Bioinformática y Biología Integrativa and Doctorado en Biotecnología, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago 8370146, Chile
| | - Daniel Aguayo
- Centro de Bioinformática y Biología Integrativa and Doctorado en Biotecnología, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago 8370146, Chile
| | - Fernando González-Nilo
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile Centro de Bioinformática y Biología Integrativa and Doctorado en Biotecnología, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago 8370146, Chile
| | - Carlos González
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
| | - Ramón Latorre
- Centro Interdisciplinario de Neurociencia de Valparaíso and Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
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Calvaresi M, Furini S, Domene C, Bottoni A, Zerbetto F. Blocking the passage: C60 geometrically clogs K(+) channels. ACS NANO 2015; 9:4827-4834. [PMID: 25873341 DOI: 10.1021/nn506164s] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Classical molecular dynamics (MD) simulations combined with docking calculations, potential of mean force estimates with the umbrella sampling method, and molecular mechanic/Poisson-Boltzmann surface area (MM-PBSA) energy calculations reveal that C60 may block K(+) channels with two mechanisms: a low affinity blockage from the extracellular side, and an open-channel block from the intracellular side. The presence of a low affinity binding-site at the extracellular entrance of the channel is in agreement with the experimental results showing a fast and reversible block without use-dependence, from the extracellular compartment. Our simulation protocol suggests the existence of another binding site for C60 located in the channel cavity at the intracellular entrance of the selectivity filter. The escape barrier from this binding site is ∼21 kcal/mol making the corresponding kinetic rate of the order of minutes. The analysis of the change in solvent accessible surface area upon C60 binding shows that binding at this site is governed purely by shape complementarity, and that the molecular determinants of binding are conserved in the entire family of K(+) channels. The presence of this high-affinity binding site conserved among different K(+) channels may have serious implications for the toxicity of carbon nanomaterials.
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Affiliation(s)
- Matteo Calvaresi
- †Dipartimento di Chimica "G. Ciamician", Alma Mater Studiorum - Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Simone Furini
- ‡Dipartimento di Biotecnologie Mediche, Università di Siena, viale M. Bracci 12, I-53100 Siena, Italy
| | - Carmen Domene
- §Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
- ⊥Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Andrea Bottoni
- †Dipartimento di Chimica "G. Ciamician", Alma Mater Studiorum - Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Francesco Zerbetto
- †Dipartimento di Chimica "G. Ciamician", Alma Mater Studiorum - Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy
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42
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Wang J. Estimation of the quality of refined protein crystal structures. Protein Sci 2015; 24:661-9. [PMID: 25581292 DOI: 10.1002/pro.2639] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/30/2014] [Accepted: 01/05/2015] [Indexed: 01/13/2023]
Abstract
Crystallographic R work and R free values, which are measures of the ability of the models of macromolecular structures to explain the crystallographic data on which they are based, are often used to assess structure quality. It is widely known, and confirmed here that both are sensitive to the methods used to compute them, and can be manipulated to improve the apparent quality of the model. As an alternative it is proposed here that the quality of crystallographic models should be assessed using a global goodness-of-fit metric RO2A /R work where RO2A is the number of reflections used for refinement divided by the number of nonhydrogen atoms in the structure, and R work is the working R-factor of the refined structure. Also, analysis of structures in the Protein Data Bank suggests that many data sets have been truncated at high resolution, thereby improving the R-factor statistics. To discourage this practice, it is proposed that the resolution of a dataset be defined as the resolution of the shell of data where <I/σI > falls to 1. The proposed goodness-of-fit metric encourages investigators to use all the data available rather than a truncated subset.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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43
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Marchesi A, Arcangeletti M, Mazzolini M, Torre V. Proton transfer unlocks inactivation in cyclic nucleotide-gated A1 channels. J Physiol 2015; 593:857-70. [PMID: 25480799 DOI: 10.1113/jphysiol.2014.284216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/28/2014] [Indexed: 01/12/2023] Open
Abstract
KEY POINTS Desensitization and inactivation provide a form of short-term memory controlling the firing patterns of excitable cells and adaptation in sensory systems. Unlike many of their cousin K(+) channels, cyclic nucleotide-gated (CNG) channels are thought not to desensitize or inactivate. Here we report that CNG channels do inactivate and that inactivation is controlled by extracellular protons. Titration of a glutamate residue within the selectivity filter destabilizes the pore architecture, which collapses towards a non-conductive, inactivated state in a process reminiscent of the usual C-type inactivation observed in many K(+) channels. These results indicate that inactivation in CNG channels represents a regulatory mechanism that has been neglected thus far, with possible implications in several physiological processes ranging from signal transduction to growth cone navigation. ABSTRACT Ion channels control ionic fluxes across biological membranes by residing in any of three functionally distinct states: deactivated (closed), activated (open) or inactivated (closed). Unlike many of their cousin K(+) channels, cyclic nucleotide-gated (CNG) channels do not desensitize or inactivate. Using patch recording techniques, we show that when extracellular pH (pHo ) is decreased from 7.4 to 6 or lower, wild-type CNGA1 channels inactivate in a voltage-dependent manner. pHo titration experiments show that at pHo < 7 the I-V relationships are outwardly rectifying and that inactivation is coupled to current rectification. Single-channel recordings indicate that a fast mechanism of proton blockage underlines current rectification while inactivation arises from conformational changes downstream from protonation. Furthermore, mutagenesis and ionic substitution experiments highlight the role of the selectivity filter in current decline, suggesting analogies with the C-type inactivation observed in K(+) channels. Analysis with Markovian models indicates that the non-independent binding of two protons within the transmembrane electrical field explains both the voltage-dependent blockage and the inactivation. Low pH, by inhibiting the CNGA1 channels in a state-dependent manner, may represent an unrecognized endogenous signal regulating CNG physiological functions in diverse tissues.
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Affiliation(s)
- Arin Marchesi
- Neurobiology Sector, International School for Advanced Studies (SISSA), Trieste, Italy
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Bannister ML, Thomas NL, Sikkel MB, Mukherjee S, Maxwell C, MacLeod KT, George CH, Williams AJ. The mechanism of flecainide action in CPVT does not involve a direct effect on RyR2. Circ Res 2015; 116:1324-35. [PMID: 25648700 DOI: 10.1161/circresaha.116.305347] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/03/2015] [Indexed: 12/17/2022]
Abstract
RATIONALE Flecainide, a class 1c antiarrhythmic, has emerged as an effective therapy in preventing arrhythmias in patients with catecholaminergic polymorphic ventricular tachycardia (CPVT) refractory to β-adrenergic receptor blockade. It has been proposed that the clinical efficacy of flecainide in CPVT is because of the combined actions of direct blockade of ryanodine receptors (RyR2) and Na(+) channel inhibition. However, there is presently no direct evidence to support the notion that flecainide blocks RyR2 Ca(2+) flux in the physiologically relevant (luminal-to-cytoplasmic) direction. The mechanism of flecainide action remains controversial. OBJECTIVE To examine, in detail, the effect of flecainide on the human RyR2 channel and to establish whether the direct blockade of physiologically relevant RyR2 ion flow by the drug contributes to its therapeutic efficacy in the clinical management of CPVT. METHODS AND RESULTS Using single-channel analysis, we show that, even at supraphysiological concentrations, flecainide did not inhibit the physiologically relevant, luminal-to-cytosolic flux of cations through the channel. Moreover, flecainide did not alter RyR2 channel gating and had negligible effect on the mechanisms responsible for the sarcoplasmic reticulum charge-compensating counter current. Using permeabilized cardiac myocytes to eliminate any contribution of plasmalemmal Na(+) channels to the observed actions of the drug at the cellular level, flecainide did not inhibit RyR2-dependent sarcoplasmic reticulum Ca(2+) release. CONCLUSIONS The principal action of flecainide in CPVT is not via a direct interaction with RyR2. Our data support a model of flecainide action in which Na(+)-dependent modulation of intracellular Ca(2+) handling attenuates RyR2 dysfunction in CPVT.
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Affiliation(s)
- Mark L Bannister
- From the Institute of Molecular and Experimental Medicine, Wales Heart Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom (M.L.B., N.L.T., S.M., C.M., C.H.G., A.J.W.); and Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom (M.B.S., K.T.M.)
| | - N Lowri Thomas
- From the Institute of Molecular and Experimental Medicine, Wales Heart Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom (M.L.B., N.L.T., S.M., C.M., C.H.G., A.J.W.); and Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom (M.B.S., K.T.M.)
| | - Markus B Sikkel
- From the Institute of Molecular and Experimental Medicine, Wales Heart Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom (M.L.B., N.L.T., S.M., C.M., C.H.G., A.J.W.); and Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom (M.B.S., K.T.M.)
| | - Saptarshi Mukherjee
- From the Institute of Molecular and Experimental Medicine, Wales Heart Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom (M.L.B., N.L.T., S.M., C.M., C.H.G., A.J.W.); and Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom (M.B.S., K.T.M.)
| | - Chloe Maxwell
- From the Institute of Molecular and Experimental Medicine, Wales Heart Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom (M.L.B., N.L.T., S.M., C.M., C.H.G., A.J.W.); and Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom (M.B.S., K.T.M.)
| | - Kenneth T MacLeod
- From the Institute of Molecular and Experimental Medicine, Wales Heart Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom (M.L.B., N.L.T., S.M., C.M., C.H.G., A.J.W.); and Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom (M.B.S., K.T.M.)
| | - Christopher H George
- From the Institute of Molecular and Experimental Medicine, Wales Heart Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom (M.L.B., N.L.T., S.M., C.M., C.H.G., A.J.W.); and Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom (M.B.S., K.T.M.)
| | - Alan J Williams
- From the Institute of Molecular and Experimental Medicine, Wales Heart Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom (M.L.B., N.L.T., S.M., C.M., C.H.G., A.J.W.); and Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom (M.B.S., K.T.M.).
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Aryal P, Sansom MSP, Tucker SJ. Hydrophobic gating in ion channels. J Mol Biol 2015; 427:121-30. [PMID: 25106689 PMCID: PMC4817205 DOI: 10.1016/j.jmb.2014.07.030] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/24/2014] [Accepted: 07/28/2014] [Indexed: 02/01/2023]
Abstract
Biological ion channels are nanoscale transmembrane pores. When water and ions are enclosed within the narrow confines of a sub-nanometer hydrophobic pore, they exhibit behavior not evident from macroscopic descriptions. At this nanoscopic level, the unfavorable interaction between the lining of a hydrophobic pore and water may lead to stochastic liquid-vapor transitions. These transient vapor states are "dewetted", i.e. effectively devoid of water molecules within all or part of the pore, thus leading to an energetic barrier to ion conduction. This process, termed "hydrophobic gating", was first observed in molecular dynamics simulations of model nanopores, where the principles underlying hydrophobic gating (i.e., changes in diameter, polarity, or transmembrane voltage) have now been extensively validated. Computational, structural, and functional studies now indicate that biological ion channels may also exploit hydrophobic gating to regulate ion flow within their pores. Here we review the evidence for this process and propose that this unusual behavior of water represents an increasingly important element in understanding the relationship between ion channel structure and function.
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Affiliation(s)
- Prafulla Aryal
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 2JD, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 2JD, UK.
| | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 2JD, UK.
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Wang J. On the validation of crystallographic symmetry and the quality of structures. Protein Sci 2014; 24:621-32. [PMID: 25352397 DOI: 10.1002/pro.2595] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/20/2014] [Accepted: 10/24/2014] [Indexed: 11/06/2022]
Abstract
In 2008, Zwart and colleagues observed that the fraction of the structures deposited in the PDB alleged to have "pseudosymmetry" or "special noncrystallographic symmetry" (NCS) was about 6%, and that this percentage was rising annually. A few years later, Poon and colleagues found that 2% of all the crystal structures in the PDB belonged to higher symmetry space groups than those assigned to them. Here, I report an analysis of the X-ray diffraction data deposited for this class of structures, which shows that most of the "pseudosymmetry" and "special NCS" that has been reported is in fact true crystallographic symmetry (CS). This distinction is important because the credibility of crystal structures depends heavily on quality control statistics such as Rfree that are unreliable when they are computed incorrectly, which they often are when CS is misidentified as "special NCS" or "pseudosymmetry". When mistakes of this kind are made, artificially low values of Rfree can give unjustified confidence in the accuracy of the reported structures.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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Linder T, Saxena P, Timin E, Hering S, Stary-Weinzinger A. Structural Insights into Trapping and Dissociation of Small Molecules in K+ Channels. J Chem Inf Model 2014; 54:3218-28. [DOI: 10.1021/ci500353r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tobias Linder
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Priyanka Saxena
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Eugen Timin
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Steffen Hering
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Anna Stary-Weinzinger
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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Affiliation(s)
- Geoffrey W Abbott
- 1360 Medical Surge II, Dept. of Pharmacology, School of Medicine, University of California, Irvine, CA 92697, USA.
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Molecular dynamics simulations of scorpion toxin recognition by the Ca(2+)-activated potassium channel KCa3.1. Biophys J 2014; 105:1829-37. [PMID: 24138859 DOI: 10.1016/j.bpj.2013.08.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/26/2013] [Accepted: 08/30/2013] [Indexed: 02/06/2023] Open
Abstract
The Ca(2+)-activated channel of intermediate-conductance (KCa3.1) is a target for antisickling and immunosuppressant agents. Many small peptides isolated from animal venoms inhibit KCa3.1 with nanomolar affinities and are promising drug scaffolds. Although the inhibitory effect of peptide toxins on KCa3.1 has been examined extensively, the structural basis of toxin-channel recognition has not been understood in detail. Here, the binding modes of two selected scorpion toxins, charybdotoxin (ChTx) and OSK1, to human KCa3.1 are examined in atomic detail using molecular dynamics (MD) simulations. Employing a homology model of KCa3.1, we first determine conduction properties of the channel using Brownian dynamics and ascertain that the simulated results are in accord with experiment. The model structures of ChTx-KCa3.1 and OSK1-KCa3.1 complexes are then constructed using MD simulations biased with distance restraints. The ChTx-KCa3.1 complex predicted from biased MD is consistent with the crystal structure of ChTx bound to a voltage-gated K(+) channel. The dissociation constants (Kd) for the binding of both ChTx and OSK1 to KCa3.1 determined experimentally are reproduced within fivefold using potential of mean force calculations. Making use of the knowledge we gained by studying the ChTx-KCa3.1 complex, we attempt to enhance the binding affinity of the toxin by carrying out a theoretical mutagenesis. A mutant toxin, in which the positions of two amino acid residues are interchanged, exhibits a 35-fold lower Kd value for KCa3.1 than that of the wild-type. This study provides insight into the key molecular determinants for the high-affinity binding of peptide toxins to KCa3.1, and demonstrates the power of computational methods in the design of novel toxins.
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Tikhonov DB, Bruhova I, Garden DP, Zhorov BS. State-dependent inter-repeat contacts of exceptionally conserved asparagines in the inner helices of sodium and calcium channels. Pflugers Arch 2014; 467:253-66. [DOI: 10.1007/s00424-014-1508-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 01/09/2023]
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