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Fortea E, Accardi A. A quantitative flux assay for the study of reconstituted Cl - channels and transporters. Methods Enzymol 2021; 652:243-272. [PMID: 34059284 DOI: 10.1016/bs.mie.2021.01.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The recent deluge of high-resolution structural information on membrane proteins has not been accompanied by a comparable increase in our ability to functionally interrogate these proteins. Current functional assays often are not quantitative or are performed in conditions that significantly differ from those used in structural experiments, thus limiting the mechanistic correspondence between structural and functional experiments. A flux assay to determine quantitatively the functional properties of purified and reconstituted Cl- channels and transporters in membranes of defined lipid compositions is described. An ion-sensitive electrode is used to measure the rate of Cl- efflux from proteoliposomes reconstituted with the desired protein and the fraction of vesicles containing at least one active protein. These measurements enable the quantitative determination of key molecular parameters such as the unitary transport rate, the fraction of proteins that are active, and the molecular mass of the transport protein complex. The approach is illustrated using CLC-ec1, a CLC-type H+/Cl- exchanger as an example. The assay enables the quantitative study of a wide range of Cl- transporting molecules and proteins whose activity is modulated by ligands, voltage, and membrane composition as well as the investigation of the effects of compounds that directly inhibit or activate the reconstituted transport systems. The present assay is readily adapted to the study of transport systems with diverse substrate specificities and molecular characteristics, and the necessary modifications needed are discussed.
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Affiliation(s)
- Eva Fortea
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States
| | - Alessio Accardi
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States; Department of Anesthesiology, Weill Cornell Medical College, New York, NY, United States; Department of Biochemistry, Weill Cornell Medical College, New York, NY, United States.
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2
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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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3
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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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4
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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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5
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Park E, MacKinnon R. Structure of the CLC-1 chloride channel from Homo sapiens. eLife 2018; 7:36629. [PMID: 29809153 PMCID: PMC6019066 DOI: 10.7554/elife.36629] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/15/2018] [Indexed: 11/18/2022] Open
Abstract
CLC channels mediate passive Cl− conduction, while CLC transporters mediate active Cl− transport coupled to H+ transport in the opposite direction. The distinction between CLC-0/1/2 channels and CLC transporters seems undetectable by amino acid sequence. To understand why they are different functionally we determined the structure of the human CLC-1 channel. Its ‘glutamate gate’ residue, known to mediate proton transfer in CLC transporters, adopts a location in the structure that appears to preclude it from its transport function. Furthermore, smaller side chains produce a wider pore near the intracellular surface, potentially reducing a kinetic barrier for Cl− conduction. When the corresponding residues are mutated in a transporter, it is converted to a channel. Finally, Cl− at key sites in the pore appear to interact with reduced affinity compared to transporters. Thus, subtle differences in glutamate gate conformation, internal pore diameter and Cl− affinity distinguish CLC channels and transporters. Channels and transporters are two classes of proteins that transport molecules and ions – collectively referred to as “substrates” – across cell membranes. Channels form a pore in the membrane and the substrates diffuse through passively. Transporters, on the other hand, actively pump substrates across a membrane, consuming energy in the process. Thus, channels and transporters work in distinct ways. Channels and transporters most often have unrelated structures, but there are rare examples of both existing within the same family of structurally similar proteins. CLC proteins, for example, include both chloride ion channels and transporters that pump chloride ions in one direction by harnessing the energy from hydrogen ions flowing in the other direction. It remains unclear why some CLC proteins work as channels while others are transporters, especially since the two seem indistinguishable on the basis of the order of their amino acids – the building blocks of all proteins. The conservation of the amino acid sequences implies they are structurally very similar. How then can different members perform such energetically distinct processes? Park and MacKinnon now show that the answer to this question serves as a reminder of how subtle nature can be. Indeed, while the structure of a human CLC channel (called CLC-1) is indeed similar to those of CLC transporters, one amino acid adopts a unique shape that explains why the protein cannot act as a transporter. This specific amino acid, a glutamate, is central to the exchange of chloride and hydrogen ions in CLC transporters. Park and MacKinnon show that its conformation in the CLC-1 channel stops this exchange, while leaving the pore open for the passive transport of chloride ions. Also, two other amino acids along the ion diffusion pathway in the CLC channel are smaller than their counterparts in CLC transporters, and so allow chloride ions to diffuse through more quickly. Lastly, Park and MacKinnon also note that channels do not require a wide pore: instead ions can still flow rapidly through a narrow pore if the chemical environment inside permits it. CLC proteins perform a number of important roles in humans, and mutations in CLC-encoding genes underlie numerous heritable diseases. It remains too early to know how this mechanistic study may or may not impact treatments, yet the findings will likely interest scientists working on ion conduction mechanisms and the evolution of molecular function.
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Affiliation(s)
- Eunyong Park
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Roderick MacKinnon
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
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6
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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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7
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Structure of a CLC chloride ion channel by cryo-electron microscopy. Nature 2016; 541:500-505. [PMID: 28002411 PMCID: PMC5576512 DOI: 10.1038/nature20812] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/18/2016] [Indexed: 12/18/2022]
Abstract
CLC proteins transport chloride (Cl-) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl- ions passively, whereas others are secondary active transporters that exchange two Cl- ions for one H+. The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture on the basis of sequence homology. Here we determined the structure of a bovine CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl- transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl- passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl-/H+ transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl- down its electrochemical gradient.
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8
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Carraretto L, Teardo E, Checchetto V, Finazzi G, Uozumi N, Szabo I. Ion Channels in Plant Bioenergetic Organelles, Chloroplasts and Mitochondria: From Molecular Identification to Function. MOLECULAR PLANT 2016; 9:371-395. [PMID: 26751960 DOI: 10.1016/j.molp.2015.12.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/22/2015] [Accepted: 12/01/2015] [Indexed: 06/05/2023]
Abstract
Recent technical advances in electrophysiological measurements, organelle-targeted fluorescence imaging, and organelle proteomics have pushed the research of ion transport a step forward in the case of the plant bioenergetic organelles, chloroplasts and mitochondria, leading to the molecular identification and functional characterization of several ion transport systems in recent years. Here we focus on channels that mediate relatively high-rate ion and water flux and summarize the current knowledge in this field, focusing on targeting mechanisms, proteomics, electrophysiology, and physiological function. In addition, since chloroplasts evolved from a cyanobacterial ancestor, we give an overview of the information available about cyanobacterial ion channels and discuss the evolutionary origin of chloroplast channels. The recent molecular identification of some of these ion channels allowed their physiological functions to be studied using genetically modified Arabidopsis plants and cyanobacteria. The view is emerging that alteration of chloroplast and mitochondrial ion homeostasis leads to organelle dysfunction, which in turn significantly affects the energy metabolism of the whole organism. Clear-cut identification of genes encoding for channels in these organelles, however, remains a major challenge in this rapidly developing field. Multiple strategies including bioinformatics, cell biology, electrophysiology, use of organelle-targeted ion-sensitive probes, genetics, and identification of signals eliciting specific ion fluxes across organelle membranes should provide a better understanding of the physiological role of organellar channels and their contribution to signaling pathways in plants in the future.
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Affiliation(s)
- Luca Carraretto
- Department of Biology, University of Padova, Padova 35121, Italy
| | - Enrico Teardo
- Department of Biology, University of Padova, Padova 35121, Italy; CNR Institute of Neuroscience, University of Padova, Padova 35121, Italy
| | | | - Giovanni Finazzi
- UMR 5168 Laboratoire de Physiologie Cellulaire Végétale (LPCV) CNRS/ UJF / INRA / CEA, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), CEA Grenoble, 38054 Grenoble, France.
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan.
| | - Ildiko Szabo
- Department of Biology, University of Padova, Padova 35121, Italy; CNR Institute of Neuroscience, University of Padova, Padova 35121, Italy.
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9
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Jiang T, Han W, Maduke M, Tajkhorshid E. Molecular Basis for Differential Anion Binding and Proton Coupling in the Cl(-)/H(+) Exchanger ClC-ec1. J Am Chem Soc 2016; 138:3066-75. [PMID: 26880377 DOI: 10.1021/jacs.5b12062] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cl–/H+ transporters of the CLC superfamily form a ubiquitous class of membrane proteins that catalyze stoichiometrically coupled exchange of Cl– and H+ across biological membranes. CLC transporters exchange H+ for halides and certain polyatomic anions, but exclude cations, F–, and larger physiological anions, such as PO43– and SO42–. Despite comparable transport rates of different anions, the H+ coupling in CLC transporters varies significantly depending on the chemical nature of the transported anion. Although the molecular mechanism of exchange remains unknown, studies on bacterial ClC-ec1 transporter revealed that Cl– binding to the central anion-binding site (Scen) is crucial for the anion-coupled H+ transport. Here, we show that Cl–, F–, NO3–, and SCN– display distinct binding coordinations at the Scen site and are hydrated in different manners. Consistent with the observation of differential bindings, ClC-ec1 exhibits markedly variable ability to support the formation of the transient water wires, which are necessary to support the connection of the two H+ transfer sites (Gluin and Gluex), in the presence of different anions. While continuous water wires are frequently observed in the presence of physiologically transported Cl–, binding of F– or NO3– leads to the formation of pseudo-water-wires that are substantially different from the wires formed with Cl–. Binding of SCN–, however, eliminates the water wires altogether. These findings provide structural details of anion binding in ClC-ec1 and reveal a putative atomic-level mechanism for the decoupling of H+ transport to the transport of anions other than Cl–.
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Affiliation(s)
- Tao Jiang
- Department of Biochemistry, Center for Biophysics and Computational Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
| | - Wei Han
- Department of Biochemistry, Center for Biophysics and Computational Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine , Stanford, California 94305-5207, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, Center for Biophysics and Computational Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
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10
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Khantwal CM, Abraham SJ, Han W, Jiang T, Chavan TS, Cheng RC, Elvington SM, Liu CW, Mathews II, Stein RA, Mchaourab HS, Tajkhorshid E, Maduke M. Revealing an outward-facing open conformational state in a CLC Cl(-)/H(+) exchange transporter. eLife 2016; 5. [PMID: 26799336 PMCID: PMC4769167 DOI: 10.7554/elife.11189] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/14/2016] [Indexed: 11/22/2022] Open
Abstract
CLC secondary active transporters exchange Cl- for H+. Crystal structures have suggested that the conformational change from occluded to outward-facing states is unusually simple, involving only the rotation of a conserved glutamate (Gluex) upon its protonation. Using 19F NMR, we show that as [H+] is increased to protonate Gluex and enrich the outward-facing state, a residue ~20 Å away from Gluex, near the subunit interface, moves from buried to solvent-exposed. Consistent with functional relevance of this motion, constriction via inter-subunit cross-linking reduces transport. Molecular dynamics simulations indicate that the cross-link dampens extracellular gate-opening motions. In support of this model, mutations that decrease steric contact between Helix N (part of the extracellular gate) and Helix P (at the subunit interface) remove the inhibitory effect of the cross-link. Together, these results demonstrate the formation of a previously uncharacterized 'outward-facing open' state, and highlight the relevance of global structural changes in CLC function. DOI:http://dx.doi.org/10.7554/eLife.11189.001 Cells have transporter proteins on their surface to carry molecules in and out of the cell. For example, the CLC family of transporters move two chloride ions in one direction at the same time as moving one hydrogen ion in the opposite direction. To be able to move these ions in opposite directions, transporters have to cycle through a series of shapes in which the ions can only access alternate sides of the membrane. First, the transporter adopts an 'outward-facing' shape when the ions first bind to the transporter, then it switches into the 'occluded' shape to move the ions through the membrane. Finally, the transporter takes on the 'inward-facing' shape to release the ions on the other side of the membrane. However, structural studies of CLCs suggest that the structures of these proteins do not change much while they are moving ions, which suggests that they might work in a different way. Khantwal, Abraham et al. have now used techniques called “nuclear magnetic resonance” and "double electron-electron resonance" to investigate how a CLC from a bacterium moves ions. The experiments suggest that when the transporter adopts the outward-facing shape, points on the protein known as Y419 and D417 shift their positions. Chemically linking two regions of the CLC prevented this movement and inhibited the transport of chloride ions across the membrane. Khantwal, Abraham et al. then used a computer simulation to model how the protein changes shape in more detail. This model predicts that two regions of the transporter undergo major rearrangements resulting in a gate-opening motion that widens a passage to allow the chloride ions to bind to the protein. Khantwal, Abraham et al.’s findings will prompt future studies to reveal the other shapes and how CLCs transition between them. DOI:http://dx.doi.org/10.7554/eLife.11189.002
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Affiliation(s)
- Chandra M Khantwal
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Sherwin J Abraham
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Wei Han
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, United States.,College of Medicine, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Tao Jiang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, United States.,College of Medicine, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Tanmay S Chavan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Ricky C Cheng
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Shelley M Elvington
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Corey W Liu
- Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, Stanford, United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, United States
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, United States.,College of Medicine, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
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11
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Accardi A. Structure and gating of CLC channels and exchangers. J Physiol 2015; 593:4129-38. [PMID: 26148215 DOI: 10.1113/jp270575] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 06/28/2015] [Indexed: 11/08/2022] Open
Abstract
Since their serendipitous discovery the CLC family of Cl(-) transporting proteins has been a never ending source of surprises. From their double-barrelled architecture to their complex structure and divergence as channels and transporters, the CLCs never cease to amaze biophysicists, biochemists and physiologists alike. These unusual functional properties allow the CLCs to fill diverse physiological niches, regulating processes that range from muscle contraction to acidification of intracellular organelles, nutrient accumulation and survival of bacteria to environmental stresses. Over the last 15 years, the availability of atomic-level information on the structure of the CLCs, coupled to the discovery that the family is divided into passive channels and secondary active transporters, has revolutionized our understanding of their function. These breakthroughs led to the identification of the key structural elements regulating gating, transport, selectivity and regulation by ligands. Unexpectedly, many lines of evidence indicate that the CLC exchangers function according to a non-conventional transport mechanism that defies the fundamental tenets of the alternating-access paradigm for exchange transport, paving the way for future unexpected insights into the principles underlying active transport and channel gating.
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Affiliation(s)
- Alessio Accardi
- Departments of Anaesthesiology, Physiology & Biophysics, and Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
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12
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Zifarelli G. A tale of two CLCs: biophysical insights toward understanding ClC-5 and ClC-7 function in endosomes and lysosomes. J Physiol 2015; 593:4139-50. [PMID: 26036722 DOI: 10.1113/jp270604] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 05/22/2015] [Indexed: 11/08/2022] Open
Abstract
The CLC protein family comprises both Cl(-) channels and H(+) -coupled anion transporters. The understanding of the critical role of CLC proteins in a number of physiological functions has greatly contributed to a revision of the classical paradigm that attributed to Cl(-) ions only a marginal role in human physiology. The endosomal ClC-5 and the lysosomal ClC-7 are the best characterized human CLC transporters. Their dysfunction causes Dent's disease and osteopetrosis, respectively. It had been originally proposed that they would provide a Cl(-) shunt conductance allowing efficient acidification of intracellular compartments. However, this model seems to conflict with the transport properties of these proteins and with recent physiological evidence. Currently, there is no consensus on their specific physiological role. CLC proteins present also a number of peculiar biophysical properties, such as the dimeric architecture, the co-existence of intrinsically different thermodynamic modes of transport based on similar structural principles, and the gating mechanism recently emerging for the transporters, just to name a few. This review focuses on the biophysical properties and physiological roles of ClC-5 and ClC-7.
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Affiliation(s)
- Giovanni Zifarelli
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
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13
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Jardón-Valadez E, Bondar AN, Tobias DJ. Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1837:1964-1972. [PMID: 25256652 DOI: 10.1016/j.bbabio.2014.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 10/24/2022]
Abstract
Translocation of negatively charged ions across cell membranes by ion pumps raises the question as to how protein interactions control the location and dynamics of the ion. Here we address this question by performing extensive molecular dynamics simulations of wild type and mutant halorhodopsin, a seven-helical transmembrane protein that translocates chloride ions upon light absorption. We find that inter-helical hydrogen bonds mediated by a key arginine group largely govern the dynamics of the protein and water groups coordinating the chloride ion.
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Affiliation(s)
- Eduardo Jardón-Valadez
- Departamento de Recursos de la Tierra, Universidad Autónoma Metropolitana-Lerma, Lerma de Villada, Estado de México 52005, México
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics Department of Physics, Freie University Arnimallee 14, Berlin 14195, Germany.
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
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14
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Imbrici P, Altamura C, Pessia M, Mantegazza R, Desaphy JF, Camerino DC. ClC-1 chloride channels: state-of-the-art research and future challenges. Front Cell Neurosci 2015; 9:156. [PMID: 25964741 PMCID: PMC4410605 DOI: 10.3389/fncel.2015.00156] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/08/2015] [Indexed: 01/06/2023] Open
Abstract
The voltage-dependent ClC-1 chloride channel belongs to the CLC channel/transporter family. It is a homodimer comprising two individual pores which can operate independently or simultaneously according to two gating modes, the fast and the slow gate of the channel. ClC-1 is preferentially expressed in the skeletal muscle fibers where the presence of an efficient Cl(-) homeostasis is crucial for the correct membrane repolarization and propagation of action potential. As a consequence, mutations in the CLCN1 gene cause dominant and recessive forms of myotonia congenita (MC), a rare skeletal muscle channelopathy caused by abnormal membrane excitation, and clinically characterized by muscle stiffness and various degrees of transitory weakness. Elucidation of the mechanistic link between the genetic defects and the disease pathogenesis is still incomplete and, at this time, there is no specific treatment for MC. Still controversial is the subcellular localization pattern of ClC-1 channels in skeletal muscle as well as its modulation by some intracellular factors. The expression of ClC-1 in other tissues such as in brain and heart and the possible assembly of ClC-1/ClC-2 heterodimers further expand the physiological properties of ClC-1 and its involvement in diseases. A recent de novo CLCN1 truncation mutation in a patient with generalized epilepsy indeed postulates an unexpected role of this channel in the control of neuronal network excitability. This review summarizes the most relevant and state-of-the-art research on ClC-1 chloride channels physiology and associated diseases.
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Affiliation(s)
- Paola Imbrici
- Department of Pharmacy - Drug Sciences, University of Bari “Aldo Moro”,Bari, Italy
| | - Concetta Altamura
- Department of Pharmacy - Drug Sciences, University of Bari “Aldo Moro”,Bari, Italy
| | - Mauro Pessia
- Department of Pharmacy - Drug Sciences, University of Bari “Aldo Moro”,Bari, Italy
| | - Renato Mantegazza
- Department of Pharmacy - Drug Sciences, University of Bari “Aldo Moro”,Bari, Italy
| | | | - Diana Conte Camerino
- Department of Pharmacy - Drug Sciences, University of Bari “Aldo Moro”,Bari, Italy
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15
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Basilio D, Accardi A. A Proteoliposome-Based Efflux Assay to Determine Single-molecule Properties of Cl- Channels and Transporters. J Vis Exp 2015:52369. [PMID: 25938223 PMCID: PMC4541587 DOI: 10.3791/52369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The last 15 years have been characterized by an explosion in the ability to overexpress and purify membrane proteins from prokaryotic organisms as well as from eukaryotes. This increase has been largely driven by the successful push to obtain structural information on membrane proteins. However, the ability to functionally interrogate these proteins has not advanced at the same rate and is often limited to qualitative assays of limited quantitative value, thereby limiting the mechanistic insights that they can provide. An assay to quantitatively investigate the transport activity of reconstituted Cl(-) channels or transporters is described. The assay is based on the measure of the efflux rate of Cl(-) from proteoliposomes following the addition of the K(+) ionophore valinomycin to shunt the membrane potential. An ion sensitive electrode is used to follow the time-course of ion efflux from proteoliposomes reconstituted with the desired protein. The method is highly suited for mechanistic studies, as it allows for the quantitative determination of key properties of the reconstituted protein, such as its unitary transport rate, the fraction of active protein and the molecular mass of the functional unit. The assay can also be utilized to determine the effect of small molecule compounds that directly inhibit/activate the reconstituted protein, as well as to test the modulatory effects of the membrane composition or lipid-modifying reagents. Where possible, direct comparison between results obtained using this method were found to be in good agreement with those obtained using electrophysiological approaches. The technique is illustrated using CLC-ec1, a CLC-type H(+)/Cl(-) exchanger, as a model system. The efflux assay can be utilized to study any Cl(-) conducting channel/transporter and, with minimal changes, can be adapted to study any ion-transporting protein.
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Affiliation(s)
- Daniel Basilio
- Department of Anesthesiology, Weill Cornell Medical College
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical College; Department of Physiology and Biophysics, Weill Cornell Medical College; Department of Biochemistry, Weill Cornell Medical College;
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16
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Abraham SJ, Cheng RC, Chew TA, Khantwal CM, Liu CW, Gong S, Nakamoto RK, Maduke M. 13C NMR detects conformational change in the 100-kD membrane transporter ClC-ec1. JOURNAL OF BIOMOLECULAR NMR 2015; 61:209-26. [PMID: 25631353 PMCID: PMC4398623 DOI: 10.1007/s10858-015-9898-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/13/2015] [Indexed: 05/03/2023]
Abstract
CLC transporters catalyze the exchange of Cl(-) for H(+) across cellular membranes. To do so, they must couple Cl(-) and H(+) binding and unbinding to protein conformational change. However, the sole conformational changes distinguished crystallographically are small movements of a glutamate side chain that locally gates the ion-transport pathways. Therefore, our understanding of whether and how global protein dynamics contribute to the exchange mechanism has been severely limited. To overcome the limitations of crystallography, we used solution-state (13)C-methyl NMR with labels on methionine, lysine, and engineered cysteine residues to investigate substrate (H(+)) dependent conformational change outside the restraints of crystallization. We show that methyl labels in several regions report H(+)-dependent spectral changes. We identify one of these regions as Helix R, a helix that extends from the center of the protein, where it forms the part of the inner gate to the Cl(-)-permeation pathway, to the extracellular solution. The H(+)-dependent spectral change does not occur when a label is positioned just beyond Helix R, on the unstructured C-terminus of the protein. Together, the results suggest that H(+) binding is mechanistically coupled to closing of the intracellular access-pathway for Cl(-).
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Affiliation(s)
- Sherwin J. Abraham
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94035
| | - Ricky C. Cheng
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94035
| | - Thomas A. Chew
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94035
| | - Chandra M. Khantwal
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94035
| | - Corey W. Liu
- Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, 299 Campus Drive West, D105 Fairchild Science Building, Stanford, CA 94305
| | - Shimei Gong
- Department of Molecular Physiology and Biological Physics, University of Virginia, PO Box 10011, Charlottesville, VA 22906-0011
| | - Robert K. Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, PO Box 10011, Charlottesville, VA 22906-0011
| | - Merritt Maduke
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94035
- corresponding author, , tel (650)-723-9075, fax (650)-725-8021
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17
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Miller C. In the beginning: a personal reminiscence on the origin and legacy of ClC-0, the 'Torpedo Cl(-) channel'. J Physiol 2015; 593:4085-90. [PMID: 25433078 DOI: 10.1113/jphysiol.2014.286260] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/21/2014] [Indexed: 11/08/2022] Open
Abstract
This unapologetically subjective essay recalls the Torpedo Cl(-) channel in the years when it had neither a molecular identity nor proper name (ClC-0), and membership in a large superfamily. I discuss the circumstances surrounding its discovery and subsequent research through the 1980s that revealed its unusual molecular architecture and other strange mechanistic characteristics.
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Affiliation(s)
- Christopher Miller
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
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18
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Salt acclimation of cyanobacteria and their application in biotechnology. Life (Basel) 2014; 5:25-49. [PMID: 25551682 PMCID: PMC4390839 DOI: 10.3390/life5010025] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/19/2014] [Indexed: 12/25/2022] Open
Abstract
The long evolutionary history and photo-autotrophic lifestyle of cyanobacteria has allowed them to colonize almost all photic habitats on Earth, including environments with high or fluctuating salinity. Their basal salt acclimation strategy includes two principal reactions, the active export of ions and the accumulation of compatible solutes. Cyanobacterial salt acclimation has been characterized in much detail using selected model cyanobacteria, but their salt sensing and regulatory mechanisms are less well understood. Here, we briefly review recent advances in the identification of salt acclimation processes and the essential genes/proteins involved in acclimation to high salt. This knowledge is of increasing importance because the necessary mass cultivation of cyanobacteria for future use in biotechnology will be performed in sea water. In addition, cyanobacterial salt resistance genes also can be applied to improve the salt tolerance of salt sensitive organisms, such as crop plants.
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19
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Pusch M, Zifarelli G. ClC-5: Physiological role and biophysical mechanisms. Cell Calcium 2014; 58:57-66. [PMID: 25443653 DOI: 10.1016/j.ceca.2014.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/19/2014] [Accepted: 09/20/2014] [Indexed: 01/05/2023]
Abstract
Cl(-) transport in animal cells has fundamental physiological roles and it is mediated by a variety of protein families, one of them being the CLC family of ion channels and transporters. Besides their physiological relevance, CLC proteins show peculiar biophysical properties. This review will focus on a member of the CLC protein family, the endosomal Cl(-)/H(+) antiporter ClC-5. ClC-5 mutations cause Dent's disease, a renal syndrome due to defective protein reabsorption in the proximal tubule. This established the critical function of ClC-5 for endocytosis. However, our understanding of ClC-5's molecular role in endosomes and of its biophysical properties has proved elusive in spite of important progress achieved in the last two decades. Early models in which ClC-5 would provide a shunt conductance to enable efficient endosomal acidification conflicted with the antiport activity of ClC-5 that has more recently emerged. Currently, the physiological role of ClC-5 is hotly debated and its biophysical properties are still not fully understood.
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Affiliation(s)
- Michael Pusch
- Istituto di Biofisica, CNR, Via De Marini 6, 16149 Genoa, Italy
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20
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Stölting G, Fischer M, Fahlke C. CLC channel function and dysfunction in health and disease. Front Physiol 2014; 5:378. [PMID: 25339907 PMCID: PMC4188032 DOI: 10.3389/fphys.2014.00378] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 09/12/2014] [Indexed: 01/01/2023] Open
Abstract
CLC channels and transporters are expressed in most tissues and fulfill diverse functions. There are four human CLC channels, ClC-1, ClC-2, ClC-Ka, and ClC-Kb, and five CLC transporters, ClC-3 through −7. Some of the CLC channels additionally associate with accessory subunits. Whereas barttin is mandatory for the functional expression of ClC-K, GlialCam is a facultative subunit of ClC-2 which modifies gating and thus increases the functional variability within the CLC family. Isoform-specific ion conduction and gating properties optimize distinct CLC channels for their cellular tasks. ClC-1 preferentially conducts at negative voltages, and the resulting inward rectification provides a large resting chloride conductance without interference with the muscle action potential. Exclusive opening at voltages negative to the chloride reversal potential allows for ClC-2 to regulate intracellular chloride concentrations. ClC-Ka and ClC-Kb are equally suited for inward and outward currents to support transcellular chloride fluxes. Every human CLC channel gene has been linked to a genetic disease, and studying these mutations has provided much information about the physiological roles and the molecular basis of CLC channel function. Mutations in the gene encoding ClC-1 cause myotonia congenita, a disease characterized by sarcolemmal hyperexcitability and muscle stiffness. Loss-of-function of ClC-Kb/barttin channels impairs NaCl resorption in the limb of Henle and causes hyponatriaemia, hypovolemia and hypotension in patients suffering from Bartter syndrome. Mutations in CLCN2 were found in patients with CNS disorders but the functional role of this isoform is still not understood. Recent links between ClC-1 and epilepsy and ClC-Ka and heart failure suggested novel cellular functions of these proteins. This review aims to survey the knowledge about physiological and pathophysiological functions of human CLC channels in the light of recent discoveries from biophysical, physiological, and genetic studies.
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Affiliation(s)
- Gabriel Stölting
- Institute of Complex Systems-Zelluläre Biophysik (ICS-4), Forschungszentrum Jülich Jülich, Germany
| | - Martin Fischer
- Institut für Neurophysiologie, Medizinische Hochschule Hannover Hannover, Germany
| | - Christoph Fahlke
- Institute of Complex Systems-Zelluläre Biophysik (ICS-4), Forschungszentrum Jülich Jülich, Germany
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21
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Conformational changes required for H(+)/Cl(-) exchange mediated by a CLC transporter. Nat Struct Mol Biol 2014; 21:456-63. [PMID: 24747941 PMCID: PMC4040230 DOI: 10.1038/nsmb.2814] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 03/26/2014] [Indexed: 11/08/2022]
Abstract
CLC-type exchangers mediate transmembrane Cl(-) transport. Mutations altering their gating properties cause numerous genetic disorders. However, their transport mechanism remains poorly understood. In conventional models, two gates alternatively expose substrates to the intra- or extracellular solutions. A glutamate was identified as the only gate in the CLCs, suggesting that CLCs function by a nonconventional mechanism. Here we show that transport in CLC-ec1, a prokaryotic homolog, is inhibited by cross-links constraining movement of helix O far from the transport pathway. Cross-linked CLC-ec1 adopts a wild-type-like structure, indicating stabilization of a native conformation. Movements of helix O are transduced to the ion pathway via a direct contact between its C terminus and a tyrosine that is a constitutive element of the second gate of CLC transporters. Therefore, the CLC exchangers have two gates that are coupled through conformational rearrangements outside the ion pathway.
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22
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Prerequisites to proton transport in the bacterial ClC-ec1 Cl-/H+ exchanger. Proc Natl Acad Sci U S A 2014; 111:1668-9. [PMID: 24459185 DOI: 10.1073/pnas.1323186111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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23
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Fluoride-dependent interruption of the transport cycle of a CLC Cl-/H+ antiporter. Nat Chem Biol 2013; 9:721-5. [PMID: 24036509 PMCID: PMC3805709 DOI: 10.1038/nchembio.1336] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 08/06/2013] [Indexed: 11/29/2022]
Abstract
Cl−/H+ antiporters of the CLC superfamily transport anions across biological membranes in varied physiological contexts. These proteins are weakly selective among anions commonly studied, including Cl−, Br−, I−,NO3−, and SCN−, but appear to be very selective against F−. The recent discovery of a new CLC clade of F−/H+ antiporters, which are highly selective for F− over Cl−, led us to investigate the mechanism of Cl−-over-F− selectivity by a CLC Cl−/H+ antiporter, CLC-ec1. By subjecting purified CLC-ec1 to anion transport measurements, electrophysiological recording, equilibrium ligand-binding studies, and x-ray crystallography, we show that F− binds in the Cl− transport pathway with affinity similar to Cl−, but stalls the transport cycle. Examination of various mutant antiporters implies a “lock-down” mechanism of F− inhibition, in which F−, by virtue of its unique H-bonding chemistry, greatly retards a proton-linked conformational change essential for the transport cycle of CLC-ec1.
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24
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Yan N. Structural investigation of the proton-coupled secondary transporters. Curr Opin Struct Biol 2013; 23:483-91. [DOI: 10.1016/j.sbi.2013.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 04/17/2013] [Accepted: 04/19/2013] [Indexed: 11/16/2022]
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25
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Checchetto V, Teardo E, Carraretto L, Formentin E, Bergantino E, Giacometti GM, Szabo I. Regulation of photosynthesis by ion channels in cyanobacteria and higher plants. Biophys Chem 2013; 182:51-7. [PMID: 23891570 DOI: 10.1016/j.bpc.2013.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/10/2013] [Accepted: 06/10/2013] [Indexed: 11/25/2022]
Abstract
Photosynthesis converts light energy into chemical energy, and supplies ATP and NADPH for CO2 fixation into carbohydrates and for the synthesis of several compounds which are essential for autotrophic growth. Oxygenic photosynthesis takes place in thylakoid membranes of chloroplasts and photosynthetic prokaryote cyanobacteria. An ancestral photoautotrophic prokaryote related to cyanobacteria has been proposed to give rise to chloroplasts of plants and algae through an endosymbiotic event. Indeed, photosynthetic complexes involved in the electron transport coupled to H(+) translocation and ATP synthesis are similar in higher plants and cyanobacteria. Furthermore, some of the protein and solute/ion conducting machineries also share common structure and function. Electrophysiological and biochemical evidence support the existence of ion channels in the thylakoid membrane in both types of organisms. By allowing specific ion fluxes across thylakoid membranes, ion channels have been hypothesized to either directly or indirectly regulate photosynthesis, by modulating the proton motive force. Recent molecular identification of some of the thylakoid-located channels allowed to obtain genetic proof in favor of such hypothesis. Furthermore, some ion channels of the envelope membrane in chloroplasts have also been shown to impact on this light-driven process. Here we give an overview of thylakoid/chloroplast located ion channels of higher plants and of cyanobacterium Synechocystis sp. PCC 6803. We focus on channels shown to be implicated in the regulation of photosynthesis and discuss the possible mechanisms of action.
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Affiliation(s)
- Vanessa Checchetto
- Department of Biology, University of Padova, viale G. Colombo 3, 35121 Padova, Italy
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26
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Phillips S, Brammer AE, Rodriguez L, Lim HH, Stary-Weinzinger A, Matulef K. Surprises from an unusual CLC homolog. Biophys J 2013. [PMID: 23199933 DOI: 10.1016/j.bpj.2012.08.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The chloride channel (CLC) family is distinctive in that some members are Cl(-) ion channels and others are Cl(-)/H(+) antiporters. The molecular mechanism that couples H(+) and Cl(-) transport in the antiporters remains unknown. Our characterization of a novel bacterial homolog from Citrobacter koseri, CLC-ck2, has yielded surprising discoveries about the requirements for both Cl(-) and H(+) transport in CLC proteins. First, even though CLC-ck2 lacks conserved amino acids near the Cl(-)-binding sites that are part of the CLC selectivity signature sequence, this protein catalyzes Cl(-) transport, albeit slowly. Ion selectivity in CLC-ck2 is similar to that in CLC-ec1, except that SO(4)(2-) strongly competes with Cl(-) uptake through CLC-ck2 but has no effect on CLC-ec1. Second, and even more surprisingly, CLC-ck2 is a Cl(-)/H(+) antiporter, even though it contains an isoleucine at the Glu(in) position that was previously thought to be a critical part of the H(+) pathway. CLC-ck2 is the first known antiporter that contains a nonpolar residue at this position. Introduction of a glutamate at the Glu(in) site in CLC-ck2 does not increase H(+) flux. Like other CLC antiporters, mutation of the external glutamate gate (Glu(ex)) in CLC-ck2 prevents H(+) flux. Hence, Glu(ex), but not Glu(in), is critical for H(+) permeation in CLC proteins.
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Affiliation(s)
- Sabrina Phillips
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California, USA
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27
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Garcia-Celma J, Szydelko A, Dutzler R. Functional characterization of a ClC transporter by solid-supported membrane electrophysiology. ACTA ACUST UNITED AC 2013; 141:479-91. [PMID: 23478993 PMCID: PMC3607819 DOI: 10.1085/jgp.201210927] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
EcClC, a prokaryotic member of the ClC family of chloride channels and transporters, works as coupled H+/Cl− exchanger. With a known structure and the possibility of investigating its behavior with different biochemical and biophysical techniques, the protein has become an important model system for the family. Although many aspects of its function have been previously characterized, it was difficult to measure transport on the same sample under different environmental conditions. To overcome this experimental limitation, we have studied EcClC by solid-supported membrane electrophysiology. The large transport-related transient currents and a simple way of relating transport rates to the measured signal have allowed a thorough investigation of ion selectivity, inhibition, and the dependence of transport on changes in ion concentration and pH. Our results confirm that the protein transports larger anions with about similar rates, whereas the smaller fluoride is not a substrate. We also show that 4,4′-diisothiocyano-2,2’-stilbenedisulfonic acid (DIDS), a known inhibitor of other anion transport protein, irreversibly inhibits EcClC from the intracellular side. The chloride dependence shows an apparent saturation at millimolar concentrations that resembles a similar behavior in eukaryotic ClC channels. Our experiments have also allowed us to quantify the pH dependence of transport. EcClC shows a strong activation at low pH with an apparent pKa of 4.6. The pronounced pH dependence is lost by the mutation of a conserved glutamate facing the extracellular solution that was previously shown to be an acceptor for transported protons, whereas it is largely retained by the mutation of an equivalent residue at the intracellular side. Our results have provided a quantitative basis for the transport behavior of EcClC, and they will serve as a reference for future investigations of novel electrogenic transporters with still-uncharacterized properties.
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Affiliation(s)
- Juan Garcia-Celma
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
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28
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Gradogna A, Fenollar-Ferrer C, Forrest LR, Pusch M. Dissecting a regulatory calcium-binding site of CLC-K kidney chloride channels. ACTA ACUST UNITED AC 2012; 140:681-96. [PMID: 23148261 PMCID: PMC3514729 DOI: 10.1085/jgp.201210878] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The kidney and inner ear CLC-K chloride channels, which are involved in salt absorption and endolymph production, are regulated by extracellular Ca2+ in the millimolar concentration range. Recently, Gradogna et al. (2010. J. Gen. Physiol.http://dx.doi.org/10.1085/jgp.201010455) identified a pair of acidic residues (E261 and D278) located in the loop between helices I and J as forming a putative intersubunit Ca2+-binding site in hClC-Ka. In this study, we sought to explore the properties of the binding site in more detail. First, we verified that the site is conserved in hClC-Kb and rClC-K1. In addition, we could confer Ca2+ sensitivity to the Torpedo marmorata ClC-0 channel by exchanging its I–J loop with that from ClC-Ka, demonstrating a direct role of the loop in Ca2+ binding. Based on a structure of a bacterial CLC and a new sequence alignment, we built homology models of ClC-Ka. The models suggested additional amino acids involved in Ca2+ binding. Testing mutants of these residues, we could restrict the range of plausible models and positively identify two more residues (E259 and E281) involved in Ca2+ coordination. To investigate cation specificity, we applied extracellular Zn2+, Mg2+, Ba2+, Sr2+, and Mn2+. Zn2+ blocks ClC-Ka as well as its Ca2+-insensitive mutant, suggesting that Zn2+ binds to a different site. Mg2+ does not activate CLC-Ks, but the channels are activated by Ba2+, Sr2+, and Mn2+ with a rank order of potency of Ca2+ > Ba2+ > Sr2+ = Mn2+ for the human CLC-Ks. Dose–response analysis indicates that the less potent Ba2+ has a lower affinity rather than a lower efficacy. Interestingly, rClC-K1 shows an altered rank order (Ca2+ > Sr2+ >> Ba2+), but homology models suggest that residues outside the I–J loop are responsible for this difference. Our detailed characterization of the regulatory Ca2+-binding site provides a solid basis for the understanding of the physiological modulation of CLC-K channel function in the kidney and inner ear.
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Affiliation(s)
- Antonella Gradogna
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 16149 Genoa, Italy
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29
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Fluoride resistance and transport by riboswitch-controlled CLC antiporters. Proc Natl Acad Sci U S A 2012; 109:15289-94. [PMID: 22949689 DOI: 10.1073/pnas.1210896109] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A subclass of bacterial CLC anion-transporting proteins, phylogenetically distant from long-studied CLCs, was recently shown to be specifically up-regulated by F(-). We establish here that a set of randomly selected representatives from this "CLC(F)" clade protect Escherichia coli from F(-) toxicity, and that the purified proteins catalyze transport of F(-) in liposomes. Sequence alignments and membrane transport experiments using (19)F NMR, osmotic response assays, and planar lipid bilayer recordings reveal four mechanistic traits that set CLC(F) proteins apart from all other known CLCs. First, CLC(F)s lack conserved residues that form the anion binding site in canonical CLCs. Second, CLC(F)s exhibit high anion selectivity for F(-) over Cl(-). Third, at a residue thought to distinguish CLC channels and transporters, CLC(F)s bear a channel-like valine rather than a transporter-like glutamate, and yet are F(-)/H(+) antiporters. Finally, F(-)/H(+) exchange occurs with 1:1 stoichiometry, in contrast to the usual value of 2:1.
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Dong H, Sharma M, Zhou HX, Cross TA. Glycines: role in α-helical membrane protein structures and a potential indicator of native conformation. Biochemistry 2012; 51:4779-89. [PMID: 22650985 DOI: 10.1021/bi300090x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among the growing number of membrane protein structures in the Protein Data Bank, there are many transmembrane domains that appear to be native-like; at the same time, there are others that appear to have less than complete native-like character. Hence, there is an increasing need for validation tools that distinguish native-like from non-native-like structures. Membrane mimetics used in protein structural characterizations differ in numerous physicochemical properties from native membranes and provide many opportunities for introducing non-native-like features into membrane protein structures. One possible approach for validating membrane protein structures is based on the use of glycine residues in transmembrane domains. Here, we have reviewed the membrane protein structure database and identified a set of benchmark proteins that appear to be native-like. In these structures, conserved glycine residues rarely face the lipid interstices, and many of them participate in close helix-helix packing. Glycine-based validation allowed the identification of non-native-like features in several membrane proteins and also shows the potential for verifying the native-like character for numerous other membrane protein structures.
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Affiliation(s)
- Hao Dong
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
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