1
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Kwon HC, Fairclough RH, Chen TY. Insights into CLC-0's Slow-Gating from Intracellular Proton Inhibition. Int J Mol Sci 2024; 25:7796. [PMID: 39063037 PMCID: PMC11276645 DOI: 10.3390/ijms25147796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
The opening of the Torpedo CLC-0 chloride (Cl-) channel is known to be regulated by two gating mechanisms: fast gating and slow (common) gating. The structural basis underlying the fast-gating mechanism is better understood than that of the slow-gating mechanism, which is still largely a mystery. Our previous study on the intracellular proton (H+i)-induced inhibition of the CLC-0 anionic current led to the conclusion that the inhibition results from the slow-gate closure (also called inactivation). The conclusion was made based on substantial evidence such as a large temperature dependence of the H+i inhibition similar to that of the channel inactivation, a resistance to the H+i inhibition in the inactivation-suppressed C212S mutant, and a similar voltage dependence between the current recovery from the H+i inhibition and the recovery from the channel inactivation. In this work, we further examine the mechanism of the H+i inhibition of wild-type CLC-0 and several mutants. We observe that an anion efflux through the pore of CLC-0 accelerates the recovery from the H+i-induced inhibition, a process corresponding to the slow-gate opening. Furthermore, various inactivation-suppressed mutants exhibit different current recovery kinetics, suggesting the existence of multiple inactivated states (namely, slow-gate closed states). We speculate that protonation of the pore of CLC-0 increases the binding affinity of permeant anions in the pore, thereby generating a pore blockage of ion flow as the first step of inactivation. Subsequent complex protein conformational changes further transition the CLC-0 channel to deeper inactivated states.
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Affiliation(s)
- Hwoi Chan Kwon
- Biophysics Graduate Program, University of California, Davis, CA 95618, USA; (H.C.K.); (R.H.F.)
| | - Robert H. Fairclough
- Biophysics Graduate Program, University of California, Davis, CA 95618, USA; (H.C.K.); (R.H.F.)
- Department of Neurology, University of California, Davis, CA 95618, USA
| | - Tsung-Yu Chen
- Biophysics Graduate Program, University of California, Davis, CA 95618, USA; (H.C.K.); (R.H.F.)
- Department of Neurology, University of California, Davis, CA 95618, USA
- Center for Neuroscience, University of California, 1544 Newton Court, Davis, CA 95618, USA
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2
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Xu M, Neelands T, Powers AS, Liu Y, Miller SD, Pintilie G, Bois JD, Dror RO, Chiu W, Maduke M. CryoEM structures of the human CLC-2 voltage gated chloride channel reveal a ball and chain gating mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.13.553136. [PMID: 37645939 PMCID: PMC10462068 DOI: 10.1101/2023.08.13.553136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different mammalian tissues and cell types. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating mechanisms among closely related CLC homologs has been a long-standing mystery, in part because few CLC channel structures are available, and those that exist exhibit high conformational similarity. Here, we report cryoEM structures of human CLC-2 at 2.46 - 2.76 Å, in the presence and absence of the potent and selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl--permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct apo conformations of CLC-2 involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl--permeation pathway from the intracellular side. This peptide is highly conserved among species variants of CLC-2 but is not present in any other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a "ball-and-chain" gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we show that loss of this short sequence increases the magnitude and decreases the rectification of CLC-2 currents expressed in mammalian cells. Furthermore, we show that with repetitive hyperpolarization WT CLC-2 currents increase in resemblance to the hairpin-deleted CLC-2 currents. These functional results combined with our structural data support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl--permeation pathway.
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Affiliation(s)
- Mengyuan Xu
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
| | - Torben Neelands
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
| | - Alexander S. Powers
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Department of Computer Science, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305
| | - Yan Liu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park 94025
| | - Steven D. Miller
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Grigore Pintilie
- Department of Bioengineering and Department of Microbiology and Immunology, Stanford University, Stanford, 94305
| | - J. Du Bois
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Ron O. Dror
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Computer Science, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park 94025
- Department of Bioengineering and Department of Microbiology and Immunology, Stanford University, Stanford, 94305
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
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3
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Zhang B, Zhang S, Polovitskaya MM, Yi J, Ye B, Li R, Huang X, Yin J, Neuens S, Balfroid T, Soblet J, Vens D, Aeby A, Li X, Cai J, Song Y, Li Y, Tartaglia M, Li Y, Jentsch TJ, Yang M, Liu Z. Molecular basis of ClC-6 function and its impairment in human disease. SCIENCE ADVANCES 2023; 9:eadg4479. [PMID: 37831762 PMCID: PMC10575590 DOI: 10.1126/sciadv.adg4479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 09/08/2023] [Indexed: 10/15/2023]
Abstract
ClC-6 is a late endosomal voltage-gated chloride-proton exchanger that is predominantly expressed in the nervous system. Mutated forms of ClC-6 are associated with severe neurological disease. However, the mechanistic role of ClC-6 in normal and pathological states remains largely unknown. Here, we present cryo-EM structures of ClC-6 that guided subsequent functional studies. Previously unrecognized ATP binding to cytosolic ClC-6 domains enhanced ion transport activity. Guided by a disease-causing mutation (p.Y553C), we identified an interaction network formed by Y553/F317/T520 as potential hotspot for disease-causing mutations. This was validated by the identification of a patient with a de novo pathogenic variant p.T520A. Extending these findings, we found contacts between intramembrane helices and connecting loops that modulate the voltage dependence of ClC-6 gating and constitute additional candidate regions for disease-associated gain-of-function mutations. Besides providing insights into the structure, function, and regulation of ClC-6, our work correctly predicts hotspots for CLCN6 mutations in neurodegenerative disorders.
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Affiliation(s)
- Bing Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Sensen Zhang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Maya M. Polovitskaya
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
| | - Jingbo Yi
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Binglu Ye
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Ruochong Li
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Xueying Huang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Jian Yin
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Sebastian Neuens
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Tom Balfroid
- Department of Pediatric Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Julie Soblet
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Department of Genetics, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Daphné Vens
- Pediatric Intensive Care Unit, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Alec Aeby
- Department of Pediatric Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Xiaoling Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, 110016 Shenyang, China
| | - Jinjin Cai
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Yingcai Song
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Yuanxi Li
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, 200237 Shanghai, China
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Yang Li
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Thomas J. Jentsch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
- Cryo-EM Facility Center, Southern University of Science & Technology, 518055 Shenzhen, Guangdong, China
| | - Zhiqiang Liu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
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4
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Wackett LP. Toward a molecular understanding of fluoride stress in a model Pseudomonas strain. Environ Microbiol 2022; 24:4981-4983. [PMID: 35848109 PMCID: PMC9795876 DOI: 10.1111/1462-2920.16114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/30/2022]
Affiliation(s)
- Lawrence P. Wackett
- Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology InstituteUniversity of MinnesotaSt. PaulMinnesotaUSA
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5
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Abstract
Thousands of heavily fluorinated chemicals are found in the environment, impact human and ecosystem health, and are relatively resistant to biological and chemical degradation. Their persistence in the environment is due to the inability of most microorganisms to biodegrade them. Only a very few examples of polyfluorinated compound biodegradation are known, and the reported rates are very low. This has been mostly attributed to the low chemical reactivity of the C-F bond. This Perspective goes beyond that explanation to highlight microbiological reasons why polyfluorinated compounds resist metabolism. The evolutionary and physiological impediments must be appreciated to better find, study, and harness microbes that degrade polyfluorinated compounds.
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6
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Wackett LP. Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances. Microb Biotechnol 2021; 15:773-792. [PMID: 34570953 PMCID: PMC8913905 DOI: 10.1111/1751-7915.13928] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Poly‐ and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today’s society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called ‘forever chemicals’ due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.
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Affiliation(s)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, 55108, USA
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7
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The role of pulmonary ORCC and CLC-2 channels in the response to oxidative stress. Mol Cell Toxicol 2021. [DOI: 10.1007/s13273-021-00137-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
Background
Exposure of human lung epithelial cells to the oxidant pollutant ozone (O3) alters cell Cl− currents inducing an outward rectifier effect. Among the various Cl− channels, ClC-2 and ORCC seemed to be involved in this response.
Objectives
To identify the channel related to O3 induced current changes.
Results
Down regulating the expression of ORCC and ClC-2 genes and analyzing the membrane current show that the enhancement of the current disappeared when ORCC was silenced. The contribution of ORCC and ClC-2 channels in control and O3 treated cells was obtained by a mathematical approach.
Conclusion
We suggest that O3 activates ORCC channels and slightly inhibited ClC-2 channels in the negative voltage range. These findings open the possibility of identifying the biomolecular changes induced by O3 allowing a possible pharmacological intervention towards chloride current due to oxidative stress.
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8
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Regulation of ClC-2 Chloride Channel Proteostasis by Molecular Chaperones: Correction of Leukodystrophy-Associated Defect. Int J Mol Sci 2021; 22:ijms22115859. [PMID: 34070744 PMCID: PMC8197790 DOI: 10.3390/ijms22115859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The ClC-2 channel plays a critical role in maintaining ion homeostasis in the brain and the testis. Loss-of-function mutations in the ClC-2-encoding human CLCN2 gene are linked to the white matter disease leukodystrophy. Clcn2-deficient mice display neuronal myelin vacuolation and testicular degeneration. Leukodystrophy-causing ClC-2 mutant channels are associated with anomalous proteostasis manifesting enhanced endoplasmic reticulum (ER)-associated degradation. The molecular nature of the ER quality control system for ClC-2 protein remains elusive. In mouse testicular tissues and Leydig cells, we demonstrated that endogenous ClC-2 co-existed in the same protein complex with the molecular chaperones heat shock protein 90β (Hsp90β) and heat shock cognate protein (Hsc70), as well as the associated co-chaperones Hsp70/Hsp90 organizing protein (HOP), activator of Hsp90 ATPase homolog 1 (Aha1), and FK506-binding protein 8 (FKBP8). Further biochemical analyses revealed that the Hsp90β-Hsc70 chaperone/co-chaperone system promoted mouse and human ClC-2 protein biogenesis. FKBP8 additionally facilitated membrane trafficking of ClC-2 channels. Interestingly, treatment with the Hsp90-targeting small molecule 17-allylamino-17-demethoxygeldanamycin (17-AAG) substantially boosted ClC-2 protein expression. Also, 17-AAG effectively increased both total and cell surface protein levels of leukodystrophy-causing loss-of-function ClC-2 mutant channels. Our findings highlight the therapeutic potential of 17-AAG in correcting anomalous ClC-2 proteostasis associated with leukodystrophy.
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9
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Kwon HC, Yu Y, Fairclough RH, Chen TY. Proton-dependent inhibition, inverted voltage activation, and slow gating of CLC-0 Chloride Channel. PLoS One 2020; 15:e0240704. [PMID: 33362212 PMCID: PMC7757909 DOI: 10.1371/journal.pone.0240704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/03/2020] [Indexed: 11/21/2022] Open
Abstract
CLC-0, a prototype Cl- channel in the CLC family, employs two gating mechanisms that control its ion-permeation pore: fast gating and slow gating. The negatively-charged sidechain of a pore glutamate residue, E166, is known to be the fast gate, and the swinging of this sidechain opens or closes the pore of CLC-0 on the millisecond time scale. The other gating mechanism, slow gating, operates with much slower kinetics in the range of seconds to tens or even hundreds of seconds, and it is thought to involve still-unknown conformational rearrangements. Here, we find that low intracellular pH (pHi) facilitates the closure of the CLC-0’s slow gate, thus generating current inhibition. The rate of low pHi-induced current inhibition increases with intracellular H+ concentration ([H+]i)—the time constants of current inhibition by low pHi = 4.5, 5.5 and 6 are roughly 0.1, 1 and 10 sec, respectively, at room temperature. In comparison, the time constant of the slow gate closure at pHi = 7.4 at room temperature is hundreds of seconds. The inhibition by low pHi is significantly less prominent in mutants favoring the slow-gate open state (such as C212S and Y512A), further supporting the fact that intracellular H+ enhances the slow-gate closure in CLC-0. A fast inhibition by low pHi causes an apparent inverted voltage-dependent activation in the wild-type CLC-0, a behavior similar to those in some channel mutants such as V490W in which only membrane hyperpolarization can open the channel. Interestingly, when V490W mutation is constructed in the background of C212S or Y512A mutation, the inverted voltage-dependent activation disappears. We propose that the slow kinetics of CLC-0’s slow-gate closure may be due to low [H+]i rather than due to the proposed large conformational change of the channel protein. Our results also suggest that the inverted voltage-dependent opening observed in some mutant channels may result from fast closure of the slow gate by the mutations.
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Affiliation(s)
- Hwoi Chan Kwon
- Biophysics Graduate Program, University of California, Davis, California, United States of America
| | - Yawei Yu
- BMCDB Graduate Program, University of California, Davis, California, United States of America
| | - Robert H. Fairclough
- Biophysics Graduate Program, University of California, Davis, California, United States of America
- BMCDB Graduate Program, University of California, Davis, California, United States of America
- Center for Neuroscience, University of California, Davis, California, United States of America
| | - Tsung-Yu Chen
- Biophysics Graduate Program, University of California, Davis, California, United States of America
- BMCDB Graduate Program, University of California, Davis, California, United States of America
- Department of Neurology, University of California, Davis, California, United States of America
- Center for Neuroscience, University of California, Davis, California, United States of America
- * E-mail:
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10
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Barrett PQ, Guagliardo NA, Bayliss DA. Ion Channel Function and Electrical Excitability in the Zona Glomerulosa: A Network Perspective on Aldosterone Regulation. Annu Rev Physiol 2020; 83:451-475. [PMID: 33176563 DOI: 10.1146/annurev-physiol-030220-113038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aldosterone excess is a pathogenic factor in many hypertensive disorders. The discovery of numerous somatic and germline mutations in ion channels in primary hyperaldosteronism underscores the importance of plasma membrane conductances in determining the activation state of zona glomerulosa (zG) cells. Electrophysiological recordings describe an electrically quiescent behavior for dispersed zG cells. Yet, emerging data indicate that in native rosette structures in situ, zG cells are electrically excitable, generating slow periodic voltage spikes and coordinated bursts of Ca2+ oscillations. We revisit data to understand how a multitude of conductances may underlie voltage/Ca2+ oscillations, recognizing that zG layer self-renewal and cell heterogeneity may complicate this task. We review recent data to understand rosette architecture and apply maxims derived from computational network modeling to understand rosette function. The challenge going forward is to uncover how the rosette orchestrates the behavior of a functional network of conditional oscillators to control zG layer performance and aldosterone secretion.
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Affiliation(s)
- Paula Q Barrett
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA; , ,
| | - Nick A Guagliardo
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA; , ,
| | - Douglas A Bayliss
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA; , ,
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11
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Zhang S, Liu Y, Zhang B, Zhou J, Li T, Liu Z, Li Y, Yang M. Molecular insights into the human CLC-7/Ostm1 transporter. SCIENCE ADVANCES 2020; 6:eabb4747. [PMID: 32851177 PMCID: PMC7423370 DOI: 10.1126/sciadv.abb4747] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/29/2020] [Indexed: 05/14/2023]
Abstract
CLC family proteins translocate chloride ions across cell membranes to maintain the membrane potential, regulate the transepithelial Cl- transport, and control the intravesicular pH among different organelles. CLC-7/Ostm1 is an electrogenic Cl-/H+ antiporter that mainly resides in lysosomes and osteoclast ruffled membranes. Mutations in human CLC-7/Ostm1 lead to lysosomal storage disorders and severe osteopetrosis. Here, we present the cryo-electron microscopy (cryo-EM) structure of the human CLC-7/Ostm1 complex and reveal that the highly glycosylated Ostm1 functions like a lid positioned above CLC-7 and interacts extensively with CLC-7 within the membrane. Our complex structure reveals a functionally crucial domain interface between the amino terminus, TMD, and CBS domains of CLC-7. Structural analyses and electrophysiology studies suggest that the domain interaction interfaces affect the slow gating kinetics of CLC-7/Ostm1. Thus, our study deepens understanding of CLC-7/Ostm1 transporter and provides insights into the molecular basis of the disease-related mutations.
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Affiliation(s)
- Sensen Zhang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yang Liu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Bing Zhang
- Department of Anesthesiology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China
| | - Jun Zhou
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tianyu Li
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhiqiang Liu
- Department of Anesthesiology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China
- Corresponding author. (Z.L.); (Y.L.); (M.Y.)
| | - Yang Li
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Corresponding author. (Z.L.); (Y.L.); (M.Y.)
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Corresponding author. (Z.L.); (Y.L.); (M.Y.)
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12
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Fu SJ, Hu MC, Peng YJ, Fang HY, Hsiao CT, Chen TY, Jeng CJ, Tang CY. CUL4-DDB1-CRBN E3 Ubiquitin Ligase Regulates Proteostasis of ClC-2 Chloride Channels: Implication for Aldosteronism and Leukodystrophy. Cells 2020; 9:cells9061332. [PMID: 32466489 PMCID: PMC7348978 DOI: 10.3390/cells9061332] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 12/27/2022] Open
Abstract
Voltage-gated ClC-2 channels are essential for chloride homeostasis. Complete knockout of mouse ClC-2 leads to testicular degeneration and neuronal myelin vacuolation. Gain-of-function and loss-of-function mutations in the ClC-2-encoding human CLCN2 gene are linked to the genetic diseases aldosteronism and leukodystrophy, respectively. The protein homeostasis (proteostasis) mechanism of ClC-2 is currently unclear. Here, we aimed to identify the molecular mechanism of endoplasmic reticulum-associated degradation of ClC-2, and to explore the pathophysiological significance of disease-associated anomalous ClC-2 proteostasis. In both heterologous expression system and native neuronal and testicular cells, ClC-2 is subject to significant regulation by cullin-RING E3 ligase-mediated polyubiquitination and proteasomal degradation. The cullin 4 (CUL4)-damage-specific DNA binding protein 1 (DDB1)-cereblon (CRBN) E3 ubiquitin ligase co-exists in the same complex with and promotes the degradation of ClC-2 channels. The CRBN-targeting immunomodulatory drug lenalidomide and the cullin E3 ligase inhibitor MLN4924 promotes and attenuates, respectively, proteasomal degradation of ClC-2. Analyses of disease-related ClC-2 mutants reveal that aldosteronism and leukodystrophy are associated with opposite alterations in ClC-2 proteostasis. Modifying CUL4 E3 ligase activity with lenalidomide and MLN4924 ameliorates disease-associated ClC-2 proteostasis abnormality. Our results highlight the significant role and therapeutic potential of CUL4 E3 ubiquitin ligase in regulating ClC-2 proteostasis.
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Affiliation(s)
- Ssu-Ju Fu
- Department of Physiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan; (S.-J.F.); (M.-C.H.); (Y.-J.P.); (H.-Y.F.); (C.-T.H.)
| | - Meng-Chun Hu
- Department of Physiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan; (S.-J.F.); (M.-C.H.); (Y.-J.P.); (H.-Y.F.); (C.-T.H.)
| | - Yi-Jheng Peng
- Department of Physiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan; (S.-J.F.); (M.-C.H.); (Y.-J.P.); (H.-Y.F.); (C.-T.H.)
| | - Hsin-Yu Fang
- Department of Physiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan; (S.-J.F.); (M.-C.H.); (Y.-J.P.); (H.-Y.F.); (C.-T.H.)
| | - Cheng-Tsung Hsiao
- Department of Physiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan; (S.-J.F.); (M.-C.H.); (Y.-J.P.); (H.-Y.F.); (C.-T.H.)
- Department of Neurology, Taipei Veterans General Hospital, Taipei 12217, Taiwan
| | - Tsung-Yu Chen
- Center for Neuroscience and Department of Neurology, University of California, Davis, CA 95616, USA;
| | - Chung-Jiuan Jeng
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei 12212, Taiwan
- Brain Research Center, National Yang-Ming University, Taipei 12212, Taiwan
- Correspondence: (C.-J.J.); (C.-Y.T.)
| | - Chih-Yung Tang
- Department of Physiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan; (S.-J.F.); (M.-C.H.); (Y.-J.P.); (H.-Y.F.); (C.-T.H.)
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
- Correspondence: (C.-J.J.); (C.-Y.T.)
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13
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Wang Z, Swanson JMJ, Voth GA. Local conformational dynamics regulating transport properties of a Cl - /H + antiporter. J Comput Chem 2020; 41:513-519. [PMID: 31633205 PMCID: PMC7184886 DOI: 10.1002/jcc.26093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 09/17/2019] [Accepted: 10/03/2019] [Indexed: 11/08/2022]
Abstract
ClC-ec1 is a Cl- /H+ antiporter that exchanges Cl- and H+ ions across the membrane. Experiments have demonstrated that several mutations, including I109F, decrease the Cl- and H+ transport rates by an order of magnitude. Using reactive molecular dynamics simulations of explicit proton transport across the central region in the I109F mutant, a two-dimensional free energy profile has been constructed that is consistent with the experimental transport rates. The importance of a phenylalanine gate formed by F109 and F357 and its influence on hydration connectivity through the central proton transport pathway is revealed. This work demonstrates how seemingly subtle changes in local conformational dynamics can dictate hydration changes and thus transport properties. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Zhi Wang
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | | | - Gregory A. Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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14
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Jeng CJ, Fu SJ, You CY, Peng YJ, Hsiao CT, Chen TY, Tang CY. Defective Gating and Proteostasis of Human ClC-1 Chloride Channel: Molecular Pathophysiology of Myotonia Congenita. Front Neurol 2020; 11:76. [PMID: 32117034 PMCID: PMC7026490 DOI: 10.3389/fneur.2020.00076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/22/2020] [Indexed: 01/17/2023] Open
Abstract
The voltage-dependent ClC-1 chloride channel, whose open probability increases with membrane potential depolarization, belongs to the superfamily of CLC channels/transporters. ClC-1 is almost exclusively expressed in skeletal muscles and is essential for stabilizing the excitability of muscle membranes. Elucidation of the molecular structures of human ClC-1 and several CLC homologs provides important insight to the gating and ion permeation mechanisms of this chloride channel. Mutations in the human CLCN1 gene, which encodes the ClC-1 channel, are associated with a hereditary skeletal muscle disease, myotonia congenita. Most disease-causing CLCN1 mutations lead to loss-of-function phenotypes in the ClC-1 channel and thus increase membrane excitability in skeletal muscles, consequently manifesting as delayed relaxations following voluntary muscle contractions in myotonic subjects. The inheritance pattern of myotonia congenita can be autosomal dominant (Thomsen type) or recessive (Becker type). To date over 200 myotonia-associated ClC-1 mutations have been identified, which are scattered throughout the entire protein sequence. The dominant inheritance pattern of some myotonia mutations may be explained by a dominant-negative effect on ClC-1 channel gating. For many other myotonia mutations, however, no clear relationship can be established between the inheritance pattern and the location of the mutation in the ClC-1 protein. Emerging evidence indicates that the effects of some mutations may entail impaired ClC-1 protein homeostasis (proteostasis). Proteostasis of membrane proteins comprises of biogenesis at the endoplasmic reticulum (ER), trafficking to the surface membrane, and protein turn-over at the plasma membrane. Maintenance of proteostasis requires the coordination of a wide variety of different molecular chaperones and protein quality control factors. A number of regulatory molecules have recently been shown to contribute to post-translational modifications of ClC-1 and play critical roles in the ER quality control, membrane trafficking, and peripheral quality control of this chloride channel. Further illumination of the mechanisms of ClC-1 proteostasis network will enhance our understanding of the molecular pathophysiology of myotonia congenita, and may also bring to light novel therapeutic targets for skeletal muscle dysfunction caused by myotonia and other pathological conditions.
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Affiliation(s)
- Chung-Jiuan Jeng
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Ssu-Ju Fu
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Ying You
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Jheng Peng
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Cheng-Tsung Hsiao
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tsung-Yu Chen
- Center for Neuroscience, University of California, Davis, Davis, CA, United States
| | - Chih-Yung Tang
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan.,College of Medicine, Graduate Institute of Brain and Mind Sciences, National Taiwan University, Taipei, Taiwan
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15
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Hall AE, Engevik MA, Oezguen N, Haag A, Versalovic J. ClC transporter activity modulates histidine catabolism in Lactobacillus reuteri by altering intracellular pH and membrane potential. Microb Cell Fact 2019; 18:212. [PMID: 31830990 PMCID: PMC6909576 DOI: 10.1186/s12934-019-1264-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Histamine is a key mediator of the anti-inflammatory activity conferred by the probiotic organism Lactobacillus reuteri ATCC PTA 6475 in animal models of colitis and colorectal cancer. In L. reuteri, histamine synthesis and secretion requires L-histidine decarboxylase and a L-histidine/histamine exchanger. Chloride channel (ClC)-family proton/chloride antiporters have been proposed to act as electrochemical shunts in conjunction with amino acid decarboxylase systems, correcting ion imbalances generated by decarboxylation through fixed ratio exchange of two chloride ions for one proton. This family is unique among transporters by facilitating ion flux in either direction. Here we examine the histidine decarboxylase system in relation to ClC antiporters in the probiotic organism Lactobacillus reuteri. RESULTS In silico analyses reveal that L. reuteri possesses two ClC transporters, EriC and EriC2, as well as a complete histidine decarboxylase gene cluster (HDC) for the synthesis and export of histamine. When the transport activity of either proton/chloride antiporter is disrupted by genetic manipulation, bacterial histamine output is reduced. Using fluorescent reporter assays, we further show that ClC transporters affect histamine output by altering intracellular pH and membrane potential. ClC transport also alters the expression and activity of two key HDC genes: the histidine decarboxylase (hdcA) and the histidine/histamine exchanger (hdcP). CONCLUSIONS Histamine production is a potentially beneficial feature for intestinal microbes by promoting long-term colonization and suppression of inflammation and host immune responses. ClC transporters may serve as tunable modulators for histamine production by L. reuteri and other gut microbes.
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Affiliation(s)
- Anne E Hall
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, 77030, USA
- Infectious Disease Laboratories, Akron Children's Hospital, Akron, OH, 44308, USA
| | - Melinda A Engevik
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Anthony Haag
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, 77030, USA
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Pathology, Texas Children's Hospital, Houston, TX, 77030, USA.
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16
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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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17
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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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18
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Min D, Jefferson RE, Qi Y, Wang JY, Arbing MA, Im W, Bowie JU. Unfolding of a ClC chloride transporter retains memory of its evolutionary history. Nat Chem Biol 2018; 14:489-496. [PMID: 29581582 PMCID: PMC6038805 DOI: 10.1038/s41589-018-0025-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/12/2018] [Indexed: 11/12/2022]
Abstract
ClC chloride channels and transporters are important for chloride homeostasis in species from bacteria to human. Mutations in ClC proteins cause genetically inherited diseases, some of which are likely to have folding defects. The ClC proteins present a challenging and unusual biological folding problem because they are large membrane proteins possessing a complex architecture with many re-entrant helices that go only part way through membrane and loop back out. Here we were able to examine the unfolding of the E. coli ClC transporter, ClC-ec1, using single-molecule forced unfolding methods. We find that the protein can be separated into two stable halves that unfold independently. The independence of the two domains is consistent with an evolutionary model in which the two halves arose from independent folding subunits that later fused together. Maintaining smaller folding domains of lesser complexity within large membrane proteins may be an advantageous strategy to avoid misfolding traps.
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Affiliation(s)
- Duyoung Min
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert E Jefferson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yifei Qi
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Jing Yang Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mark A Arbing
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. .,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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19
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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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20
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Pinelli L, Nissant A, Edwards A, Lourdel S, Teulon J, Paulais M. Dual regulation of the native ClC-K2 chloride channel in the distal nephron by voltage and pH. J Gen Physiol 2017; 148:213-26. [PMID: 27574292 PMCID: PMC5004338 DOI: 10.1085/jgp.201611623] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/07/2016] [Indexed: 12/23/2022] Open
Abstract
ClC-K2 is present on the basolateral membrane of kidney epithelial cells, but little is known about its single channel properties. Pinelli et al. record unitary ClC-K2 currents from intercalated cells of mouse connecting tubules and investigate their regulation by voltage, pH, Cl−, and Ca2+. ClC-K2, a member of the ClC family of Cl− channels and transporters, forms the major basolateral Cl− conductance in distal nephron epithelial cells and therefore plays a central role in renal Cl− absorption. However, its regulation remains largely unknown because of the fact that recombinant ClC-K2 has not yet been studied at the single-channel level. In the present study, we investigate the effects of voltage, pH, Cl−, and Ca2+ on native ClC-K2 in the basolateral membrane of intercalated cells from the mouse connecting tubule. The ∼10-pS channel shows a steep voltage dependence such that channel activity increases with membrane depolarization. Intracellular pH (pHi) and extracellular pH (pHo) differentially modulate the voltage dependence curve: alkaline pHi flattens the curve by causing an increase in activity at negative voltages, whereas alkaline pHo shifts the curve toward negative voltages. In addition, pHi, pHo, and extracellular Ca2+ strongly increase activity, mainly because of an increase in the number of active channels with a comparatively minor effect on channel open probability. Furthermore, voltage alters both the number of active channels and their open probability, whereas intracellular Cl− has little influence. We propose that changes in the number of active channels correspond to them entering or leaving an inactivated state, whereas modulation of open probability corresponds to common gating by these channels. We suggest that pH, through the combined effects of pHi and pHo on ClC-K2, might be a key regulator of NaCl absorption and Cl−/HCO3− exchange in type B intercalated cells.
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Affiliation(s)
- Laurent Pinelli
- Sorbonne Universités, Université Pierre-et-Marie-Curie Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Institut National de la Santé et de la Recherche Médicale, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Centre National de la Recherche Scientifique ERL 8228, Centre de Recherche des Cordeliers, F-75006 Paris, France
| | - Antoine Nissant
- Sorbonne Universités, Université Pierre-et-Marie-Curie Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Institut National de la Santé et de la Recherche Médicale, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Centre National de la Recherche Scientifique ERL 8228, Centre de Recherche des Cordeliers, F-75006 Paris, France
| | - Aurélie Edwards
- Sorbonne Universités, Université Pierre-et-Marie-Curie Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Institut National de la Santé et de la Recherche Médicale, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Centre National de la Recherche Scientifique ERL 8228, Centre de Recherche des Cordeliers, F-75006 Paris, France
| | - Stéphane Lourdel
- Sorbonne Universités, Université Pierre-et-Marie-Curie Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Institut National de la Santé et de la Recherche Médicale, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Centre National de la Recherche Scientifique ERL 8228, Centre de Recherche des Cordeliers, F-75006 Paris, France
| | - Jacques Teulon
- Sorbonne Universités, Université Pierre-et-Marie-Curie Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Institut National de la Santé et de la Recherche Médicale, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Centre National de la Recherche Scientifique ERL 8228, Centre de Recherche des Cordeliers, F-75006 Paris, France
| | - Marc Paulais
- Sorbonne Universités, Université Pierre-et-Marie-Curie Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Institut National de la Santé et de la Recherche Médicale, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006 Paris, France Centre National de la Recherche Scientifique ERL 8228, Centre de Recherche des Cordeliers, F-75006 Paris, France
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21
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Chakraborty K, Leung K, Krishnan Y. High lumenal chloride in the lysosome is critical for lysosome function. eLife 2017; 6. [PMID: 28742019 PMCID: PMC5526669 DOI: 10.7554/elife.28862] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 06/23/2017] [Indexed: 12/31/2022] Open
Abstract
Lysosomes are organelles responsible for the breakdown and recycling of cellular machinery. Dysfunctional lysosomes give rise to lysosomal storage disorders as well as common neurodegenerative diseases. Here, we use a DNA-based, fluorescent chloride reporter to measure lysosomal chloride in Caenorhabditis elegans as well as murine and human cell culture models of lysosomal diseases. We find that the lysosome is highly enriched in chloride, and that chloride reduction correlates directly with a loss in the degradative function of the lysosome. In nematodes and mammalian cell culture models of diverse lysosomal disorders, where previously only lysosomal pH dysregulation has been described, massive reduction of lumenal chloride is observed that is ~103 fold greater than the accompanying pH change. Reducing chloride within the lysosome impacts Ca2+ release from the lysosome and impedes the activity of specific lysosomal enzymes indicating a broader role for chloride in lysosomal function. DOI:http://dx.doi.org/10.7554/eLife.28862.001 In cells, worn out proteins and other unnecessary materials are sent to small compartments called lysosomes to be broken down and recycled. Lysosomes contain many different proteins including some that break down waste material into recyclable fragments and others that transport the fragments out of the lysosome. If any of these proteins do not work, waste products build up and cause disease. There are around 70 such lysosomal storage diseases, each arising from a different lysosomal protein not working correctly. A recently developed “nanodevice” called Clensor can measure the levels of chloride ions inside cells. Clensor is constructed from DNA, and its fluorescence changes when it detects chloride ions. Although chloride ions have many biological roles, chloride ion levels had not been measured inside a living organism. Now, Chakraborty et al. – including some of the researchers who developed Clensor – have used this nanodevice to examine chloride ion levels in the lysosomes of the roundworm Caenorhabditis elegans. This revealed that the lysosomes contain high levels of chloride ions. Furthermore, reducing the amount of chloride in the lysosomes made them worse at breaking down waste. Do lysosomes affected by lysosome storage diseases also contain low levels of chloride ions? To find out, Chakraborty et al. used Clensor to study C. elegans worms and mouse and human cells whose lysosomes accumulate waste products. In all these cases, the levels of chloride in the diseased lysosomes were much lower than normal. This had a number of effects on how the lysosomes worked, such as reducing the activity of key lysosomal proteins. Chakraborty et al. also found that Clensor can be used to distinguish between different lysosomal storage diseases. This means that in the future, Clensor (or similar methods that directly measure chloride ion levels in lysosomes) may be useful not just for research purposes. They may also be valuable for diagnosing lysosomal storage diseases early in infancy that, if left undiagnosed, are fatal. DOI:http://dx.doi.org/10.7554/eLife.28862.002
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Affiliation(s)
- Kasturi Chakraborty
- Department of Chemistry, University of Chicago, Chicago, United States.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, United States
| | - KaHo Leung
- Department of Chemistry, University of Chicago, Chicago, United States.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, United States
| | - Yamuna Krishnan
- Department of Chemistry, University of Chicago, Chicago, United States.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, United States
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22
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Yu Y, Tsai MF, Yu WP, Chen TY. Modulation of the slow/common gating of CLC channels by intracellular cadmium. ACTA ACUST UNITED AC 2017; 146:495-508. [PMID: 26621774 PMCID: PMC4664824 DOI: 10.1085/jgp.201511413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cd2+ binding to the CLC channel dimer interface inhibits slow gating by altering subunit interactions. Members of the CLC family of Cl− channels and transporters are homodimeric integral membrane proteins. Two gating mechanisms control the opening and closing of Cl− channels in this family: fast gating, which regulates opening and closing of the individual pores in each subunit, and slow (or common) gating, which simultaneously controls gating of both subunits. Here, we found that intracellularly applied Cd2+ reduces the current of CLC-0 because of its inhibition on the slow gating. We identified CLC-0 residues C229 and H231, located at the intracellular end of the transmembrane domain near the dimer interface, as the Cd2+-coordinating residues. The inhibition of the current of CLC-0 by Cd2+ was greatly enhanced by mutation of I225W and V490W at the dimer interface. Biochemical experiments revealed that formation of a disulfide bond within this Cd2+-binding site is also affected by mutation of I225W and V490W, indicating that these two mutations alter the structure of the Cd2+-binding site. Kinetic studies showed that Cd2+ inhibition appears to be state dependent, suggesting that structural rearrangements may occur in the CLC dimer interface during Cd2+ modulation. Mutations of I290 and I556 of CLC-1, which correspond to I225 and V490 of CLC-0, respectively, have been shown previously to cause malfunction of CLC-1 Cl− channel by altering the common gating. Our experimental results suggest that mutations of the corresponding residues in CLC-0 change the subunit interaction and alter the slow gating of CLC-0. The effect of these mutations on modulations of slow gating of CLC channels by intracellular Cd2+ likely depends on their alteration of subunit interactions.
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Affiliation(s)
- Yawei Yu
- Center for Neuroscience and Department of Neurology, University of California, Davis, Davis, CA 95618 Center for Neuroscience and Department of Neurology, University of California, Davis, Davis, CA 95618
| | - Ming-Feng Tsai
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453
| | - Wei-Ping Yu
- Center for Neuroscience and Department of Neurology, University of California, Davis, Davis, CA 95618 Center for Neuroscience and Department of Neurology, University of California, Davis, Davis, CA 95618
| | - Tsung-Yu Chen
- Center for Neuroscience and Department of Neurology, University of California, Davis, Davis, CA 95618 Center for Neuroscience and Department of Neurology, University of California, Davis, Davis, CA 95618
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23
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Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter. Biophys J 2016; 110:1334-45. [PMID: 27028643 DOI: 10.1016/j.bpj.2016.02.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/05/2016] [Accepted: 02/08/2016] [Indexed: 11/22/2022] Open
Abstract
Multiscale reactive molecular dynamics simulations are used to study proton transport through the central region of ClC-ec1, a widely studied ClC transporter that enables the stoichiometric exchange of 2 Cl(-) ions for 1 proton (H(+)). It has long been known that both Cl(-) and proton transport occur through partially congruent pathways, and that their exchange is strictly coupled. However, the nature of this coupling and the mechanism of antiporting remain topics of debate. Here multiscale simulations have been used to characterize proton transport between E203 (Glu(in)) and E148 (Glu(ex)), the internal and external intermediate proton binding sites, respectively. Free energy profiles are presented, explicitly accounting for the binding of Cl(-) along the central pathway, the dynamically coupled hydration changes of the central region, and conformational changes of Glu(in) and Glu(ex). We find that proton transport between Glu(in) and Glu(ex) is possible in both the presence and absence of Cl(-) in the central binding site, although it is facilitated by the anion presence. These results support the notion that the requisite coupling between Cl(-) and proton transport occurs elsewhere (e.g., during proton uptake or release). In addition, proton transport is explored in the E203K mutant, which maintains proton permeation despite the substitution of a basic residue for Glu(in). This collection of calculations provides for the first time, to our knowledge, a detailed picture of the proton transport mechanism in the central region of ClC-ec1 at a molecular level.
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24
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Lee S, Mayes HB, Swanson JMJ, Voth GA. The Origin of Coupled Chloride and Proton Transport in a Cl -/H + Antiporter. J Am Chem Soc 2016; 138:14923-14930. [PMID: 27783900 PMCID: PMC5114699 DOI: 10.1021/jacs.6b06683] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The ClC family of transmembrane proteins
functions throughout nature
to control the transport of Cl– ions across biological
membranes. ClC-ec1 from Escherichia coli is an antiporter,
coupling the transport of Cl– and H+ ions
in opposite directions and driven by the concentration gradients of
the ions. Despite keen interest in this protein, the molecular mechanism
of the Cl–/H+ coupling has not been fully
elucidated. Here, we have used multiscale simulation to help identify
the essential mechanism of the Cl–/H+ coupling. We find that the highest barrier for proton transport
(PT) from the intra- to extracellular solution is attributable to
a chemical reaction, the deprotonation of glutamic acid 148 (E148).
This barrier is significantly reduced by the binding of Cl– in the “central” site (Cl–cen), which displaces E148 and thereby facilitates its deprotonation.
Conversely, in the absence of Cl–cen E148
favors the “down” conformation, which results in a much
higher cumulative rotation and deprotonation barrier that effectively
blocks PT to the extracellular solution. Thus, the rotation of E148
plays a critical role in defining the Cl–/H+ coupling. As a control, we have also simulated PT in the
ClC-ec1 E148A mutant to further understand the role of this residue.
Replacement with a non-protonatable residue greatly increases the
free energy barrier for PT from E203 to the extracellular solution,
explaining the experimental result that PT in E148A is blocked whether
or not Cl–cen is present. The results
presented here suggest both how a chemical reaction can control the
rate of PT and also how it can provide a mechanism for a coupling
of the two ion transport processes.
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Affiliation(s)
- Sangyun Lee
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Heather B Mayes
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Jessica M J Swanson
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
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25
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Sharma T, Dreyer I, Kochian L, Piñeros MA. The ALMT Family of Organic Acid Transporters in Plants and Their Involvement in Detoxification and Nutrient Security. FRONTIERS IN PLANT SCIENCE 2016; 7:1488. [PMID: 27757118 PMCID: PMC5047901 DOI: 10.3389/fpls.2016.01488] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 09/20/2016] [Indexed: 05/02/2023]
Abstract
About a decade ago, members of a new protein family of anion channels were discovered on the basis of their ability to confer on plants the tolerance toward toxic aluminum ions in the soil. The efflux of Al3+-chelating malate anions through these channels is stimulated by external Al3+ ions. This feature of a few proteins determined the name of the entire protein family as Aluminum-activated Malate Transporters (ALMT). Meanwhile, after several years of research, it is known that the physiological roles of ALMTs go far beyond Al-detoxification. In this review article we summarize the current knowledge on this transporter family and assess their involvement in diverse physiological processes.
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Affiliation(s)
- Tripti Sharma
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, TalcaChile
| | - Ingo Dreyer
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, TalcaChile
| | - Leon Kochian
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture–Agricultural Research Service, Cornell University, Ithaca, NYUSA
| | - Miguel A. Piñeros
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture–Agricultural Research Service, Cornell University, Ithaca, NYUSA
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26
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Lee S, Liang R, Voth GA, Swanson JMJ. Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins. J Chem Theory Comput 2016; 12:879-91. [PMID: 26734942 PMCID: PMC4750100 DOI: 10.1021/acs.jctc.5b01109] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Indexed: 11/30/2022]
Abstract
An important challenge in the simulation of biomolecular systems is a quantitative description of the protonation and deprotonation process of amino acid residues. Despite the seeming simplicity of adding or removing a positively charged hydrogen nucleus, simulating the actual protonation/deprotonation process is inherently difficult. It requires both the explicit treatment of the excess proton, including its charge defect delocalization and Grotthuss shuttling through inhomogeneous moieties (water and amino residues), and extensive sampling of coupled condensed phase motions. In a recent paper (J. Chem. Theory Comput. 2014, 10, 2729-2737), a multiscale approach was developed to map high-level quantum mechanics/molecular mechanics (QM/MM) data into a multiscale reactive molecular dynamics (MS-RMD) model in order to describe amino acid deprotonation in bulk water. In this article, we extend the fitting approach (called FitRMD) to create MS-RMD models for ionizable amino acids within proteins. The resulting models are shown to faithfully reproduce the free energy profiles of the reference QM/MM Hamiltonian for PT inside an example protein, the ClC-ec1 H(+)/Cl(-) antiporter. Moreover, we show that the resulting MS-RMD models are computationally efficient enough to then characterize more complex 2-dimensional free energy surfaces due to slow degrees of freedom such as water hydration of internal protein cavities that can be inherently coupled to the excess proton charge translocation. The FitRMD method is thus shown to be an effective way to map ab initio level accuracy into a much more computationally efficient reactive MD method in order to explicitly simulate and quantitatively describe amino acid protonation/deprotonation in proteins.
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Affiliation(s)
| | | | - Gregory A. Voth
- Department of Chemistry,
Institute for Biophysical Dynamics, James Franck Institute, and Computation
Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States
| | - Jessica M. J. Swanson
- Department of Chemistry,
Institute for Biophysical Dynamics, James Franck Institute, and Computation
Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States
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27
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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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28
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Cruz-Rangel S, De Jesús-Pérez JJ, Contreras-Vite JA, Pérez-Cornejo P, Hartzell HC, Arreola J. Gating modes of calcium-activated chloride channels TMEM16A and TMEM16B. J Physiol 2015; 593:5283-98. [PMID: 26728431 DOI: 10.1113/jp271256] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/12/2015] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS Calcium-activated chloride channels TMEM16A and TMEM16B support important physiological processes such as fast block of polyspermy, fluid secretion, control of blood pressure and sensory transduction. Given the physiological importance of TMEM16 channels, it is important to study how incoming stimuli activate these channels. Here we study how channels open and close and how the process of gating is regulated. We show that TMEM16A and TMEM16B display fast and slow gating. These gating modes are regulated by voltage and external chloride. Dual gating explains the complex time course of the anion current. Residues within the first intracellular loop of the channel influence the slow gating mode. Dual gating is an intrinsic property observed in endogenous calcium-activated chloride channels and could be relevant to physiological processes that require sustained chloride ion movement. ABSTRACT TMEM16A and TMEM16B are molecular components of the physiologically relevant calcium-activated chloride channels (CaCCs) present in many tissues. Their gating is dictated by membrane voltage (Vm ), intracellular calcium concentrations ([Ca(2+) ]i ) and external permeant anions. As a consequence, the chloride current (ICl ) kinetics is complex. For example, TMEM16A ICl activates slowly with a non-mono-exponential time course while TMEM16B ICl activates rapidly following a mono-exponential behaviour. To understand the underlying mechanism responsible for the complex activation kinetics, we recorded ICl from HEK-293 cells transiently transfected with either TMEM16A or TMEM16B as well as from mouse parotid acinar cells. Two distinct Vm -dependent gating modes were uncovered: a fast-mode on the millisecond time scale followed by a slow mode on the second time scale. Using long (20 s) depolarizing pulses both gating modes were activated, and a slowly rising ICl was recorded in whole-cell and inside-out patches. The amplitude of ICl at the end of the long pulse nearly doubled and was blocked by 100 μm tannic acid. The slow gating mode was strongly reduced by decreasing the [Cl(-) ]o from 140 to 30 mm and by altering the sequence of the first intracellular loop. Mutating 480 RSQ482 to AVK in the first intracellular loop of TMEM16B nearly abolished slow gating, but, mutating 448 AVK451 to RSQ in TMEM16A has little effect. Deleting 448 EAVK451 residues in TMEM16A reduced slow gating. We conclude that TMEM16 CaCCs have intrinsic Vm - and Cl(-) -sensitive dual gating that elicits complex ICl kinetics.
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Affiliation(s)
- Silvia Cruz-Rangel
- Physics Institute, Universidad Autónoma de San Luis Potosí, Ave. Dr. Manuel Nava #6, San Luis Potosí, SLP, 78290, México
| | - José J De Jesús-Pérez
- Physics Institute, Universidad Autónoma de San Luis Potosí, Ave. Dr. Manuel Nava #6, San Luis Potosí, SLP, 78290, México
| | - Juan A Contreras-Vite
- Physics Institute, Universidad Autónoma de San Luis Potosí, Ave. Dr. Manuel Nava #6, San Luis Potosí, SLP, 78290, México
| | - Patricia Pérez-Cornejo
- Department of Physiology, Universidad Autónoma de San Luis Potosí School of Medicine, Ave. V. Carranza 2405, San Luis Potosí, SLP, 78290, Mexico
| | - H Criss Hartzell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jorge Arreola
- Physics Institute, Universidad Autónoma de San Luis Potosí, Ave. Dr. Manuel Nava #6, San Luis Potosí, SLP, 78290, México
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29
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Cherkashin AP, Kolesnikova AS, Tarasov MV, Romanov RA, Rogachevskaja OA, Bystrova MF, Kolesnikov SS. Expression of calcium-activated chloride channels Ano1 and Ano2 in mouse taste cells. Pflugers Arch 2015; 468:305-19. [DOI: 10.1007/s00424-015-1751-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 02/03/2023]
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30
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Andrini O, Keck M, Briones R, Lourdel S, Vargas-Poussou R, Teulon J. ClC-K chloride channels: emerging pathophysiology of Bartter syndrome type 3. Am J Physiol Renal Physiol 2015; 308:F1324-34. [DOI: 10.1152/ajprenal.00004.2015] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/23/2015] [Indexed: 02/08/2023] Open
Abstract
The mutations in the CLCNKB gene encoding the ClC-Kb chloride channel are responsible for Bartter syndrome type 3, one of the four variants of Bartter syndrome in the genetically based nomenclature. All forms of Bartter syndrome are characterized by hypokalemia, metabolic alkalosis, and secondary hyperaldosteronism, but Bartter syndrome type 3 has the most heterogeneous presentation, extending from severe to very mild. A relatively large number of CLCNKB mutations have been reported, including gene deletions and nonsense or missense mutations. However, only 20 CLCNKB mutations have been functionally analyzed, due to technical difficulties regarding ClC-Kb functional expression in heterologous systems. This review provides an overview of recent progress in the functional consequences of CLCNKB mutations on ClC-Kb chloride channel activity. It has been observed that 1) all ClC-Kb mutants have an impaired expression at the membrane; and 2) a minority of the mutants combines reduced membrane expression with altered pH-dependent channel gating. Although further investigation is needed to fully characterize disease pathogenesis, Bartter syndrome type 3 probably belongs to the large family of conformational diseases, in which the mutations destabilize channel structure, inducing ClC-Kb retention in the endoplasmic reticulum and accelerated channel degradation.
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Affiliation(s)
- Olga Andrini
- UPMC Université Paris 06, UMR_S 1138, Team 3, Paris, France
- INSERM, UMR_S 872, Paris, France
| | - Mathilde Keck
- UPMC Université Paris 06, UMR_S 1138, Team 3, Paris, France
- INSERM, UMR_S 872, Paris, France
| | - Rodolfo Briones
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stéphane Lourdel
- UPMC Université Paris 06, UMR_S 1138, Team 3, Paris, France
- INSERM, UMR_S 872, Paris, France
| | - Rosa Vargas-Poussou
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Département de Génétique, Paris, France; and
- Université Paris-Descartes, Faculté de Médecine, Paris, France
| | - Jacques Teulon
- UPMC Université Paris 06, UMR_S 1138, Team 3, Paris, France
- INSERM, UMR_S 872, Paris, France
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31
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Identification of a proton-chloride antiporter (EriC) by Himar1 transposon mutagenesis in Lactobacillus reuteri and its role in histamine production. Antonie van Leeuwenhoek 2014; 105:579-92. [PMID: 24488273 DOI: 10.1007/s10482-014-0113-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 01/01/2014] [Indexed: 12/21/2022]
Abstract
The gut microbiome may modulate intestinal immunity by luminal conversion of dietary amino acids to biologically active signals. The model probiotic organism Lactobacillus reuteri ATCC PTA 6475 is indigenous to the human microbiome, and converts the amino acid L-histidine to the biogenic amine, histamine. Histamine suppresses tumor necrosis factor (TNF) production by human myeloid cells and is a product of L-histidine decarboxylation, which is a proton-facilitated reaction. A transposon mutagenesis strategy was developed based on a single-plasmid nisin-inducible Himar1 transposase/transposon delivery system for L. reuteri. A highly conserved proton-chloride antiporter gene (eriC), a gene widely present in the gut microbiome was discovered by Himar1 transposon (Tn)-mutagenesis presented in this study. Genetic inactivation of eriC by transposon insertion and genetic recombineering resulted in reduced ability of L. reuteri to inhibit TNF production by activated human myeloid cells, diminished histamine production by the bacteria and downregulated expression of histidine decarboxylase cluster genes compared to those of WT 6475. EriC belongs to a large family of ion transporters that includes chloride channels and proton-chloride antiporters and may facilitate the availability of protons for the decarboxylation reaction, resulting in histamine production by L. reuteri. This report leverages the tools of bacterial genetics for probiotic gene discovery. The findings highlight the widely conserved nature of ion transporters in bacteria and how ion transporters are coupled with amino acid decarboxylation and contribute to microbiome-mediated immunomodulation.
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Alexander SPH, Benson HE, Faccenda E, Pawson AJ, Sharman JL, Catterall WA, Spedding M, Peters JA, Harmar AJ. The Concise Guide to PHARMACOLOGY 2013/14: ion channels. Br J Pharmacol 2013; 170:1607-51. [PMID: 24528239 PMCID: PMC3892289 DOI: 10.1111/bph.12447] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Concise Guide to PHARMACOLOGY 2013/14 provides concise overviews of the key properties of over 2000 human drug targets with their pharmacology, plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. The full contents can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.12444/full. Ion channels are one of the seven major pharmacological targets into which the Guide is divided, with the others being G protein-coupled receptors, ligand-gated ion channels, catalytic receptors, nuclear hormone receptors, transporters and enzymes. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. A new landscape format has easy to use tables comparing related targets. It is a condensed version of material contemporary to late 2013, which is presented in greater detail and constantly updated on the website www.guidetopharmacology.org, superseding data presented in previous Guides to Receptors and Channels. It is produced in conjunction with NC-IUPHAR and provides the official IUPHAR classification and nomenclature for human drug targets, where appropriate. It consolidates information previously curated and displayed separately in IUPHAR-DB and the Guide to Receptors and Channels, providing a permanent, citable, point-in-time record that will survive database updates.
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Affiliation(s)
- Stephen PH Alexander
- School of Life Sciences, University of Nottingham Medical SchoolNottingham, NG7 2UH, UK
- *
Author for correspondence;
| | - Helen E Benson
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | - Elena Faccenda
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | - Adam J Pawson
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | - Joanna L Sharman
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | - William A Catterall
- University of Washington, School of Medicine, Department of PharmacologyBox 357280, Seattle, WA 98195-7280, USA
| | | | - John A Peters
- Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of DundeeDundee, DD1 9SY, UK
| | - Anthony J Harmar
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
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CLCNKB mutations causing mild Bartter syndrome profoundly alter the pH and Ca2+ dependence of ClC-Kb channels. Pflugers Arch 2013; 466:1713-23. [DOI: 10.1007/s00424-013-1401-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 10/30/2013] [Accepted: 11/01/2013] [Indexed: 10/26/2022]
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Characterization of the mouse ClC-K1/Barttin chloride channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2399-409. [DOI: 10.1016/j.bbamem.2013.06.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/28/2013] [Accepted: 06/11/2013] [Indexed: 11/24/2022]
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35
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Odontoblast-like MDPC-23 cells function as odontoclasts with RANKL/M-CSF induction. Arch Oral Biol 2013; 58:272-8. [DOI: 10.1016/j.archoralbio.2012.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 04/10/2012] [Accepted: 05/29/2012] [Indexed: 01/09/2023]
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Lee TT, Zhang XD, Chuang CC, Chen JJ, Chen YA, Chen SC, Chen TY, Tang CY. Myotonia congenita mutation enhances the degradation of human CLC-1 chloride channels. PLoS One 2013; 8:e55930. [PMID: 23424641 PMCID: PMC3570542 DOI: 10.1371/journal.pone.0055930] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 01/03/2013] [Indexed: 11/18/2022] Open
Abstract
Myotonia congenita is a hereditary muscle disorder caused by mutations in the human voltage-gated chloride (Cl−) channel CLC-1. Myotonia congenita can be inherited in an autosomal recessive (Becker type) or dominant (Thomsen type) fashion. One hypothesis for myotonia congenita is that the inheritance pattern of the disease is determined by the functional consequence of the mutation on the gating of CLC-1 channels. Several disease-related mutations, however, have been shown to yield functional CLC-1 channels with no detectable gating defects. In this study, we have functionally and biochemically characterized a myotonia mutant: A531V. Despite a gating property similar to that of wild-type (WT) channels, the mutant CLC-1 channel displayed a diminished whole-cell current density and a reduction in the total protein expression level. Our biochemical analyses further demonstrated that the reduced expression of A531V can be largely attributed to an enhanced proteasomal degradation as well as a defect in protein trafficking to surface membranes. Moreover, the A531V mutant protein also appeared to be associated with excessive endosomal-lysosomal degradation. Neither the reduced protein expression nor the diminished current density was rescued by incubating A531V-expressing cells at 27°C. These results demonstrate that the molecular pathophysiology of A531V does not involve anomalous channel gating, but rather a disruption of the balance between the synthesis and degradation of the CLC-1 channel protein.
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Affiliation(s)
- Ting-Ting Lee
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Xiao-Dong Zhang
- Neuroscience Center, University of California Davis, Davis, California, United States of America
| | - Chao-Chin Chuang
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jing-Jer Chen
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-An Chen
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shu-Ching Chen
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Tsung-Yu Chen
- Neuroscience Center, University of California Davis, Davis, California, United States of America
| | - Chih-Yung Tang
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- * E-mail:
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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Krivobokova T, Briones R, Hub J, Munk A, de Groot B. Partial least-squares functional mode analysis: application to the membrane proteins AQP1, Aqy1, and CLC-ec1. Biophys J 2012; 103:786-96. [PMID: 22947940 PMCID: PMC3443789 DOI: 10.1016/j.bpj.2012.07.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 06/20/2012] [Accepted: 07/06/2012] [Indexed: 10/28/2022] Open
Abstract
We introduce an approach based on the recently introduced functional mode analysis to identify collective modes of internal dynamics that maximally correlate to an external order parameter of functional interest. Input structural data can be either experimentally determined structure ensembles or simulated ensembles, such as molecular dynamics trajectories. Partial least-squares regression is shown to yield a robust solution to the multidimensional optimization problem, with a minimal and controllable risk of overfitting, as shown by extensive cross-validation. Several examples illustrate that the partial least-squares-based functional mode analysis successfully reveals the collective dynamics underlying the fluctuations in selected functional order parameters. Applications to T4 lysozyme, the Trp-cage, the aquaporin channels Aqy1 and hAQP1, and the CLC-ec1 chloride antiporter are presented in which the active site geometry, the hydrophobic solvent-accessible surface, channel gating dynamics, water permeability (p(f)), and a dihedral angle are defined as functional order parameters. The Aqy1 case reveals a gating mechanism that connects the inner channel gating residues with the protein surface, thereby providing an explanation of how the membrane may affect the channel. hAQP1 shows how the p(f) correlates with structural changes around the aromatic/arginine region of the pore. The CLC-ec1 application shows how local motions of the gating Glu(148) couple to a collective motion that affects ion affinity in the pore.
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Affiliation(s)
- Tatyana Krivobokova
- Institute for Mathematical Stochastics and Courant Research Center (Poverty, Equity, and Growth), Georg-August-University Göttingen, Göttingen, Germany
| | - Rodolfo Briones
- Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jochen S. Hub
- Computational Molecular Biophysics Group, Department of Molecular Structural Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Axel Munk
- Institute for Mathematical Stochastics, Georg-August-University Göttingen and Statistical Inverse Problems Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L. de Groot
- Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Chen TY. Single myotonia mutation strikes multiple mechanisms of a chloride channel. J Physiol 2012; 590:3407. [PMID: 22855049 DOI: 10.1113/jphysiol.2012.238337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Tsung-Yu Chen
- Center for Neuroscience and Department of Neurology, University of California, Davis, 1544 Newton Court,Davis, CA 95618, USA.
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40
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Richman DP, Yu Y, Lee TT, Tseng PY, Yu WP, Maselli RA, Tang CY, Chen TY. Dominantly inherited myotonia congenita resulting from a mutation that increases open probability of the muscle chloride channel CLC-1. Neuromolecular Med 2012; 14:328-37. [PMID: 22790975 DOI: 10.1007/s12017-012-8190-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 06/22/2012] [Indexed: 10/28/2022]
Abstract
Myotonia congenita-inducing mutations in the muscle chloride channel CLC-1 normally result in reduced open probability (P (o)) of this channel. One well-accepted mechanism of the dominant inheritance of this disease involves a dominant-negative effect of the mutation on the function of the common-gate of this homodimeric, double-barreled molecule. We report here a family with myotonia congenita characterized by muscle stiffness and clinical and electrophysiologic myotonic phenomena transmitted in an autosomal dominant pattern. DNA sequencing of DMPK and ZNF9 genes for myotonic muscular dystrophy types I and II was normal, whereas sequencing of CLC-1 encoding gene, CLCN1, identified a single heterozygous missense mutation, G233S. Patch-clamp analyses of this mutant CLC-1 channel in Xenopus oocytes revealed an increased P (o) of the channel's fast-gate, from ~0.4 in the wild type to >0.9 in the mutant at -90 mV. In contrast, the mutant exhibits a minimal effect on the P (o) of the common-gate. These results are consistent with the structural prediction that the mutation site is adjacent to the fast-gate of the channel. Overall, the mutant could lead to a significantly reduced dynamic response of CLC-1 to membrane depolarization, from a fivefold increase in chloride conductance in the wild type to a twofold increase in the mutant-this might result in slower membrane repolarization during an action potential. Since expression levels of the mutant and wild-type subunits in artificial model cell systems were unable to explain the disease symptoms, the mechanism leading to dominant inheritance in this family remains to be determined.
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Affiliation(s)
- David P Richman
- Department of Neurology and Center for Neuroscience, University of California, Davis, CA 95616, USA.
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41
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Yu T, Wang XQ, Sang JP, Pan CX, Zou XW, Chen TY, Zou X. Influences of mutations on the electrostatic binding free energies of chloride ions in Escherichia coli ClC. J Phys Chem B 2012; 116:6431-8. [PMID: 22612693 DOI: 10.1021/jp300430f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutations in ClC channel proteins may cause serious functional changes and even diseases. The function of ClC proteins mainly manifests as Cl(-) transport, which is related to the binding free energies of chloride ions. Therefore, the influence of a mutation on ClC function can be studied by investigating the mutational effect on the binding free energies of chloride ions. The present study provides quantitative and systematic investigations on the influences of residue mutations on the electrostatic binding free energies in Escherichia coli ClC (EcClC) proteins, using all-atom molecular dynamics simulations. It was found that the change of the electrostatic binding free energy decreases linearly with the increase of the residue-chloride ion distance for a mutation. This work reveals how changes in the charge of a mutated residue and in the distance between the mutated residue and the binding site govern the variations in the electrostatic binding free energies and therefore influence the transport of chloride ions and conduction in EcClC. This work would facilitate our understanding of the mutational effects on transport of chloride ions and functions of ClC proteins and provide a guideline to estimate which residue mutations will have great influences on ClC functions.
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Affiliation(s)
- Tao Yu
- Department of Physics, Wuhan University, Wuhan 430072, PR China
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42
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Cheng MH, Coalson RD. Molecular dynamics investigation of Cl- and water transport through a eukaryotic CLC transporter. Biophys J 2012; 102:1363-71. [PMID: 22455919 DOI: 10.1016/j.bpj.2012.01.056] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 01/19/2012] [Accepted: 01/24/2012] [Indexed: 11/29/2022] Open
Abstract
Early crystal structures of prokaryotic CLC proteins identified three Cl(-) binding sites: internal (S(int)), central (S(cen)), and external (S(ext)). A conserved external GLU (GLU(ex)) residue acts as a gate competing for S(ext). Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLU(ex) competes instead for S(cen). Here, we use molecular dynamics simulations to investigate Cl(-) transport through CmCLC. The gating and Cl(-)/H(+) transport cycle are inferred through comparative molecular dynamics simulations with protonated and deprotonated GLU(ex) in the presence/absence of external potentials. Adaptive biasing force calculations are employed to estimate the potential of mean force profiles associated with transport of a Cl(-) ion from S(ext) to S(int), depending on the Cl(-) occupancy of other sites. Our simulations demonstrate that protonation of GLU(ex) is essential for Cl(-) transport from S(ext) to S(cen). The S(cen) site may be occupied by two Cl(-) ions simultaneously due to a high energy barrier (∼8 Kcal/mol) for a single Cl(-) ion to translocate from S(cen) to S(int). Binding two Cl(-) ions to S(cen) induces a continuous water wire from S(cen) to the extracellular solution through the side chain of the GLU(ex) gate. This may initiate deprotonation of GLU(ex), which then drives the two Cl(-) ions out of S(cen) toward the intracellular side via two putative Cl(-) transport paths. Finally, a conformational cycle is proposed that would account for the exchange stoichiometry.
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Affiliation(s)
- Mary Hongying Cheng
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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43
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Physiology and pathophysiology of CLC-1: mechanisms of a chloride channel disease, myotonia. J Biomed Biotechnol 2011; 2011:685328. [PMID: 22187529 PMCID: PMC3237021 DOI: 10.1155/2011/685328] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 07/18/2011] [Accepted: 09/10/2011] [Indexed: 12/22/2022] Open
Abstract
The CLC-1 chloride channel, a member of the CLC-channel/transporter family, plays important roles for the physiological functions of skeletal muscles. The opening of this chloride channel is voltage dependent and is also regulated by protons and chloride ions. Mutations of the gene encoding CLC-1 result in a genetic disease, myotonia congenita, which can be inherited as an autosmal dominant (Thomsen type) or an autosomal recessive (Becker type) pattern. These mutations are scattered throughout the entire protein sequence, and no clear relationship exists between the inheritance pattern of the mutation and the location of the mutation in the channel protein. The inheritance pattern of some but not all myotonia mutants can be explained by a working hypothesis that these mutations may exert a “dominant negative” effect on the gating function of the channel. However, other mutations may be due to different pathophysiological mechanisms, such as the defect of protein trafficking to membranes. Thus, the underlying mechanisms of myotonia are likely to be quite diverse, and elucidating the pathophysiology of myotonia mutations will require the understanding of multiple molecular/cellular mechanisms of CLC-1 channels in skeletal muscles, including molecular operation, protein synthesis, and membrane trafficking mechanisms.
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Baykov AA, Tuominen HK, Lahti R. The CBS domain: a protein module with an emerging prominent role in regulation. ACS Chem Biol 2011; 6:1156-63. [PMID: 21958115 DOI: 10.1021/cb200231c] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Regulatory CBS (cystathionine β-synthase) domains exist as two or four tandem copies in thousands of cytosolic and membrane-associated proteins from all kingdoms of life. Mutations in the CBS domains of human enzymes and membrane channels are associated with an array of hereditary diseases. Four CBS domains encoded within a single polypeptide or two identical polypeptides (each having a pair of CBS domains at the subunit interface) form a highly conserved disk-like structure. CBS domains act as autoinhibitory regulatory units in some proteins and activate or further inhibit protein function upon binding to adenosine nucleotides (AMP, ADP, ATP, S-adenosyl methionine, NAD, diadenosine polyphosphates). As a result of the differential effects of the nucleotides, CBS domain-containing proteins can sense cell energy levels. Significant conformational changes are induced in CBS domains by bound ligands, highlighting the structural basis for their effects.
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Affiliation(s)
- Alexander A. Baykov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Heidi K. Tuominen
- Department of Biochemistry and Food Chemistry, University of Turku, Turku FIN-20014, Finland
| | - Reijo Lahti
- Department of Biochemistry and Food Chemistry, University of Turku, Turku FIN-20014, Finland
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45
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The discovery of slowness: low-capacity transport and slow anion channel gating by the glutamate transporter EAAT5. Biophys J 2011; 100:2623-32. [PMID: 21641307 DOI: 10.1016/j.bpj.2011.04.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/15/2011] [Accepted: 04/18/2011] [Indexed: 01/12/2023] Open
Abstract
Excitatory amino acid transporters (EAATs) control the glutamate concentration in the synaptic cleft by glial and neuronal glutamate uptake. Uphill glutamate transport is achieved by the co-/countertransport of Na(+) and other ions down their concentration gradients. Glutamate transporters also display an anion conductance that is activated by the binding of Na(+) and glutamate but is not thermodynamically coupled to the transport process. Of the five known glutamate transporter subtypes, the retina-specific subtype EAAT5 has the largest conductance relative to glutamate uptake activity. Our results suggest that EAAT5 behaves as a slow-gated anion channel with little glutamate transport activity. At steady state, EAAT5 was activated by glutamate, with a K(m)= 61 ± 11 μM. Binding of Na(+) to the empty transporter is associated with a K(m) = 229 ± 37 mM, and binding to the glutamate-bound form is associated with a K(m) = 76 ± 40 mM. Using laser-pulse photolysis of caged glutamate, we determined the pre-steady-state kinetics of the glutamate-induced anion current of EAAT5. This was characterized by two exponential components with time constants of 30 ± 1 ms and 200 ± 15 ms, which is an order of magnitude slower than those observed in other glutamate transporters. A voltage-jump analysis of the anion currents indicates that the slow activation behavior is caused by two slow, rate-limiting steps in the transport cycle, Na(+) binding to the empty transporter, and translocation of the fully loaded transporter. We propose a kinetic transport scheme that includes these two slow steps and can account for the experimentally observed data. Overall, our results suggest that EAAT5 may not act as a classical high-capacity glutamate transporter in the retina; rather, it may function as a slow-gated glutamate receptor and/or glutamate buffering system.
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Tseng PY, Yu WP, Liu HY, Zhang XD, Zou X, Chen TY. Binding of ATP to the CBS domains in the C-terminal region of CLC-1. ACTA ACUST UNITED AC 2011; 137:357-68. [PMID: 21444658 PMCID: PMC3068280 DOI: 10.1085/jgp.201010495] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The common gating of CLC-1 has been shown to be inhibited by intracellular adenosine triphosphate (ATP) in acidic pH conditions. Such modulation is thought to be mediated by direct binding of ATP to the cystathionine β-synthase (CBS) domains at the C-terminal cytoplasmic region of CLC-1. Guided by the crystal structure of the C-terminal domain of CLC-5, we constructed a homology model of CLC-1’s C terminus and mutated critical amino acid residues lining the potential ATP-binding site. The CLC-1 mutations V634A and E865A completely abolished the ATP inhibition of CLC-1, consistent with the loss of ATP binding seen with the corresponding mutations in CLC-5. Mutating two other residues, V613 and V860, also disrupted the ATP modulation of CLC-1. However, placing aromatic amino acids at position 634 increases the apparent ATP affinity. Mutant cycle analyses showed that the modulation effects of ATP and cytidine triphosphate on wild-type CLC-1 and the V634F mutant were nonadditive, suggesting that the side chain of amino acid at position 634 interacts with the base moiety of the nucleotide. The mutation effects of V634F and V613A on the ATP modulation were also nonadditive, which is consistent with the assertion suggested from the homology model that these two residues may both interact with the bound nucleotide. These results provide evidence for a direct ATP binding for modulating the function of CLC-1 and suggest an overall conserved architecture of the ATP-binding sites in CLC-1 and CLC-5. This study also demonstrates that CLC-1 is a convenient experimental model for studying the interaction of nucleotides/nucleosides with the CBS domain.
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Affiliation(s)
- Pang-Yen Tseng
- Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
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47
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Abstract
August Krogh proposed that freshwater fishes (and other freshwater animals) maintain body NaCl homoeostasis by extracting these ions from the environment via separate Na(+) /NH(4)(+) and Cl(-) /HCO(3)(-) exchangers in the gill epithelium. Subsequent data from other laboratories suggested that Na(+) uptake was more probably coupled to H(+) secretion via a vesicular proton pump (V-ATPase) electrically coupled to a Na(+) channel. However, despite uncertainty about electrochemical gradients, evidence has accrued that epithelial Na(+) /H(+) exchange indeed may be an alternative pathway for Na(+) uptake. The specific pathways for Na(+) uptake may be species and environment specific. An apical Cl(-) /HCO(3)(-) exchanger is generally accepted for most species (some species do not extract Cl(-) from freshwater), but the relative roles of anion exchanger-like (SLC4A1) vs. pendrin-like (SLC26Z4) exchangers are unknown, and also may be species specific. Most recently, data have supported the presence of an apical Na(+) + Cl(-) cotransporter (NCC-type), despite thermodynamic uncertainty. Ammonia extrusion may be via NH(3) diffusing through the paracellular junctions or NH(4) (+) substitution on both basolateral and apical ionic exchangers (Na(+) + K(+) -ATPase; Na(+) + K(+) + Cl(-) - cotransporter; and Na(+) /H(+) exchanger), but recent evidence suggests that Rhesus-glycoproteins mediate both basolateral and apical movement of ammonia.
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Affiliation(s)
- D H Evans
- Department of Biology, University of Florida, Gainesville, FL 32611, USA.
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48
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Rivetta A, Kuroda T, Slayman C. Anion currents in yeast K+ transporters (TRK) characterize a structural homologue of ligand-gated ion channels. Pflugers Arch 2011; 462:315-30. [PMID: 21556692 DOI: 10.1007/s00424-011-0959-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 03/13/2011] [Accepted: 03/14/2011] [Indexed: 11/26/2022]
Abstract
Patch clamp studies of the potassium-transport proteins TRK1,2 in Saccharomyces cerevisiae have revealed large chloride efflux currents: at clamp voltages negative to -100 mV, and intracellular chloride concentrations >10 mM (J. Membr. Biol. 198:177, 2004). Stationary-state current-voltage analysis led to an in-series two-barrier model for chloride activation: the lower barrier (α) being 10-13 kcal/mol located ~30% into the membrane from the cytoplasmic surface; and the higher one (β) being 12-16 kcal/mol located at the outer surface. Measurements carried out with lyotrophic anions and osmoprotective solutes have now demonstrated the following new properties: (1) selectivity for highly permeant anions changes with extracellular pH; at pH(o)= 5.5: I(-)≈ Br(-) >Cl(-) >SCN(-) >NO (3)(-) , and at pH(o) 7.5: I(-)≈ Br(-) > SCN(-) > NO(3)(-) >Cl(-). (2) NO(2)(-) acts like "superchoride", possibly enhancing the channel's intrinsic permeability to Cl(-). (3) SCN(-) and NO(3)(-) block chloride permeability. (4) The order of selectivity for several slightly permeant anions (at pH(o)= 5.5 only) is formate>gluconate>acetate>>phosphate(-1). (5) All anion conductances are modulated (choked) by osmoprotective solutes. (6) The data and descriptive two-barrier model evoke a hypothetical structure (Biophys. J. 77:789, 1999) consisting of an intramembrane homotetramer of fungal TRK molecules, arrayed radially around a central cluster of four single helices (TM7) from each monomer. (7) That tetrameric cluster would resemble the hydrophobic core of (pentameric) ligand-gated ion channels, and would suggest voltage-modulated hydrophobic gating to underlie anion permeation.
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Affiliation(s)
- Alberto Rivetta
- Department of Cellular and Molecular Physiology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
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Lubiprostone activates Cl- secretion via cAMP signaling and increases membrane CFTR in the human colon carcinoma cell line, T84. Dig Dis Sci 2011; 56:339-51. [PMID: 21140215 DOI: 10.1007/s10620-010-1495-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 11/10/2010] [Indexed: 12/19/2022]
Abstract
BACKGROUND Lubiprostone, used clinically (b.i.d.) to treat constipation, has been reported to increase transepithelial Cl(-) transport in T84 cells by activating ClC-2 channels. AIM To identify the underlying signaling pathway, we explored the effects of short-term and overnight lubiprostone treatment on second messenger signaling and Cl(-) transport. METHODS Cl(-) transport was assessed either as I(sc) across T84 monolayers grown on Transwells and mounted in Ussing chambers or by the iodide efflux assay. [cAMP](i) was measured by enzyme immunoassay, and [Ca(2+)](i) by Fluo-3 fluorescence. Quantitation of apical cell surface CFTR protein levels was assessed by Western blotting and biotinylation with the EZ-Link Sulfo-NHS-LC-LC-Biotin. ClC-2 mRNA level was studied by RT-PCR. RESULTS Lubiprostone and the cAMP stimulator, forskolin, caused comparable and maximal increases of I(sc) in T84 cells. The I(sc) effects of lubiprostone and forskolin were each suppressed if the tissue had previously been treated with the other agent. These responses were unaltered even if the monolayers were treated with lubiprostone overnight. Lubiprostone-induced increases in iodide efflux were ~80% of those obtained with forskolin. Lubiprostone increased [cAMP](i). H89, bumetanide, or CFTR(inh)-172 greatly attenuated lubiprostone-stimulated Cl(-) secretion, whereas the ClC-2 inhibitor CdCl(2) did not. Compared to controls, FSK-treatment increased membrane-associated CFTR by 1.9 fold, and lubiprostone caused a 2.6-fold increase in apical membrane CFTR as seen by immunoblotting following cell surface biotinylation. CONCLUSIONS Lubiprostone activates Cl(-) secretion in T84 cells via cAMP, protein kinase A, and by increasing apical membrane CFTR protein.
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A three-state multi-ion kinetic model for conduction properties of ClC-0 chloride channel. Biophys J 2010; 99:464-71. [PMID: 20643064 DOI: 10.1016/j.bpj.2010.04.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2010] [Revised: 04/16/2010] [Accepted: 04/23/2010] [Indexed: 11/21/2022] Open
Abstract
A three-state, multiion kinetic model was proposed to enable the conduction properties of the mammalian channel ClC-0 to be well characterized. Using this rate-theory based model, the current-voltage and conductance-concentration relations were obtained. The five parameters needed were determined by fitting the data of conduction experiments of the wild-type ClC-0 and its K519C mutant. The model was then tested against available calculation and simulation data, and the energy differences between distinct chloride-occupancy states computed agreed with an independent calculation on the binding free energies solved by using the Poisson-Boltzmann equation. The average ion number of conduction and the ion passing duration calculated closely resembled the values obtained from Brownian dynamics simulations. According to the model, the decrease of conductance caused by mutating residue K519 to C519 can be attributed to the effect of K519C mutation on translocation rate constants. Our study sets up a theoretical model for ion permeation and conductance in ClC-0. It provides a starting point for experimentalists to test the three-state model, and would help in understanding the conduction mechanism of ClC-0.
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