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Kacher J, Sokolova OS, Tarek M. A Deep Learning Approach to Uncover Voltage-Gated Ion Channels' Intermediate States. J Phys Chem B 2024; 128:8724-8736. [PMID: 39213618 DOI: 10.1021/acs.jpcb.4c03182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Owing to recent advancements in cryo-electron microscopy, voltage-gated ion channels have gained a greater comprehension of their structural characteristics. However, a significant enigma remains unsolved for a large majority of these channels: their gating mechanism. This mechanism, which encompasses the conformational changes between open and closed states, is pivotal to their proper functioning. Beyond the binary states of open and closed, an ensemble of intermediate states defines the transition path in-between. Due to the lack of experimental data, one might resort to molecular dynamics simulations as an alternative to decipher these states and the transitions between them. However, the high-energy barriers and the colossal time scales involved hinder access to the latter. We present here an application of deep learning as a reliable pipeline for a comprehensive exploration of voltage-gated ion channel conformational rearrangements during gating. We showcase the pipeline performance specifically on the Kv1.2 voltage sensor domain and confront the results with existing data. We demonstrate how our physics-based deep learning approach contributes to the theoretical understanding of these channels and how it might provide further insights into the exploration of channelopathies.
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Affiliation(s)
- Julia Kacher
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119234 Moscow, Russia
- Shenzhen MSU-BIT University, 1 International University Park Road, Dayun New Town, Longgang District, Shenzhen 518172, China
| | - Mounir Tarek
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
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2
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Peisley A, Hernandez CC, Dahir NS, Koepping L, Raczkowski A, Su M, Ghamari-Langroudi M, Ji X, Gimenez LE, Cone RD. Structure of the Ion Channel Kir7.1 and Implications for its Function in Normal and Pathophysiologic States. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597981. [PMID: 38895219 PMCID: PMC11185801 DOI: 10.1101/2024.06.07.597981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Hereditary defects in the function of the Kir7.1 in the retinal pigment epithelium are associated with the ocular diseases retinitis pigmentosa, Leber congenital amaurosis, and snowflake vitreal degeneration. Studies also suggest that Kir7.1 may be regulated by a GPCR, the melanocortin-4 receptor, in certain hypothalamic neurons. We present the first structures of human Kir7.1 and describe the conformational bias displayed by two pathogenic mutations, R162Q and E276A, to provide an explanation for the basis of disease and illuminate the gating pathway. We also demonstrate the structural basis for the blockade of the channel by a small molecule ML418 and demonstrate that channel blockade in vivo activates MC4R neurons in the paraventricular nucleus of the hypothalamus (PVH), inhibiting food intake and inducing weight loss. Preliminary purification, and structural and pharmacological characterization of an in tandem construct of MC4R and Kir7.1 suggests that the fusion protein forms a homotetrameric channel that retains regulation by liganded MC4R molecules.
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Affiliation(s)
- Alys Peisley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | | | - Naima S. Dahir
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Laura Koepping
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | | | - Min Su
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | | | - Xinrui Ji
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Luis E. Gimenez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Roger D. Cone
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Molecular and Integrative Physiology, School of Medicine, University of Michigan, Ann Arbor, MI
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI
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3
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Huang Y, Kumar S, Lee J, Lü W, Du J. Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution. Nat Struct Mol Biol 2024:10.1038/s41594-024-01316-4. [PMID: 38773335 DOI: 10.1038/s41594-024-01316-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 04/12/2024] [Indexed: 05/23/2024]
Abstract
Channel enzymes represent a class of ion channels with enzymatic activity directly or indirectly linked to their channel function. We investigated a TRPM2 chanzyme from choanoflagellates that integrates two seemingly incompatible functions into a single peptide: a channel module activated by ADP-ribose with high open probability and an enzyme module (NUDT9-H domain) consuming ADP-ribose at a remarkably slow rate. Using time-resolved cryogenic-electron microscopy, we captured a complete series of structural snapshots of gating and catalytic cycles, revealing the coupling mechanism between channel gating and enzymatic activity. The slow kinetics of the NUDT9-H enzyme module confers a self-regulatory mechanism: ADPR binding triggers NUDT9-H tetramerization, promoting channel opening, while subsequent hydrolysis reduces local ADPR, inducing channel closure. We further demonstrated how the NUDT9-H domain has evolved from a structurally semi-independent ADP-ribose hydrolase module in early species to a fully integrated component of a gating ring essential for channel activation in advanced species.
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Affiliation(s)
- Yihe Huang
- Van Andel Institute, Grand Rapids, MI, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Junuk Lee
- Van Andel Institute, Grand Rapids, MI, USA
| | - Wei Lü
- Van Andel Institute, Grand Rapids, MI, USA.
| | - Juan Du
- Van Andel Institute, Grand Rapids, MI, USA.
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4
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Lam AHC, Cooke A, Wright H, Lawson DM, Charpentier M. Evolution of endosymbiosis-mediated nuclear calcium signaling in land plants. Curr Biol 2024; 34:2212-2220.e7. [PMID: 38642549 DOI: 10.1016/j.cub.2024.03.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
The ability of fungi to establish mycorrhizal associations with plants and enhance the acquisition of mineral nutrients stands out as a key feature of terrestrial life. Evidence indicates that arbuscular mycorrhizal (AM) association is a trait present in the common ancestor of land plants,1,2,3,4 suggesting that AM symbiosis was an important adaptation for plants in terrestrial environments.5 The activation of nuclear calcium signaling in roots is essential for AM within flowering plants.6 Given that the earliest land plants lacked roots, whether nuclear calcium signals are required for AM in non-flowering plants is unknown. To address this question, we explored the functional conservation of symbiont-induced nuclear calcium signals between the liverwort Marchantia paleacea and the legume Medicago truncatula. In M. paleacea, AM fungi penetrate the rhizoids and form arbuscules in the thalli.7 Here, we demonstrate that AM germinating spore exudate (GSE) activates nuclear calcium signals in the rhizoids of M. paleacea and that this activation is dependent on the nuclear-localized ion channel DOES NOT MAKE INFECTIONS 1 (MpaDMI1). However, unlike flowering plants, MpaDMI1-mediated calcium signaling is only required for the thalli colonization but not for the AM penetration within rhizoids. We further demonstrate that the mechanism of regulation of DMI1 has diverged between M. paleacea and M. truncatula, including a key amino acid residue essential to sustain DMI1 in an inactive state. Our study reveals functional evolution of nuclear calcium signaling between liverworts and flowering plants and opens new avenues of research into the mechanism of endosymbiosis signaling.
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Affiliation(s)
- Anson H C Lam
- John Innes Centre, Cell and Developmental Biology Department, Norwich Research Park, Norwich NR4 7UH, UK
| | - Aisling Cooke
- John Innes Centre, Cell and Developmental Biology Department, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hannah Wright
- John Innes Centre, Cell and Developmental Biology Department, Norwich Research Park, Norwich NR4 7UH, UK
| | - David M Lawson
- John Innes Centre, Biochemistry and Metabolism Department, Norwich Research Park, Norwich NR4 7UH, UK
| | - Myriam Charpentier
- John Innes Centre, Cell and Developmental Biology Department, Norwich Research Park, Norwich NR4 7UH, UK.
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5
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Liu J, Lu J, Ji W, Lu G, Wang J, Ye T, Jiang Y, Zheng J, Yu P, Liu N, Jiang Y, Mao L. Ion-Selective Micropipette Sensor for In Vivo Monitoring of Sodium Ion with Crown Ether-Encapsulated Metal-Organic Framework Subnanopores. Anal Chem 2024; 96:2651-2657. [PMID: 38306178 DOI: 10.1021/acs.analchem.3c05366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
In vivo sensing of the dynamics of ions with high selectivity is essential for gaining molecular insights into numerous physiological and pathological processes. In this work, we report an ion-selective micropipette sensor (ISMS) through the integration of functional crown ether-encapsulated metal-organic frameworks (MOFs) synthesized in situ within the micropipette tip. The ISMS features distinctive sodium ion (Na+) conduction and high selectivity toward Na+ sensing. The selectivity is attributed to the synergistic effects of subnanoconfined space and the specific coordination of 18-crown-6 toward potassium ions (K+), which largely increase the steric hindrance and transport resistance for K+ to pass through the ISMS. Furthermore, the ISMS exhibits high stability and sensitivity, facilitating real-time monitoring of Na+ dynamics in the living rat brain during spreading of the depression events process. In light of the diversity of crown ethers and MOFs, we believe this study paves the way for a nanofluidic platform for in vivo sensing and neuromorphic electrochemical sensing.
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Affiliation(s)
- Jiahao Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiahao Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Wenliang Ji
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Guangwen Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiao Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Tingyan Ye
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, China
| | - Yisha Jiang
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, China
| | - Juanjuan Zheng
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nannan Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, China
| | - Yanan Jiang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lanqun Mao
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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Niu J, Ma B, Shen J, Chi H, Zhou H, Lu Z, Lu F, Zhu P. Structure-Guided Steric Hindrance Engineering of Devosia Strain A6-243 Quinone-Dependent Dehydrogenase to Enhance Its Catalytic Efficiency. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:549-558. [PMID: 38153089 DOI: 10.1021/acs.jafc.3c07179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Deoxynivalenol (DON), the most widely distributed mycotoxin worldwide, causes severe health risks for humans and animals. Quinone-dependent dehydrogenase derived from Devosia strain A6-243 (DADH) can degrade DON into less toxic 3-keto-DON and then aldo-keto reductase AKR13B3 can reduce 3-keto-DON into relatively nontoxic 3-epi-DON. However, the poor catalytic efficiency of DADH made it unsuitable for practical applications, and it has become the rate-limiting step of the two-step enzymatic cascade catalysis. Here, structure-guided steric hindrance engineering was employed to enhance the catalytic efficiency of DADH. After the steric hindrance engineering, the best mutant, V429G/N431V/T432V/L434V/F537A (M5-1), showed an 18.17-fold increase in specific activity and an 11.04-fold increase in catalytic efficiency (kcat/Km) compared with that of wild-type DADH. Structure-based computational analysis provided information on the increased catalytic efficiency in the directions that attenuated steric hindrance, which was attributed to the reshaped substrate-binding pocket with an expanded catalytic binding cavity and a favorable attack distance. Tunnel analysis suggested that reshaping the active cavity by mutation might alter the shape and size of the enzyme tunnels or form one new enzyme tunnel, which might contribute to the improved catalytic efficiency of M5-1. These findings provide a promising strategy to enhance the catalytic efficiency by steric hindrance engineering.
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Affiliation(s)
- Jiafeng Niu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Ma
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Shen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huimin Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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7
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Min Q, Gao Y, Wang Y. Bioelectricity in dental medicine: a narrative review. Biomed Eng Online 2024; 23:3. [PMID: 38172866 PMCID: PMC10765628 DOI: 10.1186/s12938-023-01189-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Bioelectric signals, whether exogenous or endogenous, play crucial roles in the life processes of organisms. Recently, the significance of bioelectricity in the field of dentistry is steadily gaining greater attention. OBJECTIVE This narrative review aims to comprehensively outline the theory, physiological effects, and practical applications of bioelectricity in dental medicine and to offer insights into its potential future direction. It attempts to provide dental clinicians and researchers with an electrophysiological perspective to enhance their clinical practice or fundamental research endeavors. METHODS An online computer search for relevant literature was performed in PubMed, Web of Science and Cochrane Library, with the keywords "bioelectricity, endogenous electric signal, electric stimulation, dental medicine." RESULTS Eventually, 288 documents were included for review. The variance in ion concentration between the interior and exterior of the cell membrane, referred to as transmembrane potential, forms the fundamental basis of bioelectricity. Transmembrane potential has been established as an essential regulator of intercellular communication, mechanotransduction, migration, proliferation, and immune responses. Thus, exogenous electric stimulation can significantly alter cellular action by affecting transmembrane potential. In the field of dental medicine, electric stimulation has proven useful for assessing pulp condition, locating root apices, improving the properties of dental biomaterials, expediting orthodontic tooth movement, facilitating implant osteointegration, addressing maxillofacial malignancies, and managing neuromuscular dysfunction. Furthermore, the reprogramming of bioelectric signals holds promise as a means to guide organism development and intervene in disease processes. Besides, the development of high-throughput electrophysiological tools will be imperative for identifying ion channel targets and precisely modulating bioelectricity in the future. CONCLUSIONS Bioelectricity has found application in various concepts of dental medicine but large-scale, standardized, randomized controlled clinical trials are still necessary in the future. In addition, the precise, repeatable and predictable measurement and modulation methods of bioelectric signal patterns are essential research direction.
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Affiliation(s)
- Qingqing Min
- Department of Endodontics, Wuxi Stomatology Hospital, Wuxi, 214000, China
| | - Yajun Gao
- Department of Endodontics, Wuxi Stomatology Hospital, Wuxi, 214000, China
| | - Yao Wang
- Department of Implantology, Wuxi Stomatology Hospital, Wuxi, 214000, China.
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8
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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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9
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Huang J, Chen J. Hydrophobic gating in bundle-crossing ion channels: a case study of TRPV4. Commun Biol 2023; 6:1094. [PMID: 37891195 PMCID: PMC10611814 DOI: 10.1038/s42003-023-05471-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Transmembrane ion channels frequently regulate ion permeation by forming bundle crossing of the pore-lining helices when deactivated. The resulting physical constriction is believed to serve as the de facto gate that imposes the major free energy barrier to ion permeation. Intriguingly, many ion channels also contain highly hydrophobic inner pores enclosed by bundle crossing, which can undergo spontaneous dewetting and give rise to a "vapor barrier" to block ion flow even in the absence of physical constriction. Using atomistic simulations, we show that hydrophobic gating and bundle-crossing mechanisms co-exist and complement one and another in the human TRPV4 channel. In particular, a single hydrophilic mutation in the lower pore can increase pore hydration and reduce the ion permeation free energy barrier by about half without affecting the bundle crossing. We believe that hydrophobic gating may play a key role in other bundle-crossing ion channels with hydrophobic inner pores.
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Affiliation(s)
- Jian Huang
- Department of Chemistry University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Jianhan Chen
- Department of Chemistry University of Massachusetts Amherst, Amherst, MA, 01003, USA.
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10
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Maisat W, Yuki K. Volatile anesthetic isoflurane exposure facilitates Enterococcus biofilm infection. FASEB J 2023; 37:e23186. [PMID: 37665578 PMCID: PMC10495085 DOI: 10.1096/fj.202301128r] [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: 06/06/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
Enterococcus faecalis (E. faecalis) is one of the major pathogenic bacteria responsible for surgical site infections. Biofilm infections are major hospital-acquired infections. Previous studies suggested that ions could regulate biofilm formation in microbes. Volatile anesthetics, frequently administered in surgical setting, target ion channels. Here, we investigated the role of ion channels/transporters and volatile anesthetics in the biofilm formation by E. faecalis MMH594 strain and its ion transporter mutants. We found that a chloride transporter mutant significantly reduced biofilm formation compared to the parental strain. Downregulation of teichoic acid biosynthesis in the chloride transporter mutant impaired biofilm matrix formation and cellular adhesion, leading to mitigated biofilm formation. Among anesthetics, isoflurane exposure enhanced biofilm formation in vitro and in vivo. The upregulation of de novo purine biosynthesis pathway by isoflurane exposure potentially enhanced biofilm formation, an essential process for DNA, RNA, and ATP synthesis. We also demonstrated that isoflurane exposure to E. faecalis increased cyclic-di-AMP and extracellular DNA production, consistent with the increased purine biosynthesis. We further showed that isoflurane enhanced the enzymatic activity of phosphoribosyl pyrophosphate synthetase (PRPP-S). With the hypothesis that isoflurane directly bound to PRPP-S, we predicted isoflurane binding site on it using rigid docking. Our study provides a better understanding of the underlying mechanisms of E. faecalis biofilm formation and highlights the potential impact of an ion transporter and volatile anesthetic on this process. These findings may lead to the development of novel strategies for preventing E. faecalis biofilm formation and improving patient outcomes in clinical settings.
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Affiliation(s)
- Wiriya Maisat
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children’s Hospital, Boston, MA, USA
- Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Anesthesiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Koichi Yuki
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children’s Hospital, Boston, MA, USA
- Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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11
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Catacuzzeno L, Conti F, Franciolini F. Fifty years of gating currents and channel gating. J Gen Physiol 2023; 155:e202313380. [PMID: 37410612 PMCID: PMC10324510 DOI: 10.1085/jgp.202313380] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/12/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
We celebrate this year the 50th anniversary of the first electrophysiological recordings of the gating currents from voltage-dependent ion channels done in 1973. This retrospective tries to illustrate the context knowledge on channel gating and the impact gating-current recording had then, and how it continued to clarify concepts, elaborate new ideas, and steer the scientific debate in these 50 years. The notion of gating particles and gating currents was first put forward by Hodgkin and Huxley in 1952 as a necessary assumption for interpreting the voltage dependence of the Na and K conductances of the action potential. 20 years later, gating currents were actually recorded, and over the following decades have represented the most direct means of tracing the movement of the gating charges and gaining insights into the mechanisms of channel gating. Most work in the early years was focused on the gating currents from the Na and K channels as found in the squid giant axon. With channel cloning and expression on heterologous systems, other channels as well as voltage-dependent enzymes were investigated. Other approaches were also introduced (cysteine mutagenesis and labeling, site-directed fluorometry, cryo-EM crystallography, and molecular dynamics [MD] modeling) to provide an integrated and coherent view of voltage-dependent gating in biological macromolecules. The layout of this retrospective reflects the past 50 years of investigations on gating currents, first addressing studies done on Na and K channels and then on other voltage-gated channels and non-channel structures. The review closes with a brief overview of how the gating-charge/voltage-sensor movements are translated into pore opening and the pathologies associated with mutations targeting the structures involved with the gating currents.
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Affiliation(s)
- Luigi Catacuzzeno
- Department of Chemistry Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Franco Conti
- Department of Physics, University of Genova, Genova, Italy
| | - Fabio Franciolini
- Department of Chemistry Biology and Biotechnology, University of Perugia, Perugia, Italy
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12
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Bhowmick S, Shenouda ML, Tschowri N. Osmotic stress responses and the biology of the second messenger c-di-AMP in Streptomyces. MICROLIFE 2023; 4:uqad020. [PMID: 37223731 PMCID: PMC10117811 DOI: 10.1093/femsml/uqad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Streptomyces are prolific antibiotic producers that thrive in soil, where they encounter diverse environmental cues, including osmotic challenges caused by rainfall and drought. Despite their enormous value in the biotechnology sector, which often relies on ideal growth conditions, how Streptomyces react and adapt to osmotic stress is heavily understudied. This is likely due to their complex developmental biology and an exceptionally broad number of signal transduction systems. With this review, we provide an overview of Streptomyces' responses to osmotic stress signals and draw attention to open questions in this research area. We discuss putative osmolyte transport systems that are likely involved in ion balance control and osmoadaptation and the role of alternative sigma factors and two-component systems (TCS) in osmoregulation. Finally, we highlight the current view on the role of the second messenger c-di-AMP in cell differentiation and the osmotic stress responses with specific emphasis on the two models, S. coelicolor and S. venezuelae.
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Affiliation(s)
- Sukanya Bhowmick
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Mary L Shenouda
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Natalia Tschowri
- Corresponding author. Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany. E-mail:
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13
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Huang Y, Lü W, Du J. Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533055. [PMID: 36993210 PMCID: PMC10055075 DOI: 10.1101/2023.03.16.533055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The canonical ion channels gated by chemical ligands use the free energy of agonist binding to open the channel pore, returning to a closed state upon agonist departure. A unique class of ion channels, known as channel-enzymes (chanzymes), possess additional enzymatic activity that is directly or indirectly linked to their channel function. Here we investigated a TRPM2 chanzyme from choanoflagellates, an evolutionary ancestor of all metazoan TRPM channels, which integrates two seemingly incompatible functions into a single peptide: a channel module activated by ADP ribose (ADPR) with high open probability and an enzyme module (NUDT9-H domain) consuming ADPR at a remarkably slow rate. Using time-resolved cryo- electron microscopy (cryo-EM), we captured a complete series of structural snapshots of the gating and catalytic cycles, revealing the coupling mechanism between channel gating and enzymatic activity. Our results showed that the slow kinetics of the NUDT9-H enzyme module confers a novel self-regulatory mechanism, whereby the enzyme module modulates channel gating in a binary manner. Binding of ADPR to NUDT9-H first triggers tetramerization of the enzyme modules, promoting channel opening, while the subsequent hydrolysis reaction reduces local ADPR availability, inducing channel closure. This coupling enables the ion-conducting pore to alternate rapidly between open and closed states, avoiding Mg 2+ and Ca 2+ overload. We further demonstrated how the NUDT9-H domain has evolved from a structurally semi-independent ADPR hydrolase module in early species TRPM2 to a fully integrated component of a gating ring essential for channel activation in advanced species TRPM2. Our study demonstrated an example of how organisms can adapt to their environments at the molecular level.
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14
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Liang KK. On the crucial features of a single‐file transport model for ion channels. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202200517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Kuo Kan Liang
- Department of Physics National Taiwan University Taipei Taiwan
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15
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Feng H, Wei GW. Virtual screening of DrugBank database for hERG blockers using topological Laplacian-assisted AI models. Comput Biol Med 2023; 153:106491. [PMID: 36599209 PMCID: PMC10120853 DOI: 10.1016/j.compbiomed.2022.106491] [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: 11/17/2022] [Revised: 11/29/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022]
Abstract
The human ether-a-go-go (hERG) potassium channel (Kv11.1) plays a critical role in mediating cardiac action potential. The blockade of this ion channel can potentially lead fatal disorder and/or long QT syndrome. Many drugs have been withdrawn because of their serious hERG-cardiotoxicity. It is crucial to assess the hERG blockade activity in the early stage of drug discovery. We are particularly interested in the hERG-cardiotoxicity of compounds collected in the DrugBank database considering that many DrugBank compounds have been approved for therapeutic treatments or have high potential to become drugs. Machine learning-based in silico tools offer a rapid and economical platform to virtually screen DrugBank compounds. We design accurate and robust classifiers for blockers/non-blockers and then build regressors to quantitatively analyze the binding potency of the DrugBank compounds on the hERG channel. Molecular sequences are embedded with two natural language processing (NLP) methods, namely, autoencoder and transformer. Complementary three-dimensional (3D) molecular structures are embedded with two advanced mathematical approaches, i.e., topological Laplacians and algebraic graphs. With our state-of-the-art tools, we reveal that 227 out of the 8641 DrugBank compounds are potential hERG blockers, suggesting serious drug safety problems. Our predictions provide guidance for the further experimental interrogation of DrugBank compounds' hERG-cardiotoxicity.
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Affiliation(s)
- Hongsong Feng
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, MI 48824, USA; Department of Electrical and Computer Engineering, Michigan State University, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA.
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16
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Li C, Jiang Y, Wu Z, Zhang Y, Huang C, Cheng S, You Y, Zhang P, Chen W, Mao L, Jiang L. Mixed Matrix Membrane with Penetrating Subnanochannels: A Versatile Nanofluidic Platform for Selective Metal Ion Conduction. Angew Chem Int Ed Engl 2023; 62:e202215906. [PMID: 36374215 DOI: 10.1002/anie.202215906] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Indexed: 11/16/2022]
Abstract
Biological ion channels penetrated through cell membrane form unique transport pathways for selective ionic conductance. Replicating the success of ion selectivity with mixed matrix membranes (MMMs) will enable new separation technologies but remains challenging. Herein, we report a soft substrate-assisted solution casting method to develop MMMs with penetrating subnanochannels for selective metal ion conduction. The MMMs are composed of penetrating Prussian white (PW) microcubes with subnanochannels in dense polyimide (PI) matrices, achieving selective monovalent metal ion conduction. The ion selectivity of K+ /Mg2+ is up to 14.0, and the ion conductance of K+ can reach 45.5 μS with the testing diameter of 5 mm, which can be further improved by increasing the testing area. Given the diversity of nanoporous materials and polymer matrices, we expect that the MMMs with penetrating subnanochannels could be developed into a versatile nanofluidic platform for various emerging applications.
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Affiliation(s)
- Chen Li
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
| | - Yanan Jiang
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Zihan Wu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
| | - Youcai Zhang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
| | - Cheng Huang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
| | - Sha Cheng
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
| | - Ya You
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China.,Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, 572024, P. R. China.,Hubei Longzhong Laboratory, Xiangyang, 441000, P. R. China
| | - Pengchao Zhang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China.,Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, 572024, P. R. China.,Hubei Longzhong Laboratory, Xiangyang, 441000, P. R. China
| | - Wen Chen
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
| | - Lanqun Mao
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Lei Jiang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
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17
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Matamoros M, Ng XW, Brettmann JB, Piston DW, Nichols CG. Conformational plasticity of NaK2K and TREK2 potassium channel selectivity filters. Nat Commun 2023; 14:89. [PMID: 36609575 PMCID: PMC9822992 DOI: 10.1038/s41467-022-35756-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023] Open
Abstract
The K+ channel selectivity filter (SF) is defined by TxGYG amino acid sequences that generate four identical K+ binding sites (S1-S4). Only two sites (S3, S4) are present in the non-selective bacterial NaK channel, but a four-site K+-selective SF is obtained by mutating the wild-type TVGDGN SF sequence to a canonical K+ channel TVGYGD sequence (NaK2K mutant). Using single molecule FRET (smFRET), we show that the SF of NaK2K, but not of non-selective NaK, is ion-dependent, with the constricted SF configuration stabilized in high K+ conditions. Patch-clamp electrophysiology and non-canonical fluorescent amino acid incorporation show that NaK2K selectivity is reduced by crosslinking to limit SF conformational movement. Finally, the eukaryotic K+ channel TREK2 SF exhibits essentially identical smFRET-reported ion-dependent conformations as in prokaryotic K+ channels. Our results establish the generality of K+-induced SF conformational stability across the K+ channel superfamily, and introduce an approach to study manipulation of channel selectivity.
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Affiliation(s)
- Marcos Matamoros
- Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xue Wen Ng
- Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua B Brettmann
- Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Millipore-Sigma Inc., St. Louis, MO, USA
| | - David W Piston
- Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Colin G Nichols
- Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.
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18
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Naranjo D, Diaz-Franulic I. Sweetening K-channels: what sugar taught us about permeation and gating. Front Mol Biosci 2023; 10:1063796. [PMID: 37122567 PMCID: PMC10140501 DOI: 10.3389/fmolb.2023.1063796] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
Because they enable for the modification of both viscosity and osmolarity, sugars have been used as a biophysical probe of voltage-gated K-channels for a while. Viscosity variations made it possible to measure the pore sizes in large and small conductance K-channels using techniques similar to those used in the 1980s to study the gramicidin A channel. These analyses led to the finding that the size of the internal mouth appears to be the primary cause of the conductance differences between Shaker-like channels and large conductance BK-channels. As an osmotic agent, adding sugar unilaterally causes streaming potentials that indicate H2O/K+ cotransport across the BK-channel pore. Osmotic experiments on Shaker K-channels suggest that the pore gate operation and the slow inactivation displace comparable amounts of water. Functionally isolated voltage sensors allow estimation of individual osmotic work for each voltage sensing charge during voltage-activation, reporting dramatic internal and external remodeling of the Voltage Sensing Domain´s solvent exposed surfaces. Remarkably, each charge of the VSD appears to take a unique trajectory. Thus, manipulation of viscosity and osmolarity, together with 3D structures, brings in solid grounds to harmonize function and structure in membrane proteins such as K-channels and, in a wider scope, other structurally dynamic proteins.
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Affiliation(s)
- David Naranjo
- Instituto de Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- *Correspondence: David Naranjo, ; Ignacio Diaz-Franulic,
| | - Ignacio Diaz-Franulic
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- *Correspondence: David Naranjo, ; Ignacio Diaz-Franulic,
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19
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Zahra A, Liu R, Han W, Meng H, Wang Q, Wang Y, Campbell SL, Wu J. K Ca-Related Neurological Disorders: Phenotypic Spectrum and Therapeutic Indications. Curr Neuropharmacol 2023; 21:1504-1518. [PMID: 36503451 PMCID: PMC10472807 DOI: 10.2174/1570159x21666221208091805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 12/14/2022] Open
Abstract
Although potassium channelopathies have been linked to a wide range of neurological conditions, the underlying pathogenic mechanism is not always clear, and a systematic summary of clinical manifestation is absent. Several neurological disorders have been associated with alterations of calcium-activated potassium channels (KCa channels), such as loss- or gain-of-function mutations, post-transcriptional modification, etc. Here, we outlined the current understanding of the molecular and cellular properties of three subtypes of KCa channels, including big conductance KCa channels (BK), small conductance KCa channels (SK), and the intermediate conductance KCa channels (IK). Next, we comprehensively reviewed the loss- or gain-of-function mutations of each KCa channel and described the corresponding mutation sites in specific diseases to broaden the phenotypic-genotypic spectrum of KCa-related neurological disorders. Moreover, we reviewed the current pharmaceutical strategies targeting KCa channels in KCa-related neurological disorders to provide new directions for drug discovery in anti-seizure medication.
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Affiliation(s)
- Aqeela Zahra
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
- Department of Zoology, University of Sialkot, Sialkot 51310, Pakistan
| | - Ru Liu
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Wenzhe Han
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Hui Meng
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Qun Wang
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - YunFu Wang
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Susan L. Campbell
- Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Jianping Wu
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
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20
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Rothberg BS. Interrogating the gating motions of the NaK channel. J Gen Physiol 2022; 154:e202213257. [PMID: 36326621 PMCID: PMC9640267 DOI: 10.1085/jgp.202213257] [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] [Indexed: 11/05/2022] Open
Abstract
Previous crystallographic studies depicted a physical gate of the NaK channel localized at a bundle crossing of pore-lining helices, but solution NMR studies in the current issue of JGP suggest otherwise.
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Affiliation(s)
- Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA
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21
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Shan M, Jiang C, Qin L, Cheng G. A Review of Computational Methods in Predicting hERG Channel Blockers. ChemistrySelect 2022. [DOI: 10.1002/slct.202201221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mengyi Shan
- School of Pharmaceutical Sciences Zhejiang Chinese Medical University Hangzhou 310053 People's Republic of China
| | - Chen Jiang
- QuanMin RenZheng (HangZhou) Technology Co. Ltd. China
| | - Lu‐Ping Qin
- School of Pharmaceutical Sciences Zhejiang Chinese Medical University Hangzhou 310053 People's Republic of China
| | - Gang Cheng
- School of Pharmaceutical Sciences Zhejiang Chinese Medical University Hangzhou 310053 People's Republic of China
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22
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Structure of the Human BK Ion Channel in Lipid Environment. MEMBRANES 2022; 12:membranes12080758. [PMID: 36005673 PMCID: PMC9414842 DOI: 10.3390/membranes12080758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023]
Abstract
Voltage-gated and ligand-modulated ion channels play critical roles in excitable cells. To understand the interplay among voltage sensing, ligand binding, and channel opening, the structures of ion channels in various functional states and in lipid membrane environments need to be determined. Here, the random spherically constrained (RSC) single-particle cryo-EM method was employed to study human large conductance voltage- and calcium-activated potassium (hBK or hSlo1) channels reconstituted into liposomes. The hBK structure was determined at 3.5 Å resolution in the absence of Ca2+. Instead of the common fourfold symmetry observed in ligand-modulated ion channels, a twofold symmetry was observed in hBK in liposomes. Compared with the structure of isolated hSlo1 Ca2+ sensing gating rings, two opposing subunits in hBK unfurled, resulting in a wider opening towards the transmembrane region of hBK. In the pore gate domain, two opposing subunits also moved downwards relative to the two other subunits.
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23
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Liang L, Liu H, Bartholdi D, van Haeringen A, Fernandez‐Jaén A, Peeters EEA, Xiong H, Bai X, Xu C, Ke T, Wang QK. Identification and functional analysis of two new de novo KCNMA1 variants associated with Liang-Wang syndrome. Acta Physiol (Oxf) 2022; 235:e13800. [PMID: 35156297 DOI: 10.1111/apha.13800] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023]
Abstract
AIM Loss-of-function KCNMA1 variants cause Liang-Wang syndrome (MIM #618729), a newly identified multiple malformation syndrome with a broad spectrum of developmental and neurological phenotypes. However, the full spectrum of clinical features and underlying pathogenic mechanisms need full elucidation. METHODS Exome sequencing was used to identify pathogenic variants. Patch-clamp recordings were performed to access the effects of KCNMA1 variants on BK channels. Total and membrane protein expression levels of BK channels were characterized using Western blotting. RESULTS We report identification and functional characterization of two new de novo loss-of-function KCNMA1 variants p.(A172T) and p.(A314T) with characteristics of Liang-Wang syndrome. Variant p.(A172T) is associated with developmental delay, cognitive impairment and ataxia. Mechanistically, p.(A172T) abolishes BK potassium current, inhibits Mg2+ -dependent gating, but shifts conductance-voltage (G-V) curves to more positive potentials when complexed with WT channels. Variant p.(A314T) is associated with developmental delay, intellectual disability, cognitive impairment, mild ataxia and generalized epilepsy; suppresses BK current amplitude; and shifts G-V curves to more positive potentials when expressed with WT channels. In addition, two new patients with previously reported gain-of-function variants p.(N536H) and p.(N995S) are found to show epilepsy and paroxysmal dyskinesia as reported previously, but also exhibit additional symptoms of cognitive impairment and dysmorphic features. Furthermore, variants p.(A314T) and p.(N536H) reduced total and membrane levels of BK proteins. CONCLUSION Our findings identified two new loss-of-function mutations of KCNMA1 associated with Liang-Wang syndrome, expanded the spectrum of clinical features associated with gain-of-function KCNMA1 variants and emphasized the overlapping features shared by gain-of-function and loss-of-function mutations.
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Affiliation(s)
- Lina Liang
- Center for Human Genome Research Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology Huazhong University of Science and Technology Wuhan P. R. China
| | - Huihui Liu
- Center for Human Genome Research Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology Huazhong University of Science and Technology Wuhan P. R. China
| | - Deborah Bartholdi
- Department of Human Genetics, Inselspital University Hospital Bern Bern Switzerland
| | - Arie van Haeringen
- Department of Clinical Genetics Leiden University Medical Center Leiden the Netherlands
| | - Alberto Fernandez‐Jaén
- Hospital Universitario Quirónsalud School of Medicine Universidad Europea de Madrid Madrid Spain
| | - Els E. A. Peeters
- Department of Child Neurology Juliana Children’s Hospital HAGA Medical Center The Hague the Netherlands
| | - Hongbo Xiong
- Center for Human Genome Research Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology Huazhong University of Science and Technology Wuhan P. R. China
| | - Xuemei Bai
- Center for Human Genome Research Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology Huazhong University of Science and Technology Wuhan P. R. China
| | - Chengqi Xu
- Center for Human Genome Research Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology Huazhong University of Science and Technology Wuhan P. R. China
| | - Tie Ke
- Center for Human Genome Research Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology Huazhong University of Science and Technology Wuhan P. R. China
| | - Qing K. Wang
- Center for Human Genome Research Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology Huazhong University of Science and Technology Wuhan P. R. China
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Guan F, Li T, Dong W, Guo R, Chai H, Chen Z, Ren Z, Li Y, Ye S. Novel insights into the allosteric gating mechanism of MthK channel. Natl Sci Rev 2022; 9:nwac072. [PMID: 36072506 PMCID: PMC9440719 DOI: 10.1093/nsr/nwac072] [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: 05/07/2021] [Revised: 02/28/2022] [Accepted: 03/29/2022] [Indexed: 11/29/2022] Open
Abstract
Allostery is a fundamental element during channel gating in response to an appropriate stimulus by which events occurring at one site are transmitted to distal sites to regulate activity. To address how binding of the first Ca2+ ion at one of the eight chemically identical subunits facilitates the other Ca2+-binding events in MthK, a Ca2+-gated K+ channel containing a conserved ligand-binding RCK domain, we analysed a large collection of MthK structures and performed the corresponding thermodynamic and electrophysiological measurements. These structural and functional studies led us to conclude that the conformations of the Ca2+-binding sites alternate between two quaternary states and exhibit significant differences in Ca2+ affinity. We further propose an allosteric model of the MthK-gating mechanism by which a cascade of structural events connect the initial Ca2+-binding to the final changes of the ring structure that open the ion-conduction pore. This mechanical model reveals the exquisite design that achieves the allosteric gating and could be of general relevance for the action of other ligand-gated ion channels containing the RCK domain.
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Affiliation(s)
- Fenghui Guan
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin300072, China
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Tianyu Li
- State Key Laboratory of Drug Research and Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
| | - Wei Dong
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058Zhejiang, China
| | - Rui Guo
- Department of Logistics, Tianjin University, 92 Weijin Road, Nankai District, Tianjin300072, China
| | - Hao Chai
- State Key Laboratory of Drug Research and Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
| | - Zhiqiu Chen
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
| | - Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL60607, USA
- Renz Research Inc., Westmont, IL60559, USA
| | - Yang Li
- State Key Laboratory of Drug Research and Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin300072, China
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058Zhejiang, China
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25
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Bavaharan A, Skilbeck C. Electrical signalling in prokaryotes and its convergence with quorum sensing in Bacillus. Bioessays 2022; 44:e2100193. [PMID: 35195292 DOI: 10.1002/bies.202100193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
Abstract
The importance of electrical signalling in bacteria is an emerging paradigm. Bacillus subtilis biofilms exhibit electrical communication that regulates metabolic activity and biofilm growth. Starving cells initiate oscillatory extracellular potassium signals that help even the distribution of nutrients within the biofilm and thus help regulate biofilm development. Quorum sensing also regulates biofilm growth and crucially there is convergence between electrical and quorum sensing signalling axes. This makes B. subtilis an interesting model for cell signalling research. SpoOF is predicted to act as a logic gate for signalling pathway convergence, raising interesting questions about the functional nature of this gate and the relative importance of these disparate signals on biofilm behaviour. How is an oscillating signal integrated with a quorum signal? The model presented offers rich opportunities for future experimental and theoretical modelling research. The importance of direct cell-to-cell electrical signalling in prokaryotes, so characteristic of multicellular eukaryotes, is also discussed.
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26
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Tikhonov DB, Zhorov BS. P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models. MEMBRANES 2022; 12:membranes12020229. [PMID: 35207150 PMCID: PMC8876033 DOI: 10.3390/membranes12020229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/09/2022] [Accepted: 02/09/2022] [Indexed: 01/27/2023]
Abstract
The superfamily of P-loop channels includes potassium, sodium, and calcium channels, as well as TRP channels and ionotropic glutamate receptors. A rapidly increasing number of crystal and cryo-EM structures have revealed conserved and variable elements of the channel structures. Intriguing differences are seen in transmembrane helices of channels, which may include π-helical bulges. The bulges reorient residues in the helices and thus strongly affect their intersegment contacts and patterns of ligand-sensing residues. Comparison of the experimental structures suggests that some π-bulges are dynamic: they may appear and disappear upon channel gating and ligand binding. The AlphaFold2 models represent a recent breakthrough in the computational prediction of protein structures. We compared some crystal and cryo-EM structures of P-loop channels with respective AlphaFold2 models. Folding of the regions, which are resolved experimentally, is generally similar to that predicted in the AlphaFold2 models. The models also reproduce some subtle but significant differences between various P-loop channels. However, patterns of π-bulges do not necessarily coincide in the experimental and AlphaFold2 structures. Given the importance of dynamic π-bulges, further studies involving experimental and theoretical approaches are necessary to understand the cause of the discrepancy.
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Szule JA. Hypothesis Relating the Structure, Biochemistry and Function of Active Zone Material Macromolecules at a Neuromuscular Junction. Front Synaptic Neurosci 2022; 13:798225. [PMID: 35069169 PMCID: PMC8766674 DOI: 10.3389/fnsyn.2021.798225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/14/2021] [Indexed: 12/22/2022] Open
Abstract
This report integrates knowledge of in situ macromolecular structures and synaptic protein biochemistry to propose a unified hypothesis for the regulation of certain vesicle trafficking events (i.e., docking, priming, Ca2+-triggering, and membrane fusion) that lead to neurotransmitter secretion from specialized “active zones” of presynaptic axon terminals. Advancements in electron tomography, to image tissue sections in 3D at nanometer scale resolution, have led to structural characterizations of a network of different classes of macromolecules at the active zone, called “Active Zone Material’. At frog neuromuscular junctions, the classes of Active Zone Material macromolecules “top-masts”, “booms”, “spars”, “ribs” and “pins” direct synaptic vesicle docking while “pins”, “ribs” and “pegs” regulate priming to influence Ca2+-triggering and membrane fusion. Other classes, “beams”, “steps”, “masts”, and “synaptic vesicle luminal filaments’ likely help organize and maintain the structural integrity of active zones. Extensive studies on the biochemistry that regulates secretion have led to comprehensive characterizations of the many conserved proteins universally involved in these trafficking events. Here, a hypothesis including a partial proteomic atlas of Active Zone Material is presented which considers the common roles, binding partners, physical features/structure, and relative positioning in the axon terminal of both the proteins and classes of macromolecules involved in the vesicle trafficking events. The hypothesis designates voltage-gated Ca2+ channels and Ca2+-gated K+ channels to ribs and pegs that are connected to macromolecules that span the presynaptic membrane at the active zone. SNARE proteins (Syntaxin, SNAP25, and Synaptobrevin), SNARE-interacting proteins Synaptotagmin, Munc13, Munc18, Complexin, and NSF are designated to ribs and/or pins. Rab3A and Rabphillin-3A are designated to top-masts and/or booms and/or spars. RIM, Bassoon, and Piccolo are designated to beams, steps, masts, ribs, spars, booms, and top-masts. Spectrin is designated to beams. Lastly, the luminal portions of SV2 are thought to form the bulk of the observed synaptic vesicle luminal filaments. The goal here is to help direct future studies that aim to bridge Active Zone Material structure, biochemistry, and function to ultimately determine how it regulates the trafficking events in vivo that lead to neurotransmitter secretion.
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Jiang Y, Idikuda V, Chanda B. Preparation of Giant Escherichia coli spheroplasts for Electrophysiological Recordings. Bio Protoc 2021; 11:e4261. [PMID: 35087920 PMCID: PMC8720513 DOI: 10.21769/bioprotoc.4261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 07/07/2024] Open
Abstract
Prokaryotic ion channels have been instrumental in furthering our understanding of many fundamental aspects of ion channels' structure and function. However, characterizing the biophysical properties of a prokaryotic ion channel in a native membrane system using patch-clamp electrophysiology is technically challenging. Patch-clamp is regarded as a gold standard technique to study ion channel properties in both native and heterologous expression systems. The presence of a cell wall and the small size of bacterial cells makes it impossible to directly patch clamp using microelectrodes. Here, we describe a method for the preparation of giant E. coli spheroplasts in order to investigate the electrophysiological properties of bacterial cell membranes. Spheroplasts are formed by first inhibiting bacterial cell wall synthesis, followed by enzymatic digestion of the outer cell wall in the presence of a permeabilizing agent. This protocol can be used to characterize the function of any heterologous ion channels or ion transporters expressed in E. coli membranes.
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Affiliation(s)
- Yihao Jiang
- Department of Psychiatry of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- The MOE Frontier Research Center of Brain & Brain-machine Integration, Zhejiang University School of Brain Science and Brain Medicine, China
| | - Vinay Idikuda
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for the Investigation of Membrane Excitability Diseases (CIMED)
| | - Baron Chanda
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for the Investigation of Membrane Excitability Diseases (CIMED)
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Small molecule modulation of the Drosophila Slo channel elucidated by cryo-EM. Nat Commun 2021; 12:7164. [PMID: 34887422 PMCID: PMC8660915 DOI: 10.1038/s41467-021-27435-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/18/2021] [Indexed: 12/16/2022] Open
Abstract
Slowpoke (Slo) potassium channels display extraordinarily high conductance, are synergistically activated by a positive transmembrane potential and high intracellular Ca2+ concentrations and are important targets for insecticides and antiparasitic drugs. However, it is unknown how these compounds modulate ion translocation and whether there are insect-specific binding pockets. Here, we report structures of Drosophila Slo in the Ca2+-bound and Ca2+-free form and in complex with the fungal neurotoxin verruculogen and the anthelmintic drug emodepside. Whereas the architecture and gating mechanism of Slo channels are conserved, potential insect-specific binding pockets exist. Verruculogen inhibits K+ transport by blocking the Ca2+-induced activation signal and precludes K+ from entering the selectivity filter. Emodepside decreases the conductance by suboptimal K+ coordination and uncouples ion gating from Ca2+ and voltage sensing. Our results expand the mechanistic understanding of Slo regulation and lay the foundation for the rational design of regulators of Slo and other voltage-gated ion channels. Slowpoke (Slo) channels are voltage-gated potassium channels that are activated by high intracellular Ca2+ concentrations, and they are targets for insecticides and antiparasitic drugs. Here, the authors present the cryo-EM structures of the Drosophila melanogaster Slo channel in the Ca2+-bound and Ca2+-free conformations, as well as in complex with the fungal neurotoxin verruculogen and the anthelmintic drug emodepside and discuss the mechanisms by which they affect the activity of Slo.
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Mu X, Wu T, Mao Y, Zhao Y, Xu Y, Nie Y. Iterative Alanine Scanning Mutagenesis Confers Aromatic Ketone Specificity and Activity of L‐Amine Dehydrogenases. ChemCatChem 2021. [DOI: 10.1002/cctc.202101558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Xiaoqing Mu
- Laboratory of Brewing Microbiology and Applied Enzymology School of Biotechnology Jiangnan University 214122 Wuxi P. R. China
- Key Laboratory of Industrial Biotechnology Ministry of Education School of Biotechnology Jiangnan University 214122 Wuxi P. R. China
- Suqian Jiangnan University Institute of Industrial Technology 223800 Suqian P. R. China
| | - Tao Wu
- Laboratory of Brewing Microbiology and Applied Enzymology School of Biotechnology Jiangnan University 214122 Wuxi P. R. China
- Key Laboratory of Industrial Biotechnology Ministry of Education School of Biotechnology Jiangnan University 214122 Wuxi P. R. China
- Suqian Jiangnan University Institute of Industrial Technology 223800 Suqian P. R. China
| | - Yong Mao
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences Department of Bioinformatics and Biostatistics School of Life Sciences and Biotechnology Shanghai Jiao Tong University 200240 Shanghai P. R. China
| | - Yilei Zhao
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences Department of Bioinformatics and Biostatistics School of Life Sciences and Biotechnology Shanghai Jiao Tong University 200240 Shanghai P. R. China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology School of Biotechnology Jiangnan University 214122 Wuxi P. R. China
- Key Laboratory of Industrial Biotechnology Ministry of Education School of Biotechnology Jiangnan University 214122 Wuxi P. R. China
| | - Yao Nie
- Laboratory of Brewing Microbiology and Applied Enzymology School of Biotechnology Jiangnan University 214122 Wuxi P. R. China
- Key Laboratory of Industrial Biotechnology Ministry of Education School of Biotechnology Jiangnan University 214122 Wuxi P. R. China
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31
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Sancho M, Kyle BD. The Large-Conductance, Calcium-Activated Potassium Channel: A Big Key Regulator of Cell Physiology. Front Physiol 2021; 12:750615. [PMID: 34744788 PMCID: PMC8567177 DOI: 10.3389/fphys.2021.750615] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/29/2021] [Indexed: 12/01/2022] Open
Abstract
Large-conductance Ca2+-activated K+ channels facilitate the efflux of K+ ions from a variety of cells and tissues following channel activation. It is now recognized that BK channels undergo a wide range of pre- and post-translational modifications that can dramatically alter their properties and function. This has downstream consequences in affecting cell and tissue excitability, and therefore, function. While finding the “silver bullet” in terms of clinical therapy has remained elusive, ongoing research is providing an impressive range of viable candidate proteins and mechanisms that associate with and modulate BK channel activity, respectively. Here, we provide the hallmarks of BK channel structure and function generally, and discuss important milestones in the efforts to further elucidate the diverse properties of BK channels in its many forms.
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Affiliation(s)
- Maria Sancho
- Department of Pharmacology, University of Vermont, Burlington, VT, United States
| | - Barry D Kyle
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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Wu T, Mu X, Xue Y, Xu Y, Nie Y. Structure-guided steric hindrance engineering of Bacillus badius phenylalanine dehydrogenase for efficient L-homophenylalanine synthesis. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:207. [PMID: 34689801 PMCID: PMC8543943 DOI: 10.1186/s13068-021-02055-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Direct reductive amination of prochiral 2-oxo-4-phenylbutyric acid (2-OPBA) catalyzed by phenylalanine dehydrogenase (PheDH) is highly attractive in the synthesis of the pharmaceutical chiral building block L-homophenylalanine (L-HPA) given that its sole expense is ammonia and that water is the only byproduct. Current issues in this field include a poor catalytic efficiency and a low substrate loading. RESULTS In this study, we report a structure-guided steric hindrance engineering of PheDH from Bacillus badius to create an enhanced biocatalyst for efficient L-HPA synthesis. Mutagenesis libraries based on molecular docking, double-proximity filtering, and a degenerate codon significantly increased catalytic efficiency. Seven superior mutants were acquired, and the optimal triple-site mutant, V309G/L306V/V144G, showed a 12.7-fold higher kcat value, and accordingly a 12.9-fold higher kcat/Km value, than that of the wild type. A paired reaction system comprising V309G/L306V/V144G and glucose dehydrogenase converted 1.08 M 2-OPBA to L-HPA in 210 min, and the specific space-time conversion was 30.9 mmol g-1 L-1 h-1. The substrate loading and specific space-time conversion are the highest values to date. Docking simulation revealed increases in substrate-binding volume and additional degrees of freedom of the substrate 2-OPBA in the pocket. Tunnel analysis suggested the formation of new enzyme tunnels and the expansion of existing ones. CONCLUSIONS Overall, the results show that the mutant V309G/L306V/V144G has the potential for the industrial synthesis of L-HPA. The modified steric hindrance engineering approach can be a valuable addition to the current enzyme engineering toolbox.
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Affiliation(s)
- Tao Wu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Suqian Jiangnan University Institute of Industrial Technology, Suqian, 223800, China
| | - Xiaoqing Mu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- Suqian Jiangnan University Institute of Industrial Technology, Suqian, 223800, China.
| | - Yuyan Xue
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yao Nie
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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Cui J. BK Channel Gating Mechanisms: Progresses Toward a Better Understanding of Variants Linked Neurological Diseases. Front Physiol 2021; 12:762175. [PMID: 34744799 PMCID: PMC8567085 DOI: 10.3389/fphys.2021.762175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/01/2021] [Indexed: 12/21/2022] Open
Abstract
The large conductance Ca2+-activated potassium (BK) channel is activated by both membrane potential depolarization and intracellular Ca2+ with distinct mechanisms. Neural physiology is sensitive to the function of BK channels, which is shown by the discoveries of neurological disorders that are associated with BK channel mutations. This article reviews the molecular mechanisms of BK channel activation in response to voltage and Ca2+ binding, including the recent progress since the publication of the atomistic structure of the whole BK channel protein, and the neurological disorders associated with BK channel mutations. These results demonstrate the unique mechanisms of BK channel activation and that these mechanisms are important factors in linking BK channel mutations to neurological disorders.
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Affiliation(s)
- Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO, United States
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34
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Unappreciated Roles for K+ Channels in Bacterial Physiology. Trends Microbiol 2021; 29:942-950. [DOI: 10.1016/j.tim.2020.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 01/03/2023]
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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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Function-Related Dynamics in Multi-Spanning Helical Membrane Proteins Revealed by Solution NMR. MEMBRANES 2021; 11:membranes11080604. [PMID: 34436367 PMCID: PMC8398610 DOI: 10.3390/membranes11080604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 01/02/2023]
Abstract
A primary biological function of multi-spanning membrane proteins is to transfer information and/or materials through a membrane by changing their conformations. Therefore, particular dynamics of the membrane proteins are tightly associated with their function. The semi-atomic resolution dynamics information revealed by NMR is able to discriminate function-related dynamics from random fluctuations. This review will discuss several studies in which quantitative dynamics information by solution NMR has contributed to revealing the structural basis of the function of multi-spanning membrane proteins, such as ion channels, GPCRs, and transporters.
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Mathie A, Veale EL, Golluscio A, Holden RG, Walsh Y. Pharmacological Approaches to Studying Potassium Channels. Handb Exp Pharmacol 2021; 267:83-111. [PMID: 34195873 DOI: 10.1007/164_2021_502] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this review, we consider the pharmacology of potassium channels from the perspective of these channels as therapeutic targets. Firstly, we describe the three main families of potassium channels in humans and disease states where they are implicated. Secondly, we describe the existing therapeutic agents which act on potassium channels and outline why these channels represent an under-exploited therapeutic target with potential for future drug development. Thirdly, we consider the evidence desired in order to embark on a drug discovery programme targeting a particular potassium channel. We have chosen two "case studies": activators of the two-pore domain potassium (K2P) channel TREK-2 (K2P10.1), for the treatment of pain and inhibitors of the voltage-gated potassium channel KV1.3, for use in autoimmune diseases such as multiple sclerosis. We describe the evidence base to suggest why these are viable therapeutic targets. Finally, we detail the main technical approaches available to characterise the pharmacology of potassium channels and identify novel regulatory compounds. We draw particular attention to the Comprehensive in vitro Proarrhythmia Assay initiative (CiPA, https://cipaproject.org ) project for cardiac safety, as an example of what might be both desirable and possible in the future, for ion channel regulator discovery projects.
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Affiliation(s)
- Alistair Mathie
- Medway School of Pharmacy, University of Kent, Kent, UK. .,Medway School of Pharmacy, University of Greenwich, London, UK. .,School of Engineering, Arts, Science and Technology, University of Suffolk, Ipswich, UK.
| | - Emma L Veale
- Medway School of Pharmacy, University of Kent, Kent, UK.,Medway School of Pharmacy, University of Greenwich, London, UK
| | - Alessia Golluscio
- Medway School of Pharmacy, University of Kent, Kent, UK.,Medway School of Pharmacy, University of Greenwich, London, UK
| | - Robyn G Holden
- Medway School of Pharmacy, University of Kent, Kent, UK.,Medway School of Pharmacy, University of Greenwich, London, UK
| | - Yvonne Walsh
- Medway School of Pharmacy, University of Kent, Kent, UK.,Medway School of Pharmacy, University of Greenwich, London, UK
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Bazard P, Frisina RD, Acosta AA, Dasgupta S, Bauer MA, Zhu X, Ding B. Roles of Key Ion Channels and Transport Proteins in Age-Related Hearing Loss. Int J Mol Sci 2021; 22:6158. [PMID: 34200434 PMCID: PMC8201059 DOI: 10.3390/ijms22116158] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 12/25/2022] Open
Abstract
The auditory system is a fascinating sensory organ that overall, converts sound signals to electrical signals of the nervous system. Initially, sound energy is converted to mechanical energy via amplification processes in the middle ear, followed by transduction of mechanical movements of the oval window into electrochemical signals in the cochlear hair cells, and finally, neural signals travel to the central auditory system, via the auditory division of the 8th cranial nerve. The majority of people above 60 years have some form of age-related hearing loss, also known as presbycusis. However, the biological mechanisms of presbycusis are complex and not yet fully delineated. In the present article, we highlight ion channels and transport proteins, which are integral for the proper functioning of the auditory system, facilitating the diffusion of various ions across auditory structures for signal transduction and processing. Like most other physiological systems, hearing abilities decline with age, hence, it is imperative to fully understand inner ear aging changes, so ion channel functions should be further investigated in the aging cochlea. In this review article, we discuss key various ion channels in the auditory system and how their functions change with age. Understanding the roles of ion channels in auditory processing could enhance the development of potential biotherapies for age-related hearing loss.
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Affiliation(s)
- Parveen Bazard
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
| | - Robert D. Frisina
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
- Department Communication Sciences and Disorders, College of Behavioral & Communication Sciences, Tampa, FL 33620, USA
| | - Alejandro A. Acosta
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
| | - Sneha Dasgupta
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
| | - Mark A. Bauer
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
| | - Xiaoxia Zhu
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
| | - Bo Ding
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
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39
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Stautz J, Hellmich Y, Fuss MF, Silberberg JM, Devlin JR, Stockbridge RB, Hänelt I. Molecular Mechanisms for Bacterial Potassium Homeostasis. J Mol Biol 2021; 433:166968. [PMID: 33798529 DOI: 10.1016/j.jmb.2021.166968] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Potassium ion homeostasis is essential for bacterial survival, playing roles in osmoregulation, pH homeostasis, regulation of protein synthesis, enzyme activation, membrane potential adjustment and electrical signaling. To accomplish such diverse physiological tasks, it is not surprising that a single bacterium typically encodes several potassium uptake and release systems. To understand the role each individual protein fulfills and how these proteins work in concert, it is important to identify the molecular details of their function. One needs to understand whether the systems transport ions actively or passively, and what mechanisms or ligands lead to the activation or inactivation of individual systems. Combining mechanistic information with knowledge about the physiology under different stress situations, such as osmostress, pH stress or nutrient limitation, one can identify the task of each system and deduce how they are coordinated with each other. By reviewing the general principles of bacterial membrane physiology and describing the molecular architecture and function of several bacterial K+-transporting systems, we aim to provide a framework for microbiologists studying bacterial potassium homeostasis and the many K+-translocating systems that are still poorly understood.
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Affiliation(s)
- Janina Stautz
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yvonne Hellmich
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michael F Fuss
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jakob M Silberberg
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jason R Devlin
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States.
| | - Inga Hänelt
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
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40
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Schmidpeter PAM, Nimigean CM. Correlating ion channel structure and function. Methods Enzymol 2021; 652:3-30. [PMID: 34059287 DOI: 10.1016/bs.mie.2021.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Recent developments in cryogenic electron microscopy (cryo-EM) led to an exponential increase in high-resolution structures of membrane proteins, and in particular ion channels. However, structures alone can only provide limited information about the workings of these proteins. In order to understand ion channel function and regulation in molecular detail, the obtained structural data need to be correlated to functional states of the same protein. Here, we describe several techniques that can be employed to study ion channel structure and function in vitro and under defined, similar conditions. Lipid nanodiscs provide a native-like environment for membrane proteins and have become a valuable tool in membrane protein structural biology and biophysics. Combined with liposome-based flux assays for the kinetic analysis of ion channel activity as well as electrophysiological recordings, researchers now have access to an array of experimental techniques allowing for detailed structure-function correlations using purified components. Two examples are presented where we put emphasis on the lipid environment and time-resolved techniques together with mutations and protein engineering to interpret structural data obtained from single particle cryo-EM on cyclic nucleotide-gated or Ca2+-gated K+ channels. Furthermore, we provide short protocols for all the assays used in our work so that others can adapt these techniques to their experimental needs. Comprehensive structure-function correlations are essential in order to pharmacologically target channelopathies.
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Affiliation(s)
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States.
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41
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Xu Z, Fang N, Zhao Y. Calix[4]trap: A Bioinspired Host Equipped with Dual Selection Mechanisms. J Am Chem Soc 2021; 143:3162-3168. [PMID: 33606533 DOI: 10.1021/jacs.0c12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Regulation of recognition events evolving in time and space is vital for living organisms. During evolution, organisms have developed distinct and orthogonal mechanisms to achieve selective recognition, avoiding mutual interference. Although the merging of multiple selection mechanisms into a single artificial host may lead to a more adaptable recognition system with unparalleled selectivity, successful implementation of this strategy is rare. Inspired by the intriguing structures and recognition properties of two well-known biological ion binders-valinomycin and K+ channels-we herein report a series of hosts equipped with dual guest selection mechanisms. These hosts simultaneously possess a preorganized binding cavity and a confined ion translocation tunnel, which are crucial to the record-setting K+/Na+ selectivity and versatile capabilities to discriminate against a wide range of ion pairs, such as K+/Rb+, K+/Ba2+, and Rb+/Cs+. Mechanistic studies verify that the host's portal is capable of discriminating cations by their size, enabling varied ion uptake rates. The confined tunnel bearing consecutive binding sites promotes complete desolvation of ions during their inclusion into the buried cavity, mimicking the ion translocation within ion channels. Our results demonstrate that the capability to manipulate guest recognition both in equilibrium and out-of-equilibrium states allows the host to effectively discriminate diverse guests via distinct mechanisms. The strategy to merge orthogonal selection mechanisms paves a new avenue to creating more robust hosts that may function in complex biological environments where many recognition events occur concurrently.
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Affiliation(s)
- Zhenchuang Xu
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Nie Fang
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yanchuan Zhao
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China.,Key Laboratory of Energy Regulation Materials, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
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42
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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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43
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Abstract
Potassium channels are the most diverse and ubiquitous family of ion channels found in cells. The Ca2+ and voltage gated members form a subfamily that play a variety of roles in both excitable and non-excitable cells and are further classified on the basis of their single channel conductance to form the small conductance (SK), intermediate conductance (IK) and big conductance (BK) K+ channels.In this chapter, we will focus on the mechanisms underlying the gating of BK channels, whose function is modified in different tissues by different splice variants as well as the expanding array of regulatory accessory subunits including β, γ and LINGO subunits. We will examine how BK channels are modified by these regulatory subunits and describe how the channel gating is altered by voltage and Ca2+ whilst setting this in context with the recently published structures of the BK channel. Finally, we will discuss how BK and other calcium-activated channels are modulated by novel ion channel modulators and describe some of the challenges associated with trying to develop compounds with sufficient efficacy, potency and selectivity to be of therapeutic benefit.
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44
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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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45
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Hou X, Outhwaite IR, Pedi L, Long SB. Cryo-EM structure of the calcium release-activated calcium channel Orai in an open conformation. eLife 2020; 9:62772. [PMID: 33252040 PMCID: PMC7723414 DOI: 10.7554/elife.62772] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
The calcium release-activated calcium channel Orai regulates Ca2+ entry into non-excitable cells and is required for proper immune function. While the channel typically opens following Ca2+ release from the endoplasmic reticulum, certain pathologic mutations render the channel constitutively open. Previously, using one such mutation (H206A), we obtained low (6.7 Å) resolution X-ray structural information on Drosophila melanogaster Orai in an open conformation (Hou et al., 2018). Here we present a structure of this open conformation at 3.3 Å resolution using fiducial-assisted cryo-electron microscopy. The improved structure reveals the conformations of amino acids in the open pore, which dilates by outward movements of subunits. A ring of phenylalanine residues repositions to expose previously shielded glycine residues to the pore without significant rotational movement of the associated helices. Together with other hydrophobic amino acids, the phenylalanines act as the channel's gate. Structured M1-M2 turrets, not evident previously, form the channel's extracellular entrance.
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Affiliation(s)
- Xiaowei Hou
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Ian R Outhwaite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Leanne Pedi
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Stephen Barstow Long
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
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46
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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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47
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Isayenkov SV, Dabravolski SA, Pan T, Shabala S. Phylogenetic Diversity and Physiological Roles of Plant Monovalent Cation/H + Antiporters. FRONTIERS IN PLANT SCIENCE 2020; 11:573564. [PMID: 33123183 PMCID: PMC7573149 DOI: 10.3389/fpls.2020.573564] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/02/2020] [Indexed: 05/23/2023]
Abstract
The processes of plant nutrition, stress tolerance, plant growth, and development are strongly dependent on transport of mineral nutrients across cellular membranes. Plant membrane transporters are key components of these processes. Among various membrane transport proteins, the monovalent cation proton antiporter (CPA) superfamily mediates a broad range of physiological and developmental processes such as ion and pH homeostasis, development of reproductive organs, chloroplast operation, and plant adaptation to drought and salt stresses. CPA family includes plasma membrane-bound Na+/H+ exchanger (NhaP) and intracellular Na+/H+ exchanger NHE (NHX), K+ efflux antiporter (KEA), and cation/H+ exchanger (CHX) family proteins. In this review, we have completed the phylogenetic inventory of CPA transporters and undertaken a comprehensive evolutionary analysis of their development. Compared with previous studies, we have significantly extended the range of plant species, including green and red algae and Acrogymnospermae into phylogenetic analysis. Our data suggest that the multiplication and complexation of CPA isoforms during evolution is related to land colonisation by higher plants and associated with an increase of different tissue types and development of reproductive organs. The new data extended the number of clades for all groups of CPAs, including those for NhaP/SOS, NHE/NHX, KEA, and CHX. We also critically evaluate the latest findings on the biological role, physiological functions and regulation of CPA transporters in relation to their structure and phylogenetic position. In addition, the role of CPA members in plant tolerance to various abiotic stresses is summarized, and the future priority directions for CPA studies in plants are discussed.
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Affiliation(s)
- Stanislav V. Isayenkov
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics NAS of Ukraine, Kyiv, Ukraine
| | - Siarhei A. Dabravolski
- Department of Clinical Diagnostics, Vitebsk State Academy of Veterinary Medicine [UO VGAVM], Vitebsk, Belarus
| | - Ting Pan
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
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48
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Cazarin CA, Dalmagro AP, Gonçalves AE, Boeing T, Silva LMD, Corrêa R, Klein-Júnior LC, Pinto BC, Lorenzett TS, Sobrinho TUDC, Fátima ÂD, Lage TCDA, Fernandes SA, Souza MMD. Usnic acid enantiomers restore cognitive deficits and neurochemical alterations induced by Aβ 1-42 in mice. Behav Brain Res 2020; 397:112945. [PMID: 33022354 DOI: 10.1016/j.bbr.2020.112945] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/25/2020] [Accepted: 09/26/2020] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia with a complex pathophysiology not fully elucidated but with limited pharmacological treatment. The Usnic acid (UA) is a lichen secondary metabolite found in two enantiomeric forms: (R)-(+)-UA or (S)-(-)-UA, with antioxidant and anti-inflammatory potential. Thus, given the role of neuroinflammation and oxidative injury in the AD, this study aimed to investigate experimentally the cognitive enhancing and anti-neuroinflammatory effects of UA enantiomers. First, the interactions of UA on acetylcholinesterase (AChE) was assessed by molecular docking and its inhibitory capability on AChE was assessed in vitro. In vivo trials investigated the effects of UA enantiomers in mice exposed to Aβ1-42 peptide (400 pmol/mice) intracerebroventricularly (i.c.v.). For this, mice were treated orally during 24 days with (R)-(+)-UA or (S)-(-)-UA at 25, 50, or 100 mg/kg, vehicle, or donepezil (2 mg/kg). Animals were submitted to the novel object recognized, Morris water maze, and inhibitory-avoidance task to assess the cognitive deficits. Additionally, UA antioxidant capacity and neuroinflammatory biomarkers were measured at the cortex and hippocampus from mice. Our results indicated that UA enantiomers evoked complex-receptor interaction with AChE like galantamine in silico. Also, UA enantiomers improved the learning and memory of the animals and in parallel decreased the myeloperoxidase activity and the lipid hydroperoxides (LOOH) on the cortex and hippocampus and reduced the IL-1β levels on the hippocampus. In summary, UA restored the cognitive deficits, as well as the signs of LOOH and neuroinflammation induced by Aβ1-42 administration in mice.
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Affiliation(s)
- Camila Andre Cazarin
- Pharmaceutical Sciences Postgraduate Program, Center of Health Sciences, Universidade do Vale do Itajaí, CEP 88302-202, Itajaí, Santa Catarina, Brazil.
| | - Ana Paula Dalmagro
- Pharmaceutical Sciences Postgraduate Program, Center of Health Sciences, Universidade do Vale do Itajaí, CEP 88302-202, Itajaí, Santa Catarina, Brazil
| | - Ana Elisa Gonçalves
- Pharmaceutical Sciences Postgraduate Program, Center of Health Sciences, Universidade do Vale do Itajaí, CEP 88302-202, Itajaí, Santa Catarina, Brazil
| | - Thaise Boeing
- Pharmaceutical Sciences Postgraduate Program, Center of Health Sciences, Universidade do Vale do Itajaí, CEP 88302-202, Itajaí, Santa Catarina, Brazil
| | - Luísa Mota da Silva
- Pharmaceutical Sciences Postgraduate Program, Center of Health Sciences, Universidade do Vale do Itajaí, CEP 88302-202, Itajaí, Santa Catarina, Brazil
| | - Rogério Corrêa
- Pharmaceutical Sciences Postgraduate Program, Center of Health Sciences, Universidade do Vale do Itajaí, CEP 88302-202, Itajaí, Santa Catarina, Brazil
| | - Luiz Carlos Klein-Júnior
- Pharmaceutical Sciences Postgraduate Program, Center of Health Sciences, Universidade do Vale do Itajaí, CEP 88302-202, Itajaí, Santa Catarina, Brazil
| | - Bernardo Carlesso Pinto
- School of Health Sciences, Universidade do Vale do Itajaí, CEP 88302-202, Itajaí, Santa Catarina, Brazil
| | - Thaís Savoldi Lorenzett
- School of Health Sciences, Universidade do Vale do Itajaí, CEP 88302-202, Itajaí, Santa Catarina, Brazil
| | | | - Ângelo de Fátima
- Department of Chemistry, Universidade Federal de Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | | | - Sergio Antonio Fernandes
- Department of Chemistry, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, Minas Gerais, Brazil
| | - Márcia Maria de Souza
- Pharmaceutical Sciences Postgraduate Program, Center of Health Sciences, Universidade do Vale do Itajaí, CEP 88302-202, Itajaí, Santa Catarina, Brazil
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49
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Langan PS, Vandavasi VG, Kopec W, Sullivan B, Afonne PV, Weiss KL, de Groot BL, Coates L. The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. IUCRJ 2020; 7:835-843. [PMID: 32939275 PMCID: PMC7467165 DOI: 10.1107/s2052252520008271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Protein dynamics are essential to function. One example of this is the various gating mechanisms within ion channels, which are transmembrane proteins that act as gateways into the cell. Typical ion channels switch between an open and closed state via a conformational transition which is often triggered by an external stimulus, such as ligand binding or pH and voltage differences. The atomic resolution structure of a potassium-selective ion channel named NaK2K has allowed us to observe that a hydro-phobic residue at the bottom of the selectivity filter, Phe92, appears in dual conformations. One of the two conformations of Phe92 restricts the diameter of the exit pore around the selectivity filter, limiting ion flow through the channel, while the other conformation of Phe92 provides a larger-diameter exit pore from the selectivity filter. Thus, it can be concluded that Phe92 acts as a hydro-phobic gate, regulating the flow of ions through the selectivity filter.
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Affiliation(s)
- Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- Lentigen Technologies, 910 Clopper Road, Gaithersburg, MD 20878, USA
| | - Venu Gopal Vandavasi
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - Wojciech Kopec
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Pavel V. Afonne
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Bert L. de Groot
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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50
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Gessner G, Rühl P, Westerhausen M, Hoshi T, Heinemann SH. Fe 2+-Mediated Activation of BK Ca Channels by Rapid Photolysis of CORM-S1 Releasing CO and Fe 2. ACS Chem Biol 2020; 15:2098-2106. [PMID: 32667185 DOI: 10.1021/acschembio.0c00282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heme catabolism by heme oxygenase (HO) with a decrease in intracellular heme concentration and a concomitant local release of CO and Fe2+ has the potential to regulate BKCa channels. Here, we show that the iron-based photolabile CO-releasing molecule CORM-S1 [dicarbonyl-bis(cysteamine)iron(II)] coreleases CO and Fe2+, making it a suitable light-triggered source of these downstream products of HO activity. To investigate the impact of CO, iron, and cysteamine on BKCa channel activation, human Slo1 (hSlo1) was expressed in HEK293T cells and studied with electrophysiological methods. Whereas hSlo1 channels are activated by CO and even more strongly by Fe2+, Fe3+ and cysteamine possess only marginal activating potency. Investigation of hSlo1 mutants revealed that Fe2+ modulates the channels mainly through the Mg2+-dependent activation mechanism. Flash photolysis of CORM-S1 suits for rapid and precise delivery of Fe2+ and CO in biological settings.
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Affiliation(s)
- Guido Gessner
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Philipp Rühl
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Matthias Westerhausen
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, D-07740 Jena, Germany
| | - Toshinori Hoshi
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania United States
| | - Stefan H. Heinemann
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, D-07745 Jena, Germany
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