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Xu M, Neelands T, Powers AS, Liu Y, Miller SD, Pintilie GD, Bois JD, Dror RO, Chiu W, Maduke M. CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism. eLife 2024; 12:RP90648. [PMID: 38345841 PMCID: PMC10942593 DOI: 10.7554/elife.90648] [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] [Indexed: 02/15/2024] Open
Abstract
CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different tissues. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating among closely related homologs has been a long-standing mystery, in part because few CLC channel structures are available. Here, we report cryoEM structures of human CLC-2 at 2.46 - 2.76 Å, in the presence and absence of the selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl--permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct conformations involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl--permeation pathway. This peptide is highly conserved among species variants of CLC-2 but is not present in other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a "ball-and-chain" gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl--permeation pathway.
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Affiliation(s)
- Mengyuan Xu
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Torben Neelands
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Alexander S Powers
- Department of Chemistry, Stanford UniversityStanfordUnited States
- Department of Computer Science, Stanford UniversityStanfordUnited States
- Department of Structural Biology, Stanford UniversityStanfordUnited States
- Institute for Computational and Mathematical Engineering, Stanford UniversityStanfordUnited States
| | - Yan Liu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford UniversityStanfordUnited States
| | - Steven D Miller
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Grigore D Pintilie
- Department of Bioengineering and Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - J Du Bois
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Ron O Dror
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
- Department of Computer Science, Stanford UniversityStanfordUnited States
- Department of Structural Biology, Stanford UniversityStanfordUnited States
- Institute for Computational and Mathematical Engineering, Stanford UniversityStanfordUnited States
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford UniversityStanfordUnited States
- Department of Bioengineering and Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
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Xu M, Neelands T, Powers AS, Liu Y, Miller SD, Pintilie G, Bois JD, Dror RO, Chiu W, Maduke M. CryoEM structures of the human CLC-2 voltage gated chloride channel reveal a ball and chain gating mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.13.553136. [PMID: 37645939 PMCID: PMC10462068 DOI: 10.1101/2023.08.13.553136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different mammalian tissues and cell types. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating mechanisms among closely related CLC homologs has been a long-standing mystery, in part because few CLC channel structures are available, and those that exist exhibit high conformational similarity. Here, we report cryoEM structures of human CLC-2 at 2.46 - 2.76 Å, in the presence and absence of the potent and selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl--permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct apo conformations of CLC-2 involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl--permeation pathway from the intracellular side. This peptide is highly conserved among species variants of CLC-2 but is not present in any other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a "ball-and-chain" gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we show that loss of this short sequence increases the magnitude and decreases the rectification of CLC-2 currents expressed in mammalian cells. Furthermore, we show that with repetitive hyperpolarization WT CLC-2 currents increase in resemblance to the hairpin-deleted CLC-2 currents. These functional results combined with our structural data support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl--permeation pathway.
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Affiliation(s)
- Mengyuan Xu
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
| | - Torben Neelands
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
| | - Alexander S. Powers
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Department of Computer Science, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305
| | - Yan Liu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park 94025
| | - Steven D. Miller
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Grigore Pintilie
- Department of Bioengineering and Department of Microbiology and Immunology, Stanford University, Stanford, 94305
| | - J. Du Bois
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Ron O. Dror
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Computer Science, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park 94025
- Department of Bioengineering and Department of Microbiology and Immunology, Stanford University, Stanford, 94305
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
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Zhang B, Zhang S, Polovitskaya MM, Yi J, Ye B, Li R, Huang X, Yin J, Neuens S, Balfroid T, Soblet J, Vens D, Aeby A, Li X, Cai J, Song Y, Li Y, Tartaglia M, Li Y, Jentsch TJ, Yang M, Liu Z. Molecular basis of ClC-6 function and its impairment in human disease. SCIENCE ADVANCES 2023; 9:eadg4479. [PMID: 37831762 PMCID: PMC10575590 DOI: 10.1126/sciadv.adg4479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 09/08/2023] [Indexed: 10/15/2023]
Abstract
ClC-6 is a late endosomal voltage-gated chloride-proton exchanger that is predominantly expressed in the nervous system. Mutated forms of ClC-6 are associated with severe neurological disease. However, the mechanistic role of ClC-6 in normal and pathological states remains largely unknown. Here, we present cryo-EM structures of ClC-6 that guided subsequent functional studies. Previously unrecognized ATP binding to cytosolic ClC-6 domains enhanced ion transport activity. Guided by a disease-causing mutation (p.Y553C), we identified an interaction network formed by Y553/F317/T520 as potential hotspot for disease-causing mutations. This was validated by the identification of a patient with a de novo pathogenic variant p.T520A. Extending these findings, we found contacts between intramembrane helices and connecting loops that modulate the voltage dependence of ClC-6 gating and constitute additional candidate regions for disease-associated gain-of-function mutations. Besides providing insights into the structure, function, and regulation of ClC-6, our work correctly predicts hotspots for CLCN6 mutations in neurodegenerative disorders.
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Affiliation(s)
- Bing Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Sensen Zhang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Maya M. Polovitskaya
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
| | - Jingbo Yi
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Binglu Ye
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Ruochong Li
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Xueying Huang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Jian Yin
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Sebastian Neuens
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Tom Balfroid
- Department of Pediatric Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Julie Soblet
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Department of Genetics, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Daphné Vens
- Pediatric Intensive Care Unit, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Alec Aeby
- Department of Pediatric Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Xiaoling Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, 110016 Shenyang, China
| | - Jinjin Cai
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Yingcai Song
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Yuanxi Li
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, 200237 Shanghai, China
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Yang Li
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Thomas J. Jentsch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
- Cryo-EM Facility Center, Southern University of Science & Technology, 518055 Shenzhen, Guangdong, China
| | - Zhiqiang Liu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
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Yue Z, Li C, Voth GA. The role of conformational change and key glutamic acid residues in the ClC-ec1 antiporter. Biophys J 2023; 122:1068-1085. [PMID: 36698313 PMCID: PMC10111279 DOI: 10.1016/j.bpj.2023.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
The triple glutamine (Q) mutant (QQQ) structure of a Cl-/H+ antiporter from Escherichia coli (ClC-ec1) displaying a novel backbone arrangement has been used to challenge the long-held notion that Cl-/H+ antiporters do not operate through large conformational motions. The QQQ mutant substitutes the glutamine residue for an external glutamate E148, an internal glutamate E203, and a third glutamate E113 that hydrogen-bonds with E203. However, it is unknown if QQQ represents a physiologically relevant state, as well as how the protonation of the wild-type glutamates relates to the global dynamics. We herein apply continuous constant-pH molecular dynamics to investigate the H+-coupled dynamics of ClC-ec1. Although any large-scale conformational rearrangement upon acidification would be due to the accumulation of excess charge within the protein, protonation of the glutamates significantly impacts mainly the local structure and dynamics. Despite the fact that the extracellular pore enlarges at acidic pHs, an occluded ClC-ec1 within the active pH range of 3.5-7.5 requires a protonated E148 to facilitate extracellular Cl- release. E203 is also involved in the intracellular H+ transfer as an H+ acceptor. The water wire connection of E148 with the intracellular solution is regulated by the charge states of the E113/E203 dyad with coupled proton titration. However, the dynamics extracted from our simulations are not QQQ-like, indicating that the QQQ mutant does not represent the behavior of the wild-type ClC-ec1. These findings reinforce the necessity of having a protonatable residue at the E203 position in ClC-ec1 and suggest that a higher level of complexity exists for the intracellular H+ transfer in Cl-/H+ antiporters.
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Affiliation(s)
- Zhi Yue
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Chenghan Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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Abstract
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Affiliation(s)
- Kaleigh A Remick
- Department of Microbiology, Cornell University, New York, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, New York, NY, United States.
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Yue Z, Bernardi A, Li C, Mironenko AV, Swanson JMJ. Toward a Multipathway Perspective: pH-Dependent Kinetic Selection of Competing Pathways and the Role of the Internal Glutamate in Cl -/H + Antiporters. J Phys Chem B 2021; 125:7975-7984. [PMID: 34260231 PMCID: PMC8409247 DOI: 10.1021/acs.jpcb.1c03304] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Canonical descriptions of multistep biomolecular transformations generally follow a single-pathway viewpoint, with a series of transitions through intermediates converting reactants to products or repeating a conformational cycle. However, mounting evidence suggests that more complexity and pathway heterogeneity are mechanistically relevant due to the statistical distribution of multiple interconnected rate processes. Making sense of such pathway complexity remains a significant challenge. To better understand the role and relevance of pathway heterogeneity, we herein probe the chemical reaction network of a Cl-/H+ antiporter, ClC-ec1, and analyze reaction pathways using multiscale kinetic modeling (MKM). This approach allows us to describe the nature of the competing pathways and how they change as a function of pH. We reveal that although pH-dependent Cl-/H+ transport rates are largely regulated by the charge state of amino acid E148, the charge state of E203 determines relative contributions from coexisting pathways and can shift the flux pH-dependence. The selection of pathways via E203 explains how ionizable mutations (D/H/K/R) would impact the ClC-ec1 bioactivity from a kinetic perspective and lends further support to the indispensability of an internal glutamate in ClC antiporters. Our results demonstrate how quantifying the kinetic selection of competing pathways under varying conditions leads to a deeper understanding of the Cl-/H+ exchange mechanism and can suggest new approaches for mechanistic control.
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Affiliation(s)
- Zhi Yue
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Austen Bernardi
- Department of Chemistry, Biological Chemistry Program, and Center for Cell and Genome Science, The University of Utah, Salt Lake City, Utah 84112, United States
| | - Chenghan Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander V. Mironenko
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jessica M. J. Swanson
- Department of Chemistry, Biological Chemistry Program, and Center for Cell and Genome Science, The University of Utah, Salt Lake City, Utah 84112, United States
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