1
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Reynolds CJ, Gillen CM, Burke R, Tsering Y, Loucks E, Judd-Mole S, Dow JA, Romero MF. Drosophila ClC-c Is a Homolog of Human CLC-5 and a New Model for Dent Disease Type 1. KIDNEY360 2024; 5:414-426. [PMID: 38233994 PMCID: PMC11000744 DOI: 10.34067/kid.0000000000000352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
Key Points Drosophila can be a model for Dent Disease type 1. Drosophila Clc-C mutations function similar to human CLC-5 Dent 1 mutations. Background Drosophila serve as exceptional alternative models for in vivo and ex vivo research and may provide an avenue for in-depth investigation for human ClC-5 and Dent disease type 1 (DD1). The Drosophila ClC-c (CG5284) has sequence homology with human ClC-5 and is hypothesized to encompass similar functional and phenotypical roles with ClC-5 and variants that cause DD1. Methods Ion transport function and activity of Drosophila ClC-c and homologous DD1 variants were assessed by voltage clamp electrophysiology. Membrane localization was demonstrated in Drosophila expressing a GFP-labeled construct of ClC-c. Genetic expression of an RNAi against ClC-c mRNA was used to generate a knockdown fly that serves as a DD1 disease model. Tubule secretion of cations and protein were assessed, as well as the crystal formation in the Malpighian tubules. Results Voltage clamp experiments demonstrate that ClC-c is voltage-gated with Cl−-dependent and pH-sensitive currents. Inclusion of homologous DD1 mutations pathogenic variants (S393L, R494W, and Q777X) impairs ClC-c ion transport activity. In vivo expression of ClC-c-eGFP in Malpighian tubules reveals that the membrane transporter localizes to the apical membrane and nearby cytosolic regions. RNAi knockdown of ClC-c (48% decreased mRNA expression) causes increased secretion of both urinary protein and Ca2+ and increased occurrence of spontaneous tubule crystals. Conclusions Drosophila ClC-c shows orthologous function and localization to human ClC-5. Thus, Drosophila and ClC-c regulation may be useful for future investigations of Cl− transport, Ca2+ homeostasis, and urinary protein loss in DD1.
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Affiliation(s)
- Carmen J. Reynolds
- Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, Minnesota
| | | | - Richard Burke
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Yula Tsering
- Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, Minnesota
- University of Minnesota-Rochester, Rochester, Minnesota
| | - Emi Loucks
- Department of Biology, Kenyon College, Gambier, Ohio
| | - Sebastian Judd-Mole
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Julian A.T. Dow
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Michael F. Romero
- Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, Minnesota
- Nephrology and Hypertension, Mayo Clinic College of Medicine & Science, Rochester, Minnesota
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2
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Asgharpour S, Chi LA, Spehr M, Carloni P, Alfonso-Prieto M. Fluoride Transport and Inhibition Across CLC Transporters. Handb Exp Pharmacol 2024; 283:81-100. [PMID: 36042142 DOI: 10.1007/164_2022_593] [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] [Indexed: 12/29/2022]
Abstract
The Chloride Channel (CLC) family includes proton-coupled chloride and fluoride transporters. Despite their similar protein architecture, the former exchange two chloride ions for each proton and are inhibited by fluoride, whereas the latter efficiently transport one fluoride in exchange for one proton. The combination of structural, mutagenesis, and functional experiments with molecular simulations has pinpointed several amino acid changes in the permeation pathway that capitalize on the different chemical properties of chloride and fluoride to fine-tune protein function. Here we summarize recent findings on fluoride inhibition and transport in the two prototypical members of the CLC family, the chloride/proton transporter from Escherichia coli (CLC-ec1) and the fluoride/proton transporter from Enterococcus casseliflavus (CLCF-eca).
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Affiliation(s)
- Somayeh Asgharpour
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - L América Chi
- Laboratory for the Design and Development of New Drugs and Biotechnological Innovation, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México, Mexico
| | - Marc Spehr
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - Paolo Carloni
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany.
- Department of Physics, RWTH Aachen University, Aachen, Germany.
- JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich, Jülich, Germany.
- JARA-HPC, Forschungszentrum Jülich, Jülich, Germany.
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.
- Medical Faculty, Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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3
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Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl -/H + Antiporter. Molecules 2021; 26:molecules26226956. [PMID: 34834047 PMCID: PMC8625536 DOI: 10.3390/molecules26226956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/09/2021] [Accepted: 11/16/2021] [Indexed: 11/17/2022] Open
Abstract
Intracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl− anion and a proton (H+), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at neutral pH. However, a structure of the WT protein at acidic pH is not available, making it difficult to assess the global conformational rearrangements that support a pH-dependent gating mechanism. To enable modeling of the CLC-ec1 dimer at acidic pH, we have applied molecular dynamics simulations (MD) featuring a new force field modification scheme—termed an Equilibrium constant pH approach (ECpH). The ECpH method utilizes linear interpolation between the force field parameters of protonated and deprotonated states of titratable residues to achieve a representation of pH-dependence in a narrow range of physiological pH values. Simulations of the CLC-ec1 dimer at neutral and acidic pH comparing ECpH-MD to canonical MD, in which the pH-dependent protonation is represented by a binary scheme, substantiates the better agreement of the conformational changes and the final model with experimental data from NMR, cross-link and AFM studies, and reveals structural elements that support the gate-opening at pH 4.5, including the key glutamates Gluin and Gluex.
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4
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Affiliation(s)
- Chris Miller
- Department of Biochemistry, Brandeis University, Waltham, MA
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5
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Chiariello MG, Alfonso-Prieto M, Ippoliti E, Fahlke C, Carloni P. Mechanisms Underlying Proton Release in CLC-type F -/H + Antiporters. J Phys Chem Lett 2021; 12:4415-4420. [PMID: 33950673 DOI: 10.1021/acs.jpclett.1c00361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The CLC family of anion channels and transporters includes Cl-/H+ exchangers (blocked by F-) and F-/H+ exchangers (or CLCFs). CLCFs contain a glutamate (E318) in the central anion-binding site that is absent in CLC Cl-/H+ exchangers. The X-ray structure of the protein from Enterococcus casseliflavus (CLCF-eca) shows that E318 tightly binds to F- when the gating glutamate (E118; highly conserved in the CLC family) faces the extracellular medium. Here, we use classical and DFT-based QM/MM metadynamics simulations to investigate proton transfer and release by CLCF-eca. After up to down movement of protonated E118, both glutamates combine with F- to form a triad, from which protons and F- anions are released as HF. Our results illustrate how glutamate insertion into the central anion-binding site of CLCF-eca permits the release of H+ to the cytosol as HF, thus enabling a net 1:1 F-/H+ stoichiometry.
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Affiliation(s)
- Maria Gabriella Chiariello
- Institute for Advanced Simulation (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, Forschungszentrum Jülich, 52425 Jülich, Germany
- JARA-HPC, Forschungszentrum Jülich, 54245 Jülich, Germany
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulation (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany
- Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Emiliano Ippoliti
- Institute for Advanced Simulation (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany
- JARA-HPC, Forschungszentrum Jülich, 54245 Jülich, Germany
| | - Christoph Fahlke
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Paolo Carloni
- Institute for Advanced Simulation (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany
- JARA-HPC, Forschungszentrum Jülich, 54245 Jülich, Germany
- Department of Physics, RWTH Aachen University, 52056 Aachen, Germany
- JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich, 52425 Jülich, Germany
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6
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Leisle L, Xu Y, Fortea E, Lee S, Galpin JD, Vien M, Ahern CA, Accardi A, Bernèche S. Divergent Cl - and H + pathways underlie transport coupling and gating in CLC exchangers and channels. eLife 2020; 9:e51224. [PMID: 32343228 PMCID: PMC7274781 DOI: 10.7554/elife.51224] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
The CLC family comprises H+-coupled exchangers and Cl- channels, and mutations causing their dysfunction lead to genetic disorders. The CLC exchangers, unlike canonical 'ping-pong' antiporters, simultaneously bind and translocate substrates through partially congruent pathways. How ions of opposite charge bypass each other while moving through a shared pathway remains unknown. Here, we use MD simulations, biochemical and electrophysiological measurements to identify two conserved phenylalanine residues that form an aromatic pathway whose dynamic rearrangements enable H+ movement outside the Cl- pore. These residues are important for H+ transport and voltage-dependent gating in the CLC exchangers. The aromatic pathway residues are evolutionarily conserved in CLC channels where their electrostatic properties and conformational flexibility determine gating. We propose that Cl- and H+ move through physically distinct and evolutionarily conserved routes through the CLC channels and transporters and suggest a unifying mechanism that describes the gating mechanism of both CLC subtypes.
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Affiliation(s)
- Lilia Leisle
- Department of Anesthesiology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Yanyan Xu
- SIB Swiss Institute of Bioinformatics, University of BaselBaselSwitzerland
- Biozentrum, University of BaselBaselSwitzerland
| | - Eva Fortea
- Department of Physiology and Biophysics, Weill Cornell Medical CollegeNew YorkUnited States
| | - Sangyun Lee
- Department of Anesthesiology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of MedicineIowa CityUnited States
| | - Malvin Vien
- Department of Anesthesiology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of MedicineIowa CityUnited States
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical CollegeNew YorkUnited States
- Department of Physiology and Biophysics, Weill Cornell Medical CollegeNew YorkUnited States
- Department of Biochemistry, Weill Cornell Medical CollegeNew YorkUnited States
| | - Simon Bernèche
- SIB Swiss Institute of Bioinformatics, University of BaselBaselSwitzerland
- Biozentrum, University of BaselBaselSwitzerland
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7
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McKiernan KA, Koster AK, Maduke M, Pande VS. Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating. PLoS Comput Biol 2020; 16:e1007530. [PMID: 32226009 PMCID: PMC7145265 DOI: 10.1371/journal.pcbi.1007530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 04/09/2020] [Accepted: 11/05/2019] [Indexed: 12/18/2022] Open
Abstract
This work reports a dynamical Markov state model of CLC-2 "fast" (pore) gating, based on 600 microseconds of molecular dynamics (MD) simulation. In the starting conformation of our CLC-2 model, both outer and inner channel gates are closed. The first conformational change in our dataset involves rotation of the inner-gate backbone along residues S168-G169-I170. This change is strikingly similar to that observed in the cryo-EM structure of the bovine CLC-K channel, though the volume of the intracellular (inner) region of the ion conduction pathway is further expanded in our model. From this state (inner gate open and outer gate closed), two additional states are observed, each involving a unique rotameric flip of the outer-gate residue GLUex. Both additional states involve conformational changes that orient GLUex away from the extracellular (outer) region of the ion conduction pathway. In the first additional state, the rotameric flip of GLUex results in an open, or near-open, channel pore. The equilibrium population of this state is low (∼1%), consistent with the low open probability of CLC-2 observed experimentally in the absence of a membrane potential stimulus (0 mV). In the second additional state, GLUex rotates to occlude the channel pore. This state, which has a low equilibrium population (∼1%), is only accessible when GLUex is protonated. Together, these pathways model the opening of both an inner and outer gate within the CLC-2 selectivity filter, as a function of GLUex protonation. Collectively, our findings are consistent with published experimental analyses of CLC-2 gating and provide a high-resolution structural model to guide future investigations.
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Affiliation(s)
- Keri A. McKiernan
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Anna K. Koster
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- Department of Molecular & Cellular Physiology, Stanford University, Stanford, California, United States of America
| | - Merritt Maduke
- Department of Molecular & Cellular Physiology, Stanford University, Stanford, California, United States of America
| | - Vijay S. Pande
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
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8
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Mutation of external glutamate residue reveals a new intermediate transport state and anion binding site in a CLC Cl -/H + antiporter. Proc Natl Acad Sci U S A 2019; 116:17345-17354. [PMID: 31409705 DOI: 10.1073/pnas.1901822116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The CLC family of proteins are involved in a variety of physiological processes to control cellular chloride concentration. Two distinct classes of CLC proteins, Cl- channels and Cl-/H+ antiporters, have been functionally and structurally investigated over the last several decades. Previous studies have suggested that the conformational heterogeneity of the critical glutamate residue, Gluex, could explain the transport cycle of CLC-type Cl-/H+ antiporters. However, the presence of multiple conformations (Up, Middle, and Down) of the Gluex has been suggested from combined structural snapshots of 2 different CLC antiporters: CLC-ec1 from Escherichia coli and cmCLC from a thermophilic red alga, Cyanidioschyzon merolae Thus, we aimed to investigate further the heterogeneity of Gluex-conformations in CLC-ec1, the most deeply studied CLC antiporter, at both functional and structural levels. Here, we show that the crystal structures of the Gluex mutant E148D and wild-type CLC-ec1 with varying anion concentrations suggest a structural intermediate, the "Midlow" conformation. We also found that an extra anion can be located above the external Cl--binding site in the E148D mutant when the anion concentration is high. Moreover, we observed that a carboxylate in solution can occupy either the external or central Cl--binding site in the ungated E148A mutant using an anomalously detectable short carboxylic acid, bromoacetate. These results lend credibility to the idea that the Gluex can take at least 3 distinct conformational states during the transport cycle of a single CLC antiporter.
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9
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Duster AW, Garza CM, Aydintug BO, Negussie MB, Lin H. Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel. J Chem Theory Comput 2019; 15:892-905. [DOI: 10.1021/acs.jctc.8b01128] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adam W. Duster
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Christina M. Garza
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Baris O. Aydintug
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Mikias B. Negussie
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Hai Lin
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
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10
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Last NB, Stockbridge RB, Wilson AE, Shane T, Kolmakova-Partensky L, Koide A, Koide S, Miller C. A CLC-type F -/H + antiporter in ion-swapped conformations. Nat Struct Mol Biol 2018; 25:601-606. [PMID: 29941917 PMCID: PMC6044475 DOI: 10.1038/s41594-018-0082-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/31/2018] [Indexed: 11/09/2022]
Abstract
Fluoride/proton antiporters of the CLCF family combat F- toxicity in bacteria by exporting this halide from the cytoplasm. These transporters belong to the widespread CLC superfamily but display transport properties different from those of the well-studied Cl-/H+ antiporters. Here, we report a structural and functional investigation of these F--transport proteins. Crystal structures of a CLCF homolog from Enterococcus casseliflavus are captured in two conformations with simultaneous accessibility of F- and H+ ions via separate pathways on opposite sides of the membrane. Manipulation of a key glutamate residue critical for H+ and F- transport reverses the anion selectivity of transport; replacement of the glutamate with glutamine or alanine completely inhibits F- and H+ transport while allowing for rapid uncoupled flux of Cl-. The structural and functional results lead to a 'windmill' model of CLC antiport wherein F- and H+ simultaneously move through separate ion-specific pathways that switch sidedness during the transport cycle.
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Affiliation(s)
- Nicholas B Last
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | - Randy B Stockbridge
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | - Ashley E Wilson
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | - Tania Shane
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | | | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Health, New York University School of Medicine, New York, NY, USA
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Christopher Miller
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA.
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11
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Jentsch TJ, Pusch M. CLC Chloride Channels and Transporters: Structure, Function, Physiology, and Disease. Physiol Rev 2018; 98:1493-1590. [DOI: 10.1152/physrev.00047.2017] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
CLC anion transporters are found in all phyla and form a gene family of eight members in mammals. Two CLC proteins, each of which completely contains an ion translocation parthway, assemble to homo- or heteromeric dimers that sometimes require accessory β-subunits for function. CLC proteins come in two flavors: anion channels and anion/proton exchangers. Structures of these two CLC protein classes are surprisingly similar. Extensive structure-function analysis identified residues involved in ion permeation, anion-proton coupling and gating and led to attractive biophysical models. In mammals, ClC-1, -2, -Ka/-Kb are plasma membrane Cl−channels, whereas ClC-3 through ClC-7 are 2Cl−/H+-exchangers in endolysosomal membranes. Biological roles of CLCs were mostly studied in mammals, but also in plants and model organisms like yeast and Caenorhabditis elegans. CLC Cl−channels have roles in the control of electrical excitability, extra- and intracellular ion homeostasis, and transepithelial transport, whereas anion/proton exchangers influence vesicular ion composition and impinge on endocytosis and lysosomal function. The surprisingly diverse roles of CLCs are highlighted by human and mouse disorders elicited by mutations in their genes. These pathologies include neurodegeneration, leukodystrophy, mental retardation, deafness, blindness, myotonia, hyperaldosteronism, renal salt loss, proteinuria, kidney stones, male infertility, and osteopetrosis. In this review, emphasis is laid on biophysical structure-function analysis and on the cell biological and organismal roles of mammalian CLCs and their role in disease.
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Affiliation(s)
- Thomas J. Jentsch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) and Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany; and Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Genova, Italy
| | - Michael Pusch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) and Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany; and Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Genova, Italy
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12
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Wang CH, Duster AW, Aydintug BO, Zarecki MG, Lin H. Chloride Ion Transport by the E. coli CLC Cl -/H + Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study. Front Chem 2018; 6:62. [PMID: 29594103 PMCID: PMC5859129 DOI: 10.3389/fchem.2018.00062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 02/26/2018] [Indexed: 01/05/2023] Open
Abstract
We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl- ion migration through the transmembrane domain of a prototypical E. coli CLC Cl-/H+ antiporter by employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found to be critical for full access of the channel entrance by Cl-. Moving the anion into the external binding site (Sext) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl- traveled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl- exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl- along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing π bonds (e.g., the Tyr445 side chain), while the charges of the H atoms coordinating Cl- changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers (~10 kcal/mol) than the MM PMF (~2 kcal/mol). Binding energy calculations indicated that the interactions between Cl- and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing π bonds, missing the stabilizations of the Cl- ion due to electron delocalization. The results suggested that it is important to explore these quantum effects for accurate descriptions of the Cl- transport.
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Affiliation(s)
- Chun-Hung Wang
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Adam W Duster
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Baris O Aydintug
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - MacKenzie G Zarecki
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Hai Lin
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
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13
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Mayes HB, Lee S, White AD, Voth GA, Swanson JMJ. Multiscale Kinetic Modeling Reveals an Ensemble of Cl -/H + Exchange Pathways in ClC-ec1 Antiporter. J Am Chem Soc 2018; 140:1793-1804. [PMID: 29332400 PMCID: PMC5812667 DOI: 10.1021/jacs.7b11463] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Despite several years of research, the ion exchange mechanisms in chloride/proton antiporters and many other coupled transporters are not yet understood at the molecular level. Here, we present a novel approach to kinetic modeling and apply it to ion exchange in ClC-ec1. Our multiscale kinetic model is developed by (1) calculating the state-to-state rate coefficients with reactive and polarizable molecular dynamics simulations, (2) optimizing these rates in a global kinetic network, and (3) predicting new electrophysiological results. The model shows that the robust Cl:H exchange ratio (2.2:1) can indeed arise from kinetic coupling without large protein conformational changes, indicating a possible facile evolutionary connection to chloride channels. The E148 amino acid residue is shown to couple chloride and proton transport through protonation-dependent blockage of the central anion binding site and an anion-dependent pKa value, which influences proton transport. The results demonstrate how an ensemble of different exchange pathways, as opposed to a single series of transitions, culminates in the macroscopic observables of the antiporter, such as transport rates, chloride/proton stoichiometry, and pH dependence.
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Affiliation(s)
- Heather B Mayes
- Department of Chemistry, The University of Chicago , Chicago, Illinois 60637, United States.,Department of Chemical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Sangyun Lee
- Department of Chemistry, The University of Chicago , Chicago, Illinois 60637, United States.,Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | - Andrew D White
- Department of Chemistry, The University of Chicago , Chicago, Illinois 60637, United States.,Department of Chemical Engineering, University of Rochester , Rochester, New York 14627-0166, United States
| | - Gregory A Voth
- Department of Chemistry, The University of Chicago , Chicago, Illinois 60637, United States.,James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Jessica M J Swanson
- Department of Chemistry, The University of Chicago , Chicago, Illinois 60637, United States
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Two Cl Ions and a Glu Compete for a Helix Cage in the CLC Proton/Cl - Antiporter. Biophys J 2017; 113:1025-1036. [PMID: 28877486 DOI: 10.1016/j.bpj.2017.07.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/30/2017] [Accepted: 07/11/2017] [Indexed: 11/21/2022] Open
Abstract
The ubiquitously expressed CLC chloride transporters are involved in a great variety of physiological functions. The CLC protein fold is shared by Cl- channels and 2Cl-:1H+ antiporters. The antiporters pump three charges per cycle across the membrane with two Cl ions moving in the opposite direction of one proton. Multiconformational continuum electrostatics was used to calculate the coupled thermodynamics of the protonation of the extracellular-facing gating Glu (Ex) and Cl- binding to the external (Sx) and central (Sc) sites in CLC-ec1, the Escherichia coli exchanger. Sx, Sc, and Ex are buried within the protein where the intersection of two helix N-termini creates a region with a strong, localized positive potential for anion binding. Our chemical potential titrations describe the thermodynamic linkage for binding the Cl- to each site and protons to Ex. We find that the 2Cl-:1H+ binding stoichiometry is a result of Cl- binding to Sx requiring H+ binding to Ex, whereas Cl- binding to Sc does not lead to proton uptake. When Sx binds a Cl-, the protonated Ex moves upward, out of the positive helix cage. The increasing Ex proton affinity on binding the first Cl- reduces the cost of binding the second Cl- at either Sx or Sc. Despite the repulsion among the anions, the lowest energy states have two anions bound in the helix cage. The state with no Cl- is not favored electrostatically, but relies on Ex blocking Sx and on the central residues Y445 and S107 blocking Sc.
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