1
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Infield DT, Strickland KM, Gaggar A, McCarty NA. The molecular evolution of function in the CFTR chloride channel. J Gen Physiol 2021; 153:212705. [PMID: 34647973 PMCID: PMC8640958 DOI: 10.1085/jgp.202012625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/11/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022] Open
Abstract
The ATP-binding cassette (ABC) transporter superfamily includes many proteins of clinical relevance, with genes expressed in all domains of life. Although most members use the energy of ATP binding and hydrolysis to accomplish the active import or export of various substrates across membranes, the cystic fibrosis transmembrane conductance regulator (CFTR) is the only known animal ABC transporter that functions primarily as an ion channel. Defects in CFTR, which is closely related to ABCC subfamily members that bear function as bona fide transporters, underlie the lethal genetic disease cystic fibrosis. This article seeks to integrate structural, functional, and genomic data to begin to answer the critical question of how the function of CFTR evolved to exhibit regulated channel activity. We highlight several examples wherein preexisting features in ABCC transporters were functionally leveraged as is, or altered by molecular evolution, to ultimately support channel function. This includes features that may underlie (1) construction of an anionic channel pore from an anionic substrate transport pathway, (2) establishment and tuning of phosphoregulation, and (3) optimization of channel function by specialized ligand–channel interactions. We also discuss how divergence and conservation may help elucidate the pharmacology of important CFTR modulators.
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Affiliation(s)
- Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA
| | | | - Amit Gaggar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL.,Program in Protease and Matrix Biology, University of Alabama at Birmingham, Birmingham, AL.,Birmingham Veterans Administration Medical Center, Birmingham, AL
| | - Nael A McCarty
- Department of Pediatrics, Emory University, Atlanta, GA.,Children's Healthcare of Atlanta Center for Cystic Fibrosis and Airways Disease Research, Emory University, Atlanta, GA
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2
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Barbieri A, Thonghin N, Shafi T, Prince SM, Collins RF, Ford RC. Structure of ABCB1/P-glycoprotein bound to the CFTR potentiator ivacaftor.. [DOI: 10.1101/2021.06.11.448073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractABCB1 (P-glycoprotein) is an ATP binding cassette transporter that is involved in the clearance of xenobiotics and it affects the disposition of many drugs in the body. Here we have studied ABCB1 in the drug-bound and drug-free states, simultaneously, using high contrast cryo-electron microscopy imaging and a Volta phase plate. The binding of the potent CFTR potentiator, ivacaftor, at a site in the central aqueous cavity is mediated by transmembrane α-helices 3,6,10,11 & 12. Binding is associated with a wider separation of the two halves of the transporter in the inward-facing state. Induced-fit changes the nucleotide binding domains in a way that may explain their increased affinity for ATP when drug is bound. Comparison of ivacaftor-bound structures of CFTR and ABCB1 suggests common features in the binding modes.
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3
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Meng X, Clews J, Ciuta AD, Martin ER, Ford RC. CFTR structure, stability, function and regulation. Biol Chem 2020; 400:1359-1370. [PMID: 30738013 DOI: 10.1515/hsz-2018-0470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/30/2019] [Indexed: 12/15/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a unique member of the ATP-binding cassette family of proteins because it has evolved into a channel. Mutations in CFTR cause cystic fibrosis, the most common genetic disease in people of European origin. The F508del mutation is found in about 90% of patients and here we present data that suggest its main effect is on CFTR stability rather than on the three-dimensional (3D) folded state. A survey of recent cryo-electron microscopy studies was carried out and this highlighted differences in terms of CFTR conformation despite similarities in experimental conditions. We further studied CFTR structure under various phosphorylation states and with the CFTR-interacting protein NHERF1. The coexistence of outward-facing and inward-facing conformations under a range of experimental conditions was suggested from these data. These results are discussed in terms of structural models for channel gating, and favour the model where the mostly disordered regulatory-region of the protein acts as a channel plug.
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Affiliation(s)
- Xin Meng
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Jack Clews
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Anca D Ciuta
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Eleanor R Martin
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Robert C Ford
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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4
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Strickland KM, Stock G, Cui G, Hwang H, Infield DT, Schmidt-Krey I, McCarty NA, Gumbart JC. ATP-Dependent Signaling in Simulations of a Revised Model of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). J Phys Chem B 2019; 123:3177-3188. [PMID: 30921517 DOI: 10.1021/acs.jpcb.8b11970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a member of the ATP-binding cassette (ABC) transporter superfamily that has uniquely evolved to function as a chloride channel. It binds and hydrolyzes ATP at its nucleotide binding domains to form a pore providing a diffusive pathway within its transmembrane domains. CFTR is the only known protein from the ABC superfamily with channel activity, and its dysfunction causes the disease cystic fibrosis. While much is known about the functional aspects of CFTR, significant gaps remain, such as the structure-function relationship underlying signaling of ATP binding. In the present work, we refined an existing homology model using an intermediate-resolution (9 Å) published cryo-electron microscopy map. The newly derived models have been simulated in equilibrium molecular dynamics simulations for a total of 2.5 μs in multiple ATP-occupancy states. Putative conformational movements connecting ATP binding with pore formation are elucidated and quantified. Additionally, new interdomain interactions between E543, K968, and K1292 have been identified and confirmed experimentally; these interactions may be relevant for signaling ATP binding and hydrolysis to the transmembrane domains and induction of pore opening.
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Affiliation(s)
- Kerry M Strickland
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Gorman Stock
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Guiying Cui
- Division of Pulmonology, Allergy and Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Center for Cystic Fibrosis and Airways Disease Research, Emory+Children's Pediatric Research Center , Emory University School of Medicine and Children's Healthcare of Atlanta , Atlanta , Georgia 30322 , United States
| | - Hyea Hwang
- School of Materials Science and Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Daniel T Infield
- Division of Pulmonology, Allergy and Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Center for Cystic Fibrosis and Airways Disease Research, Emory+Children's Pediatric Research Center , Emory University School of Medicine and Children's Healthcare of Atlanta , Atlanta , Georgia 30322 , United States
| | - Ingeborg Schmidt-Krey
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,Parker H. Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Nael A McCarty
- Division of Pulmonology, Allergy and Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Center for Cystic Fibrosis and Airways Disease Research, Emory+Children's Pediatric Research Center , Emory University School of Medicine and Children's Healthcare of Atlanta , Atlanta , Georgia 30322 , United States.,Parker H. Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - James C Gumbart
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,Parker H. Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,School of Physics , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
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5
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The structural basis of cystic fibrosis. Biochem Soc Trans 2018; 46:1093-1098. [PMID: 30154098 DOI: 10.1042/bst20180296] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 12/18/2022]
Abstract
CFTR (ABCC7) is a phospho-regulated chloride channel that is found in the apical membranes of epithelial cells, is gated by ATP and the activity of the protein is crucial in the homeostasis of the extracellular liquid layer in many organs [Annu. Rev. Biochem. (2008) 77, 701-726; Science (1989) 245, 1066-1073]. Mutations in CFTR cause the inherited disease cystic fibrosis (CF), the most common inherited condition in humans of European descent [Science (1989) 245, 1066-1073; Pflugers Arch. (2007) 453, 555-567]. The structural basis of CF will be discussed in this article.
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6
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Zhang J, Wang Y, Jiang X, Chan HC. Cystic fibrosis transmembrane conductance regulator-emerging regulator of cancer. Cell Mol Life Sci 2018; 75:1737-1756. [PMID: 29411041 PMCID: PMC11105598 DOI: 10.1007/s00018-018-2755-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/27/2017] [Accepted: 01/17/2018] [Indexed: 12/11/2022]
Abstract
Mutations of cystic fibrosis transmembrane conductance regulator (CFTR) cause cystic fibrosis, the most common life-limiting recessive genetic disease among Caucasians. CFTR mutations have also been linked to increased risk of various cancers but remained controversial for a long time. Recent studies have begun to reveal that CFTR is not merely an ion channel but also an important regulator of cancer development and progression with multiple signaling pathways identified. In this review, we will first present clinical findings showing the correlation of genetic mutations or aberrant expression of CFTR with cancer incidence in multiple cancers. We will then focus on the roles of CFTR in fundamental cellular processes including transformation, survival, proliferation, migration, invasion and epithelial-mesenchymal transition in cancer cells, highlighting the signaling pathways involved. Finally, the association of CFTR expression levels with patient prognosis, and the potential of CFTR as a cancer prognosis indicator in human malignancies will be discussed.
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Affiliation(s)
- Jieting Zhang
- Faculty of Medicine, Epithelial Cell Biology Research Center, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China
- School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China
| | - Yan Wang
- Faculty of Medicine, Epithelial Cell Biology Research Center, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China
- School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China
| | - Xiaohua Jiang
- Faculty of Medicine, Epithelial Cell Biology Research Center, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China.
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China.
- School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China.
| | - Hsiao Chang Chan
- Faculty of Medicine, Epithelial Cell Biology Research Center, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China.
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China.
- School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China.
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Chengdu, People's Republic of China.
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7
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Molinski SV, Shahani VM, Subramanian AS, MacKinnon SS, Woollard G, Laforet M, Laselva O, Morayniss LD, Bear CE, Windemuth A. Comprehensive mapping of cystic fibrosis mutations to CFTR protein identifies mutation clusters and molecular docking predicts corrector binding site. Proteins 2018; 86:833-843. [DOI: 10.1002/prot.25496] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 03/07/2018] [Accepted: 03/19/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | | | | | | | | | | | - Onofrio Laselva
- Programme in Molecular Structure and Function; Research Institute, Hospital for Sick Children; Toronto Ontario M5G 0A4 Canada
| | | | - Christine E. Bear
- Programme in Molecular Structure and Function; Research Institute, Hospital for Sick Children; Toronto Ontario M5G 0A4 Canada
- Department of Physiology; University of Toronto; Toronto Ontario M5S 1A8 Canada
- Department of Biochemistry; University of Toronto; Toronto Ontario M5S 1A8 Canada
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8
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Muimo R, Alothaid HM, Mehta A. NM23 proteins: innocent bystanders or local energy boosters for CFTR? J Transl Med 2018; 98:272-282. [PMID: 29251738 DOI: 10.1038/labinvest.2017.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/25/2017] [Accepted: 09/12/2017] [Indexed: 12/17/2022] Open
Abstract
NM23 proteins NDPK-A and -B bind to the cystic fibrosis (CF) protein CFTR in different ways from kinases such as PKA, CK2 and AMPK or linkers to cell calcium such as calmodulin and annexins. NDPK-A (not -B) interacts with CFTR through reciprocal AMPK binding/control, whereas NDPK-B (not -A) binds directly to CFTR. NDPK-B can activate G proteins without ligand-receptor coupling, so perhaps NDPK-B's binding influences energy supply local to a nucleotide-binding site (NBD1) needed for CFTR to function. Curiously, CFTR (ABC-C7) is a member of the ATP-binding cassette (ABC) protein family that does not obey 'clan rules'; CFTR channels anions and is not a pump, regulates disparate processes, is itself regulated by multiple means and is so pleiotropic that it acts as a hub that orchestrates calcium signaling through its consorts such as calmodulin/annexins. Furthermore, its multiple partners make CFTR dance to different tunes in different cellular and subcellular locations as it recycles from the plasma membrane to endosomes. CFTR function in airway apical membranes is inhibited by smoking which has been dubbed 'acquired CF'. CFTR alone among family members possesses a trap for other proteins that it unfurls as a 'fish-net' and which bears consensus phosphorylation sites for many protein kinases, with PKA being the most canonical. Recently, the site of CFTR's commonest mutation has been proposed as a knock-in mutant that alters allosteric control of kinase CK2 by log orders of activity towards calmodulin and other substrates after CFTR fragmentation. This link from CK2 to calmodulin that binds the R region invokes molecular paths that control lumen formation, which is incomplete in the tracheas of some CF-affected babies. Thus, we are poised to understand the many roles of NDPK-A and -B in CFTR function and, especially lumen formation, which is defective in the gut and lungs of many CF babies.
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Affiliation(s)
- Richmond Muimo
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Sheffield, UK
| | - Hani Mm Alothaid
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Sheffield, UK
| | - Anil Mehta
- Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
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9
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Structural effects of extracellular loop mutations in CFTR helical hairpins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1092-1098. [PMID: 29307731 DOI: 10.1016/j.bbamem.2018.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/29/2017] [Accepted: 01/02/2018] [Indexed: 01/06/2023]
Abstract
Missense mutations constitute 40% of 2000 cystic fibrosis-phenotypic mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) database, yet the precise mechanism as to how a point mutation can render the entire 1480-residue CFTR protein dysfunctional is not well-understood. Here we investigate the structural effects of two CF-phenotypic mutations - glutamic acid to glycine at position 217 (E217G) and glutamine to arginine at position 220 (Q220R) - in the extracellular (ECL2) loop region of human CFTR using helical hairpin constructs derived from transmembrane (TM) helices 3 and 4 of the first membrane domain. We systematically replaced the wild type (WT) residues E217 and Q220 with the subset of missense mutations that could arise through a single nucleotide change in their respective codons. Circular dichroism spectra of E217G revealed that a significant increase in helicity vs. WT arises in the membrane-mimetic environment of sodium dodecylsulfate (SDS) micelles, while this mutant showed a similar gel shift to WT on SDS-PAGE gels. In contrast, the CF-mutant Q220R showed similar helicity but an increased gel shift vs. WT. These structural variations are compared with the maturation levels of the corresponding mutant full-length CFTRs, which we found are reduced to approx. 50% for E217G and 30% for Q220R vs. WT. The overall results with CFTR hairpins illustrate the range of impacts that single mutations can evoke in intramolecular protein-protein and/or protein-lipid interactions - and the levels to which corresponding mutations in full-length CFTR may be flagged by quality control mechanisms during biosynthesis.
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10
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Molecular dynamics of the cryo-EM CFTR structure. Biochem Biophys Res Commun 2017; 491:986-993. [DOI: 10.1016/j.bbrc.2017.07.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 07/30/2017] [Indexed: 12/11/2022]
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11
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Simhaev L, McCarty NA, Ford RC, Senderowitz H. Molecular Dynamics Flexible Fitting Simulations Identify New Models of the Closed State of the Cystic Fibrosis Transmembrane Conductance Regulator Protein. J Chem Inf Model 2017; 57:1932-1946. [DOI: 10.1021/acs.jcim.7b00091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Luba Simhaev
- Department
of Chemistry, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Nael A. McCarty
- Division
of Pulmonology, Allergy/Immunology, Cystic Fibrosis, and Sleep, Department
of Pediatrics, Emory + Children’s Center for Cystic Fibrosis
and Airways Disease Research, Emory University School of Medicine and Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Atlanta, Georgia 30322, United States
| | - Robert C. Ford
- Faculty
of Biology Medicine and Health, University of Manchester, Oxford
Road, Manchester, M13 9PL, U.K
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12
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Hopfner KP. Invited review: Architectures and mechanisms of ATP binding cassette proteins. Biopolymers 2017; 105:492-504. [PMID: 27037766 DOI: 10.1002/bip.22843] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/24/2016] [Accepted: 03/28/2016] [Indexed: 12/29/2022]
Abstract
ATP binding cassette (ABC) ATPases form chemo-mechanical engines and switches that function in a broad range of biological processes. Most prominently, a very large family of integral membrane NTPases-ABC transporters-catalyzes the import or export of a diverse molecules across membranes. ABC proteins are also important components of the chromosome segregation, recombination, and DNA repair machineries and regulate or catalyze critical steps of ribosomal protein synthesis. Recent structural and mechanistic studies draw interesting architectural and mechanistic parallels between diverse ABC proteins. Here, I review this state of our understanding how NTP-dependent conformational changes of ABC proteins drive diverse biological processes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 492-504, 2016.
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Affiliation(s)
- Karl-Peter Hopfner
- Department Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.,Center for Integrated Protein Science Munich, Ludwigs-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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13
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Moran O. The biophysics, biochemistry and physiology of CFTR. Cell Mol Life Sci 2017; 74:1-2. [PMID: 27704173 PMCID: PMC11107758 DOI: 10.1007/s00018-016-2384-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Oscar Moran
- Istituto di Biofisica, CNR, Via De Marini, 6, 16149, Genoa, Italy.
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14
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Callebaut I, Hoffmann B, Lehn P, Mornon JP. Molecular modelling and molecular dynamics of CFTR. Cell Mol Life Sci 2017; 74:3-22. [PMID: 27717958 PMCID: PMC11107702 DOI: 10.1007/s00018-016-2385-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.
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Affiliation(s)
- Isabelle Callebaut
- UMR CNRS 7590, Museum National d'Histoire Naturelle, IRD UMR 206, IUC, Case 115, IMPMC, Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75005, Paris Cedex 05, France.
| | - Brice Hoffmann
- UMR CNRS 7590, Museum National d'Histoire Naturelle, IRD UMR 206, IUC, Case 115, IMPMC, Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75005, Paris Cedex 05, France
| | - Pierre Lehn
- INSERM U1078, SFR ScInBioS, Université de Bretagne Occidentale, Brest, France
| | - Jean-Paul Mornon
- UMR CNRS 7590, Museum National d'Histoire Naturelle, IRD UMR 206, IUC, Case 115, IMPMC, Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75005, Paris Cedex 05, France
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15
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Linsdell P. Architecture and functional properties of the CFTR channel pore. Cell Mol Life Sci 2017; 74:67-83. [PMID: 27699452 PMCID: PMC11107662 DOI: 10.1007/s00018-016-2389-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/12/2022]
Abstract
The main function of the cystic fibrosis transmembrane conductance regulator (CFTR) is as an ion channel for the movement of small anions across epithelial cell membranes. As an ion channel, CFTR must form a continuous pathway across the cell membrane-referred to as the channel pore-for the rapid electrodiffusional movement of ions. This review summarizes our current understanding of the architecture of the channel pore, as defined by electrophysiological analysis and molecular modeling studies. This includes consideration of the characteristic functional properties of the pore, definition of the overall shape of the entire extent of the pore, and discussion of how the molecular structure of distinct regions of the pore might control different facets of pore function. Comparisons are drawn with closely related proteins that are not ion channels, and also with structurally unrelated proteins with anion channel function. A simple model of pore function is also described.
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Affiliation(s)
- Paul Linsdell
- Department of Physiology and Biophysics, Dalhousie University, PO Box 15000, Halifax, NS, B3H 4R2, Canada.
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16
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Yang Z, Zhou Q, Mok L, Singh A, Swartz DJ, Urbatsch IL, Brouillette CG. Interactions and cooperativity between P-glycoprotein structural domains determined by thermal unfolding provides insights into its solution structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:48-60. [PMID: 27783926 DOI: 10.1016/j.bbamem.2016.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/19/2016] [Accepted: 10/21/2016] [Indexed: 12/16/2022]
Abstract
Structural changes in mouse P-glycoprotein (Pgp) induced by thermal unfolding were studied by differential scanning calorimetry (DSC), circular dichroism and fluorescence spectroscopy to gain insight into the solution conformation(s) of this ABC transporter that may not be apparent from current crystal structures. DSC of reconstituted Pgp showed two thermal unfolding transitions in the absence of MgATP, suggesting that each transition involved the cooperative unfolding of two or more interacting structural domains. A low calorimetric unfolding enthalpy and minimal structural changes were observed, which are hallmarks of the thermal unfolding of α-helical membrane proteins, because generally only the extramembranous regions undergo significant unfolding. Nucleotide binding increased the unfolding temperature of both transitions to the same extent, suggesting that one nucleotide binding domain (NBD) unfolds with each transition. Combined with the results from the two isolated NBDs, we propose that each DSC transition represents the cooperative unfolding of one NBD and the two contacting intracellular loops. Further, the presence of two transitions in both apo and MgATP bound wild-type Pgp suggests the NBD-dimeric conformation is transient, and that Pgp resides predominantly in the crystallographically observed inward-facing conformation with NBDs separated, even under conditions supporting continuous MgATP hydrolysis. In contrast, DSC of the vanadate-trapped MgADP·Pgp complex and the MgATP-bound catalytically inactive mutant, E552A/E1197A, show an additional transition at much higher temperature, corresponding to the unfolding of the nucleotide-trapped NBD-dimeric outward-facing conformation. The collective results indicate a strong preference for an NBD dissociated, inward-facing conformation of Pgp.
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Affiliation(s)
- Zhengrong Yang
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Qingxian Zhou
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leo Mok
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Anukriti Singh
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Douglas J Swartz
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
| | - Christie G Brouillette
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA.
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17
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Wang G, Linsley R, Norimatsu Y. External Zn2+binding to cysteine-substituted cystic fibrosis transmembrane conductance regulator constructs regulates channel gating and curcumin potentiation. FEBS J 2016; 283:2458-75. [DOI: 10.1111/febs.13752] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 05/02/2016] [Accepted: 05/11/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Guangyu Wang
- Department of Physiology and Pharmacology; Oregon Health & Sciences University; Portland OR USA
- Department of Drug Research and Development; Institute of Biophysical Medico-chemistry; Reno NV USA
- Department of Physiology and Membrane Biology; University of California School of Medicine; Davis CA USA
| | | | - Yohei Norimatsu
- Department of Physiology; Kirksville College of Osteopathic Medicine; A.T. Still University; Kirksville MO USA
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18
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Zwick M, Esposito C, Hellstern M, Seelig A. How Phosphorylation and ATPase Activity Regulate Anion Flux though the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). J Biol Chem 2016; 291:14483-98. [PMID: 27226582 DOI: 10.1074/jbc.m116.721415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 01/25/2023] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR, ABCC7), mutations of which cause cystic fibrosis, belongs to the ATP-binding cassette (ABC) transporter family and works as a channel for small anions, such as chloride and bicarbonate. Anion channel activity is known to depend on phosphorylation by cAMP-dependent protein kinase A (PKA) and CFTR-ATPase activity. Whereas anion channel activity has been extensively investigated, phosphorylation and CFTR-ATPase activity are still poorly understood. Here, we show that the two processes can be measured in a label-free and non-invasive manner in real time in live cells, stably transfected with CFTR. This study reveals three key findings. (i) The major contribution (≥90%) to the total CFTR-related ATP hydrolysis rate is due to phosphorylation by PKA and the minor contribution (≤10%) to CFTR-ATPase activity. (ii) The mutant CFTR-E1371S that is still conductive, but defective in ATP hydrolysis, is not phosphorylated, suggesting that phosphorylation requires a functional nucleotide binding domain and occurs in the post-hydrolysis transition state. (iii) CFTR-ATPase activity is inversely related to CFTR anion flux. The present data are consistent with a model in which CFTR is in a closed conformation with two ATPs bound. The open conformation is induced by ATP hydrolysis and corresponds to the post-hydrolysis transition state that is stabilized by phosphorylation and binding of chloride channel potentiators.
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Affiliation(s)
- Matthias Zwick
- From the Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Cinzia Esposito
- From the Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Manuel Hellstern
- From the Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna Seelig
- From the Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
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19
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Pollock NL, Satriano L, Zegarra-Moran O, Ford RC, Moran O. Structure of wild type and mutant F508del CFTR: A small-angle X-ray scattering study of the protein–detergent complexes. J Struct Biol 2016; 194:102-11. [DOI: 10.1016/j.jsb.2016.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
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20
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Hall JD, Wang H, Byrnes LJ, Shanker S, Wang K, Efremov IV, Chong PA, Forman-Kay JD, Aulabaugh AE. Binding screen for cystic fibrosis transmembrane conductance regulator correctors finds new chemical matter and yields insights into cystic fibrosis therapeutic strategy. Protein Sci 2016; 25:360-73. [PMID: 26444971 DOI: 10.1002/pro.2821] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/01/2015] [Indexed: 11/08/2022]
Abstract
The most common mutation in cystic fibrosis (CF) patients is deletion of F508 (ΔF508) in the first nucleotide binding domain (NBD1) of the CF transmembrane conductance regulator (CFTR). ΔF508 causes a decrease in the trafficking of CFTR to the cell surface and reduces the thermal stability of isolated NBD1; it is well established that both of these effects can be rescued by additional revertant mutations in NBD1. The current paradigm in CF small molecule drug discovery is that, like revertant mutations, a path may exist to ΔF508 CFTR correction through a small molecule chaperone binding to NBD1. We, therefore, set out to find small molecule binders of NBD1 and test whether it is possible to develop these molecules into potent binders that increase CFTR trafficking in CF-patient-derived human bronchial epithelial cells. Several fragments were identified that bind NBD1 at either the CFFT-001 site or the BIA site. However, repeated attempts to improve the affinity of these fragments resulted in only modest gains. Although these results cannot prove that there is no possibility of finding a high-affinity small molecule binder of NBD1, they are discouraging and lead us to hypothesize that the nature of these two binding sites, and isolated NBD1 itself, may not contain the features needed to build high-affinity interactions. Future work in this area may, therefore, require constructs including other domains of CFTR in addition to NBD1, if high-affinity small molecule binding is to be achieved.
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Affiliation(s)
- Justin D Hall
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
| | - Hong Wang
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
| | - Laura J Byrnes
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
| | - Suman Shanker
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
| | - Kelong Wang
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
| | - Ivan V Efremov
- Worldwide Medicinal Chemistry, , Pfizer, Cambridge, Massachusetts, 02140
| | - P Andrew Chong
- Molecular Structure and Function Program, Hospital for Sick Kids, Toronto, Ontario, M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Julie D Forman-Kay
- Molecular Structure and Function Program, Hospital for Sick Kids, Toronto, Ontario, M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ann E Aulabaugh
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
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21
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Structural Changes Fundamental to Gating of the Cystic Fibrosis Transmembrane Conductance Regulator Anion Channel Pore. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 925:13-32. [PMID: 27311317 DOI: 10.1007/5584_2016_33] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an epithelial cell anion channel. Potentiator drugs used in the treatment of cystic fibrosis act on the channel to increase overall channel function, by increasing the stability of its open state and/or decreasing the stability of its closed state. The structure of the channel in either the open state or the closed state is not currently known. However, changes in the conformation of the protein as it transitions between these two states have been studied using functional investigation and molecular modeling techniques. This review summarizes our current understanding of the architecture of the transmembrane channel pore that controls the movement of chloride and other small anions, both in the open state and in the closed state. Evidence for different kinds of changes in the conformation of the pore as it transitions between open and closed states is described, as well as the mechanisms by which these conformational changes might be controlled to regulate normal channel gating. The ways that key conformational changes might be targeted by small compounds to influence overall CFTR activity are also discussed. Understanding the changes in pore structure that might be manipulated by such small compounds is key to the development of novel therapeutic strategies for the treatment of cystic fibrosis.
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22
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Rosenberg MF, Bikadi Z, Hazai E, Starborg T, Kelley L, Chayen NE, Ford RC, Mao Q. Three-dimensional structure of the human breast cancer resistance protein (BCRP/ABCG2) in an inward-facing conformation. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1725-35. [PMID: 26249353 PMCID: PMC4528803 DOI: 10.1107/s1399004715010676] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 06/02/2015] [Indexed: 11/10/2022]
Abstract
ABCG2 is an efflux drug transporter that plays an important role in drug resistance and drug disposition. In this study, the first three-dimensional structure of human full-length ABCG2 analysed by electron crystallography from two-dimensional crystals in the absence of nucleotides and transported substrates is reported at 2 nm resolution. In this state, ABCG2 forms a symmetric homodimer with a noncrystallographic twofold axis perpendicular to the two-dimensional crystal plane, as confirmed by subtomogram averaging. This configuration suggests an inward-facing configuration similar to murine ABCB1, with the nucleotide-binding domains (NBDs) widely separated from each other. In the three-dimensional map, densities representing the long cytoplasmic extensions from the transmembrane domains that connect the NBDs are clearly visible. The structural data have allowed the atomic model of ABCG2 to be refined, in which the two arms of the V-shaped ABCG2 homodimeric complex are in a more closed and narrower conformation. The structural data and the refined model of ABCG2 are compatible with the biochemical analysis of the previously published mutagenesis studies, providing novel insight into the structure and function of the transporter.
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Affiliation(s)
- Mark F. Rosenberg
- Faculty of Life Science, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, England
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, England
| | | | - Eszter Hazai
- Faculty of Life Science, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, England
| | - Tobias Starborg
- Faculty of Life Science, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, England
| | - Lawrence Kelley
- Centre for Bioinformatics, Division of Molecular Biosciences, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, England
| | - Naomi E. Chayen
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, England
| | - Robert C. Ford
- Faculty of Life Science, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, England
| | - Qingcheng Mao
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA 98195, USA
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23
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Micoud J, Chauvet S, Scheckenbach KEL, Alfaidy N, Chanson M, Benharouga M. Involvement of the heterodimeric interface region of the nucleotide binding domain-2 (NBD2) in the CFTR quaternary structure and membrane stability. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2420-31. [PMID: 26083625 DOI: 10.1016/j.bbamcr.2015.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 06/02/2015] [Accepted: 06/12/2015] [Indexed: 11/27/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is the only member of the ATP-binding cassette (ABC) superfamily that functions as a chloride channel. The predicted structure of CFTR protein contains two membrane-spanning domains (MSDs), each followed by a nucleotide binding domain (NBD1 and NBD2). The opening of the Cl- channel is directly linked to ATP-driven tight dimerization of CFTR's NBD1 and NBD2 domains. The presence of a heterodimeric interfaces (HI) region in NBD1 and NBD2 generated a head to tail orientation necessary for channel activity. This process was also suggested to promote important conformational changes in the associated transmembrane domains of CFTR, which may impact the CFTR plasma membrane stability. To better understand the role of the individual HI region in this process, we generated recombinant CFTR protein with suppressed HI-NBD1 and HI-NBD2. Our results indicate that HI-NBD2 deletion leads to the loss of the dimerization profile of CFTR that affect its plasma membrane stability. We conclude that, in addition to its role in Cl- transport, HI-NBD2 domain confers membrane stability of CFTR by consolidating its quaternary structure through interactions with HI-NBD1 region.
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Affiliation(s)
- Julien Micoud
- Centre National de la Recherche Scientifique (CNRS), LCBM-UMR 5249, Grenoble, France; Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France
| | - Sylvain Chauvet
- Centre National de la Recherche Scientifique (CNRS), LCBM-UMR 5249, Grenoble, France; Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France
| | | | - Nadia Alfaidy
- Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1036 Grenoble, France
| | - Marc Chanson
- Laboratory of Clinical Investigation III, Geneva University Hospitals and University of Geneva, 1211 Geneva, Switzerland
| | - Mohamed Benharouga
- Centre National de la Recherche Scientifique (CNRS), LCBM-UMR 5249, Grenoble, France; Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France.
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24
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El Hiani Y, Linsdell P. Functional Architecture of the Cytoplasmic Entrance to the Cystic Fibrosis Transmembrane Conductance Regulator Chloride Channel Pore. J Biol Chem 2015; 290:15855-15865. [PMID: 25944907 DOI: 10.1074/jbc.m115.656181] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 12/19/2022] Open
Abstract
As an ion channel, the cystic fibrosis transmembrane conductance regulator must form a continuous pathway for the movement of Cl(-) and other anions between the cytoplasm and the extracellular solution. Both the structure and the function of the membrane-spanning part of this pathway are well defined. In contrast, the structure of the pathway that connects the cytoplasm to the membrane-spanning regions is unknown, and functional roles for different parts of the protein forming this pathway have not been described. We used patch clamp recording and substituted cysteine accessibility mutagenesis to identify positively charged amino acid side chains that attract cytoplasmic Cl(-) ions to the inner mouth of the pore. Our results indicate that the side chains of Lys-190, Arg-248, Arg-303, Lys-370, Lys-1041, and Arg-1048, located in different intracellular loops of the protein, play important roles in the electrostatic attraction of Cl(-) ions. Mutation and covalent modification of these residues have charge-dependent effects on the rate of Cl(-) permeation, demonstrating their functional role in maximization of Cl(-) flux. Other nearby positively charged side chains were not involved in electrostatic interactions with Cl(-). The location of these Cl(-)-attractive residues suggests that cytoplasmic Cl(-) ions enter the pore via a lateral portal located between the cytoplasmic extensions to the fourth and sixth transmembrane helices; a secondary, functionally less relevant portal might exist between the extensions to the 10th and 12th transmembrane helices. These results define the cytoplasmic mouth of the pore and show how it attracts Cl(-) ions from the cytoplasm.
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Affiliation(s)
- Yassine El Hiani
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Paul Linsdell
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
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25
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Mornon JP, Hoffmann B, Jonic S, Lehn P, Callebaut I. Full-open and closed CFTR channels, with lateral tunnels from the cytoplasm and an alternative position of the F508 region, as revealed by molecular dynamics. Cell Mol Life Sci 2015; 72:1377-403. [PMID: 25287046 PMCID: PMC11113974 DOI: 10.1007/s00018-014-1749-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 09/28/2014] [Accepted: 09/29/2014] [Indexed: 12/17/2022]
Abstract
In absence of experimental 3D structures, several homology models, based on ABC exporter 3D structures, have provided significant insights into the molecular mechanisms underlying the function of the cystic fibrosis transmembrane conductance regulator (CFTR) protein, a chloride channel whose defects are associated with cystic fibrosis (CF). Until now, these models, however, did not furnished much insights into the continuous way that ions could follow from the cytosol to the extracellular milieu in the open form of the channel. Here, we have built a refined model of CFTR, based on the outward-facing Sav1866 experimental 3D structure and integrating the evolutionary and structural information available today. Molecular dynamics simulations revealed significant conformational changes, resulting in a full-open channel, accessible from the cytosol through lateral tunnels displayed in the long intracellular loops (ICLs). At the same time, the region of nucleotide-binding domain 1 in contact with one of the ICLs and carrying amino acid F508, the deletion of which is the most common CF-causing mutation, was found to adopt an alternative but stable position. Then, in a second step, this first stable full-open conformation evolved toward another stable state, in which only a limited displacement of the upper part of the transmembrane helices leads to a closure of the channel, in a conformation very close to that adopted by the Atm1 ABC exporter, in an inward-facing conformation. These models, supported by experimental data, provide significant new insights into the CFTR structure-function relationships and into the possible impact of CF-causing mutations.
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Affiliation(s)
- Jean-Paul Mornon
- IMPMC, Sorbonne Universités, UPMC Univ Paris 06, UMR CNRS 7590, Museum National d’Histoire Naturelle, IRD UMR 206, IUC, Case 115, 4 Place Jussieu, 75005 Paris Cedex 05, France
| | - Brice Hoffmann
- IMPMC, Sorbonne Universités, UPMC Univ Paris 06, UMR CNRS 7590, Museum National d’Histoire Naturelle, IRD UMR 206, IUC, Case 115, 4 Place Jussieu, 75005 Paris Cedex 05, France
| | - Slavica Jonic
- IMPMC, Sorbonne Universités, UPMC Univ Paris 06, UMR CNRS 7590, Museum National d’Histoire Naturelle, IRD UMR 206, IUC, Case 115, 4 Place Jussieu, 75005 Paris Cedex 05, France
| | - Pierre Lehn
- INSERM U1078, SFR ScInBioS, Université de Bretagne Occidentale, Brest, France
| | - Isabelle Callebaut
- IMPMC, Sorbonne Universités, UPMC Univ Paris 06, UMR CNRS 7590, Museum National d’Histoire Naturelle, IRD UMR 206, IUC, Case 115, 4 Place Jussieu, 75005 Paris Cedex 05, France
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26
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Baroni D, Zegarra-Moran O, Moran O. Functional and pharmacological induced structural changes of the cystic fibrosis transmembrane conductance regulator in the membrane solved using SAXS. Cell Mol Life Sci 2015; 72:1363-75. [PMID: 25274064 PMCID: PMC11113906 DOI: 10.1007/s00018-014-1747-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 09/18/2014] [Accepted: 09/26/2014] [Indexed: 01/13/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel is a membrane-integral protein that belongs to the ATP-binding cassette superfamily. Mutations in the CFTR gene cause cystic fibrosis in which salt, water, and protein transports are defective in various tissues. To investigate the conformation of the CFTR in the membrane, we applied the small-angle x-ray scattering (SAXS) technique on microsomal membranes extracted from NIH/3T3 cells permanentely transfected with wild-type (WT) CFTR and with CFTR carrying the ΔF508 mutation. The electronic density profile of the membranes was calculated from the SAXS data, assuming the lipid bilayer electronic density to be composed by a series of Gaussian shells. The data indicate that membranes in the microsome vesicles, that contain mostly endoplasmic reticulum membranes, are oriented in the outside-out conformation. Phosphorylation does not change significantly the electronic density profile, while dephosphorylation produces a significant modification in the inner side of the profile. Thus, we conclude that the CFTR and its associated protein complex in microsomes are mostly phosphorylated. The electronic density profile of the ΔF508-CFTR microsomes is completely different from WT, suggesting a different assemblage of the proteins in the membranes. Low-temperature treatment of cells rescues the ΔF508-CFTR protein, resulting in a conformation that resembles the WT. Differently, treatment with the corrector VX-809 modifies the electronic profile of ΔF508-CFTR membrane, but does not recover completely the WT conformation. To our knowledge, this is the first report of a direct physical measurement of the structure of membranes containing CFTR in its native environment and in different functional and pharmacological conditions.
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Affiliation(s)
- Debora Baroni
- Istituto di Biofisica, CNR, via De Marini, 6, 16149 Genoa, Italy
| | | | - Oscar Moran
- Istituto di Biofisica, CNR, via De Marini, 6, 16149 Genoa, Italy
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27
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Belmonte L, Moran O. On the interactions between nucleotide binding domains and membrane spanning domains in cystic fibrosis transmembrane regulator: A molecular dynamic study. Biochimie 2015; 111:19-29. [DOI: 10.1016/j.biochi.2015.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/21/2015] [Indexed: 12/20/2022]
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28
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Buck TM, Jordan R, Lyons-Weiler J, Adelman JL, Needham PG, Kleyman TR, Brodsky JL. Expression of three topologically distinct membrane proteins elicits unique stress response pathways in the yeast Saccharomyces cerevisiae. Physiol Genomics 2015; 47:198-214. [PMID: 25759377 DOI: 10.1152/physiolgenomics.00101.2014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 03/04/2015] [Indexed: 01/11/2023] Open
Abstract
Misfolded membrane proteins are retained in the endoplasmic reticulum (ER) and are subject to ER-associated degradation, which clears the secretory pathway of potentially toxic species. While the transcriptional response to environmental stressors has been extensively studied, limited data exist describing the cellular response to misfolded membrane proteins. To this end, we expressed and then compared the transcriptional profiles elicited by the synthesis of three ER retained, misfolded ion channels: The α-subunit of the epithelial sodium channel, ENaC, the cystic fibrosis transmembrane conductance regulator, CFTR, and an inwardly rectifying potassium channel, Kir2.1, which vary in their mass, membrane topologies, and quaternary structures. To examine transcriptional profiles in a null background, the proteins were expressed in yeast, which was previously used to examine the degradation requirements for each substrate. Surprisingly, the proteins failed to induce a canonical unfolded protein response or heat shock response, although messages encoding several cytosolic and ER lumenal protein folding factors rose when αENaC or CFTR was expressed. In contrast, the levels of these genes were unaltered by Kir2.1 expression; instead, the yeast iron regulon was activated. Nevertheless, a significant number of genes that respond to various environmental stressors were upregulated by all three substrates, and compared with previous microarray data we deduced the existence of a group of genes that reflect a novel misfolded membrane protein response. These data indicate that aberrant proteins in the ER elicit profound yet unique cellular responses.
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Affiliation(s)
- Teresa M Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rick Jordan
- GPCL Bioinformatics Analysis Core, University of Pittsburgh, Pittsburgh, Pennsylvania; and
| | - James Lyons-Weiler
- GPCL Bioinformatics Analysis Core, University of Pittsburgh, Pittsburgh, Pennsylvania; and
| | - Joshua L Adelman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Patrick G Needham
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Thomas R Kleyman
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania;
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29
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Al-Zahrani A, Cant N, Kargas V, Rimington T, Aleksandrov L, R. Riordan J, C. Ford R. Structure of the cystic fibrosis transmembrane conductance regulator in the inward-facing conformation revealed by single particle electron microscopy. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.2.131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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30
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Qian F, Li T, Yang F, Liu L. Stoichiometry and novel gating mechanism within the cystic fibrosis transmembrane conductance regulator channel. Exp Physiol 2014; 99:1611-23. [DOI: 10.1113/expphysiol.2014.081034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Feng Qian
- Department of Medical Function; School of Medicine; Yangtze University; Jingzhou Hubei Province 434023 China
| | - Tao Li
- Department of Biology; College of Chemistry and Life Sciences; Zhejiang Normal University; Jinhua Zhejiang Province 321004 China
| | - Fei Yang
- Department of Medical Function; School of Medicine; Yangtze University; Jingzhou Hubei Province 434023 China
| | - Lian Liu
- Department of Medical Function; School of Medicine; Yangtze University; Jingzhou Hubei Province 434023 China
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31
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LaRusch J, Jung J, General IJ, Lewis MD, Park HW, Brand RE, Gelrud A, Anderson MA, Banks PA, Conwell D, Lawrence C, Romagnuolo J, Baillie J, Alkaade S, Cote G, Gardner TB, Amann ST, Slivka A, Sandhu B, Aloe A, Kienholz ML, Yadav D, Barmada MM, Bahar I, Lee MG, Whitcomb DC. Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis. PLoS Genet 2014; 10:e1004376. [PMID: 25033378 PMCID: PMC4102440 DOI: 10.1371/journal.pgen.1004376] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 03/10/2014] [Indexed: 02/07/2023] Open
Abstract
CFTR is a dynamically regulated anion channel. Intracellular WNK1-SPAK activation causes CFTR to change permeability and conductance characteristics from a chloride-preferring to bicarbonate-preferring channel through unknown mechanisms. Two severe CFTR mutations (CFTRsev) cause complete loss of CFTR function and result in cystic fibrosis (CF), a severe genetic disorder affecting sweat glands, nasal sinuses, lungs, pancreas, liver, intestines, and male reproductive system. We hypothesize that those CFTR mutations that disrupt the WNK1-SPAK activation mechanisms cause a selective, bicarbonate defect in channel function (CFTRBD) affecting organs that utilize CFTR for bicarbonate secretion (e.g. the pancreas, nasal sinus, vas deferens) but do not cause typical CF. To understand the structural and functional requirements of the CFTR bicarbonate-preferring channel, we (a) screened 984 well-phenotyped pancreatitis cases for candidate CFTRBD mutations from among 81 previously described CFTR variants; (b) conducted electrophysiology studies on clones of variants found in pancreatitis but not CF; (c) computationally constructed a new, complete structural model of CFTR for molecular dynamics simulation of wild-type and mutant variants; and (d) tested the newly defined CFTRBD variants for disease in non-pancreas organs utilizing CFTR for bicarbonate secretion. Nine variants (CFTR R74Q, R75Q, R117H, R170H, L967S, L997F, D1152H, S1235R, and D1270N) not associated with typical CF were associated with pancreatitis (OR 1.5, p = 0.002). Clones expressed in HEK 293T cells had normal chloride but not bicarbonate permeability and conductance with WNK1-SPAK activation. Molecular dynamics simulations suggest physical restriction of the CFTR channel and altered dynamic channel regulation. Comparing pancreatitis patients and controls, CFTRBD increased risk for rhinosinusitis (OR 2.3, p<0.005) and male infertility (OR 395, p<<0.0001). WNK1-SPAK pathway-activated increases in CFTR bicarbonate permeability are altered by CFTRBD variants through multiple mechanisms. CFTRBD variants are associated with clinically significant disorders of the pancreas, sinuses, and male reproductive system.
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Affiliation(s)
- Jessica LaRusch
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jinsei Jung
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Ignacio J. General
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michele D. Lewis
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Hyun Woo Park
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Randall E. Brand
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Andres Gelrud
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michelle A. Anderson
- Department of Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Peter A. Banks
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Darwin Conwell
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Christopher Lawrence
- Digestive Disease Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Joseph Romagnuolo
- Digestive Disease Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - John Baillie
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Samer Alkaade
- Department of Internal Medicine, St. Louis University School of Medicine, St Louis, Missouri, United States of America
| | - Gregory Cote
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Timothy B. Gardner
- Dartmouth-Hitchcock Medical Center, Hanover, New Hampshire, United States of America
| | - Stephen T. Amann
- North Mississippi Medical Center, Tupelo, Mississippi, United States of America
| | - Adam Slivka
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bimaljit Sandhu
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Medical Center, Richmond, Virginia, United States of America
| | - Amy Aloe
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michelle L. Kienholz
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Dhiraj Yadav
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - M. Michael Barmada
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ivet Bahar
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Min Goo Lee
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - David C. Whitcomb
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Cell Biology and Molecular Physiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Molecular modelling approaches for cystic fibrosis transmembrane conductance regulator studies. Int J Biochem Cell Biol 2014; 52:39-46. [DOI: 10.1016/j.biocel.2014.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/01/2014] [Accepted: 04/04/2014] [Indexed: 12/30/2022]
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Wei S, Roessler BC, Chauvet S, Guo J, Hartman JL, Kirk KL. Conserved allosteric hot spots in the transmembrane domains of cystic fibrosis transmembrane conductance regulator (CFTR) channels and multidrug resistance protein (MRP) pumps. J Biol Chem 2014; 289:19942-57. [PMID: 24876383 DOI: 10.1074/jbc.m114.562116] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
ATP-binding cassette (ABC) transporters are an ancient family of transmembrane proteins that utilize ATPase activity to move substrates across cell membranes. The ABCC subfamily of the ABC transporters includes active drug exporters (the multidrug resistance proteins (MRPs)) and a unique ATP-gated ion channel (cystic fibrosis transmembrane conductance regulator (CFTR)). The CFTR channel shares gating principles with conventional ligand-gated ion channels, but the allosteric network that couples ATP binding at its nucleotide binding domains (NBDs) with conformational changes in its transmembrane helices (TMs) is poorly defined. It is also unclear whether the mechanisms that govern CFTR gating are conserved with the thermodynamically distinct MRPs. Here we report a new class of gain of function (GOF) mutation of a conserved proline at the base of the pore-lining TM6. Multiple substitutions of this proline promoted ATP-free CFTR activity and activation by the weak agonist, 5'-adenylyl-β,γ-imidodiphosphate (AMP-PNP). TM6 proline mutations exhibited additive GOF effects when combined with a previously reported GOF mutation located in an outer collar of TMs that surrounds the pore-lining TMs. Each TM substitution allosterically rescued the ATP sensitivity of CFTR gating when introduced into an NBD mutant with defective ATP binding. Both classes of GOF mutations also rescued defective drug export by a yeast MRP (Yor1p) with ATP binding defects in its NBDs. We conclude that the conserved TM6 proline helps set the energy barrier to both CFTR channel opening and MRP-mediated drug efflux and that CFTR channels and MRP pumps utilize similar allosteric mechanisms for coupling conformational changes in their translocation pathways to ATP binding at their NBDs.
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Affiliation(s)
- Shipeng Wei
- From the Departments of Cell, Developmental, and Integrative Biology
| | - Bryan C Roessler
- From the Departments of Cell, Developmental, and Integrative Biology
| | - Sylvain Chauvet
- From the Departments of Cell, Developmental, and Integrative Biology
| | | | | | - Kevin L Kirk
- From the Departments of Cell, Developmental, and Integrative Biology, Neurobiology and the Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham Alabama 35294-0005
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Linsdell P. Cystic fibrosis transmembrane conductance regulator chloride channel blockers: Pharmacological, biophysical and physiological relevance. World J Biol Chem 2014; 5:26-39. [PMID: 24600512 PMCID: PMC3942540 DOI: 10.4331/wjbc.v5.i1.26] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/15/2013] [Accepted: 12/11/2013] [Indexed: 02/05/2023] Open
Abstract
Dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel causes cystic fibrosis, while inappropriate activity of this channel occurs in secretory diarrhea and polycystic kidney disease. Drugs that interact directly with CFTR are therefore of interest in the treatment of a number of disease states. This review focuses on one class of small molecules that interacts directly with CFTR, namely inhibitors that act by directly blocking chloride movement through the open channel pore. In theory such compounds could be of use in the treatment of diarrhea and polycystic kidney disease, however in practice all known substances acting by this mechanism to inhibit CFTR function lack either the potency or specificity for in vivo use. Nevertheless, this theoretical pharmacological usefulness set the scene for the development of more potent, specific CFTR inhibitors. Biophysically, open channel blockers have proven most useful as experimental probes of the structure and function of the CFTR chloride channel pore. Most importantly, the use of these blockers has been fundamental in developing a functional model of the pore that includes a wide inner vestibule that uses positively charged amino acid side chains to attract both permeant and blocking anions from the cell cytoplasm. CFTR channels are also subject to this kind of blocking action by endogenous anions present in the cell cytoplasm, and recently this blocking effect has been suggested to play a role in the physiological control of CFTR channel function, in particular as a novel mechanism linking CFTR function dynamically to the composition of epithelial cell secretions. It has also been suggested that future drugs could target this same pathway as a way of pharmacologically increasing CFTR activity in cystic fibrosis. Studying open channel blockers and their mechanisms of action has resulted in significant advances in our understanding of CFTR as a pharmacological target in disease states, of CFTR channel structure and function, and of how CFTR activity is controlled by its local environment.
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CFTR structure and cystic fibrosis. Int J Biochem Cell Biol 2014; 52:15-25. [PMID: 24534272 DOI: 10.1016/j.biocel.2014.02.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/04/2014] [Accepted: 02/06/2014] [Indexed: 12/31/2022]
Abstract
CFTR (cystic fibrosis transmembrane conductance regulator) is a member of the ATP-binding cassette family of membrane proteins. Although almost all members of this family are transporters, CFTR functions as a channel with specificity for anions, in particular chloride and bicarbonate. In this review we look at what is known about CFTR structure and function within the context of the ATP-binding cassette family. We also review current strategies aimed at obtaining the high resolution structure of the protein.
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On the structural organization of the intracellular domains of CFTR. Int J Biochem Cell Biol 2014; 52:7-14. [PMID: 24513531 DOI: 10.1016/j.biocel.2014.01.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/17/2014] [Accepted: 01/21/2014] [Indexed: 12/17/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a multidomain membrane protein forming an anion selective channel. Mutations in the gene encoding CFTR cause cystic fibrosis (CF). The intracellular side of CFTR constitutes about 80% of the total mass of the protein. This region includes domains involved in ATP-dependent gating and regulatory protein kinase-A phosphorylation sites. The high-resolution molecular structure of CFTR has not yet been solved. However, a range of lower resolution structural data, as well as functional biochemical and electrophysiological data, are now available. This information has enabled the proposition of a working model for the structural architecture of the intracellular domains of the CFTR protein.
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37
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Nakai T, Deguchi T, Frébort I, Tanizawa K, Okajima T. Identification of genes essential for the biogenesis of quinohemoprotein amine dehydrogenase. Biochemistry 2014; 53:895-907. [PMID: 24437536 DOI: 10.1021/bi401625m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural genes encoding quinohemoprotein amine dehydrogenase (QHNDH) in Gram-negative bacteria constitute a polycistronic operon together with several nearby genes, which are collectively termed "qhp". We previously showed that the qhpD gene, which lies between qhpA and qhpC (encoding the α and γ subunits of QHNDH, respectively), and the qhpE gene, which follows qhpB (encoding the β subunit), both encode enzymes specifically involved in the posttranslational modification of the γ subunit and are hence essential for QHNDH biogenesis in Paracoccus denitrificans [Ono, K., et al. (2006) J. Biol. Chem. 281, 13672-13684; Nakai, T., et al. (2012) J. Biol. Chem. 287, 6530-6538]. Here we further demonstrate that the qhpF gene, which follows qhpE, and the qhpG and qhpR genes, peripherally located in the complementary strand, are also indispensable for QHNDH biogenesis. The qhpF gene encodes an efflux ABC transporter, which probably translocates the γ subunit into the periplasm in a process coupled with hydrolysis of ATP. The qhpG gene encodes a putative FAD-dependent monooxygenase, which is required for the generation of the quinone cofactor in the γ subunit. Finally, the qhpR gene encodes an AraC family transcriptional regulator, which activates expression of the qhp operon in response to the addition of n-butylamine to the culture medium. Database analysis of the qhp genes reveals that they are very widely distributed, not only in many Gram-negative species but also in a few Gram-positive bacteria.
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Affiliation(s)
- Tadashi Nakai
- Department of Structural Molecular Biology, Institute of Scientific and Industrial Research, Osaka University , Ibaraki, Osaka 567-0047, Japan
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38
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L. Pollock N, Moran O, Baroni D, Zegarra-Moran O, C. Ford R. Characterisation of the salmon cystic fibrosis transmembrane conductance regulator protein for structural studies. AIMS MOLECULAR SCIENCE 2014. [DOI: 10.3934/molsci.2014.4.141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), a member of the ATP-binding cassette (ABC) family of membrane transport proteins. CFTR is unique among ABC proteins in that it functions not as an active transporter but as an ATP-gated Cl(-) channel. As an ion channel, the function of the CFTR transmembrane channel pore that mediates Cl(-) movement has been studied in great detail. On the other hand, only low resolution structural data is available on the transmembrane parts of the protein. The structure of the channel pore has, however, been modeled on the known structure of active transporter ABC proteins. Currently, significant barriers exist to building a unified view of CFTR pore structure and function. Reconciling functional data on the channel with indirect structural data based on other proteins with very different transport functions and substrates has proven problematic. This review summarizes current structural and functional models of the CFTR Cl(-) channel pore, including a comprehensive review of previous electrophysiological investigations of channel structure and function. In addition, functional data on the three-dimensional arrangement of pore-lining helices, as well as contemporary hypotheses concerning conformational changes in the pore that occur during channel opening and closing, are discussed. Important similarities and differences between different models of the pore highlight current gaps in our knowledge of CFTR structure and function. In order to fill these gaps, structural and functional models of the membrane-spanning pore need to become better integrated.
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Affiliation(s)
- Paul Linsdell
- Department of Physiology & Biophysics, Dalhousie University , Halifax, Nova Scotia , Canada
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40
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Verkman AS, Synder D, Tradtrantip L, Thiagarajah JR, Anderson MO. CFTR inhibitors. Curr Pharm Des 2013; 19:3529-41. [PMID: 23331030 DOI: 10.2174/13816128113199990321] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 01/16/2013] [Indexed: 12/16/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a cAMP-regulated Cl- channel whose major function is to facilitate epithelial fluid secretion. Loss-of-function mutations in CFTR cause the genetic disease cystic fibrosis. CFTR is required for transepithelial fluid transport in certain secretory diarrheas, such as cholera, and for cyst expansion in autosomal dominant polycystic kidney disease. High-throughput screening has yielded CFTR inhibitors of the thiazolidinone, glycine hydrazide and quinoxalinedione chemical classes. The glycine hydrazides target the extracellular CFTR pore, whereas the thiazolidinones and quinoxalinediones act at the cytoplasmic surface. These inhibitors have been widely used in cystic fibrosis research to study CFTR function at the cell and organ levels. The most potent CFTR inhibitor has IC50 of approximately 4 nM. Studies in animal models support the development of CFTR inhibitors for antisecretory therapy of enterotoxin-mediated diarrheas and polycystic kidney disease.
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Affiliation(s)
- Alan S Verkman
- University of California-San Francisco, CA 94143-0521, U.S.A.
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41
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Regulatory R region of the CFTR chloride channel is a dynamic integrator of phospho-dependent intra- and intermolecular interactions. Proc Natl Acad Sci U S A 2013; 110:E4427-36. [PMID: 24191035 DOI: 10.1073/pnas.1315104110] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Intrinsically disordered proteins play crucial roles in regulatory processes and often function as protein interaction hubs. Here, we present a detailed characterization of a full-length disordered hub protein region involved in multiple dynamic complexes. We performed NMR, CD, and fluorescence binding studies on the nonphosphorylated and highly PKA-phosphorylated human cystic fibrosis transmembrane conductance regulator (CFTR) regulatory region, a ∼200-residue disordered segment involved in phosphorylation-dependent regulation of channel trafficking and gating. Our data provide evidence for dynamic, phosphorylation-dependent, multisite interactions of various segments of the regulatory region for its intra- and intermolecular partners, including the CFTR nucleotide binding domains 1 and 2, a 42-residue peptide from the C terminus of CFTR, the SLC26A3 sulphate transporter and antisigma factor antagonist (STAS) domain, and 14-3-3β. Because of its large number of binding partners, multivalent binding of individually weak sites facilitates rapid exchange between free and bound states to allow the regulatory region to engage with different partners and generate a graded or rheostat-like response to phosphorylation. Our results enrich the understanding of how disordered binding segments interact with multiple targets. We present structural models consistent with our data that illustrate this dynamic aspect of phospho-regulation of CFTR by the disordered regulatory region.
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Rahman KS, Cui G, Harvey SC, McCarty NA. Modeling the conformational changes underlying channel opening in CFTR. PLoS One 2013; 8:e74574. [PMID: 24086355 PMCID: PMC3785483 DOI: 10.1371/journal.pone.0074574] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 08/05/2013] [Indexed: 12/22/2022] Open
Abstract
Mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator protein (CFTR) cause cystic fibrosis (CF), the most common life-shortening genetic disease among Caucasians. Although general features of the structure of CFTR have been predicted from homology models, the conformational changes that result in channel opening and closing have yet to be resolved. We created new closed- and open-state homology models of CFTR, and performed targeted molecular dynamics simulations of the conformational transitions in a channel opening event. The simulations predict a conformational wave that starts at the nucleotide binding domains and ends with the formation of an open conduction pathway. Changes in side-chain interactions are observed in all major domains of the protein, and experimental confirmation was obtained for a novel intra-protein salt bridge that breaks near the end of the transition. The models and simulation add to our understanding of the mechanism of ATP-dependent gating in this disease-relevant ion channel.
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Affiliation(s)
- Kazi S. Rahman
- Petit Institute of Bioengineering and Bioscience and School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Guiying Cui
- Department of Pediatrics and Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Inc., Atlanta, Georgia, United States of America
| | - Stephen C. Harvey
- Petit Institute of Bioengineering and Bioscience and School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Nael A. McCarty
- Department of Pediatrics and Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Inc., Atlanta, Georgia, United States of America
- * E-mail:
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Abstract
SbmA protein has been proposed as a dimeric secondary transporter. The protein is involved in the transport of microcins B17 and J25, bleomycin, proline-rich antimicrobial peptides, antisense peptide phosphorodiamidate morpholino oligomers, and peptide nucleic acids into the Escherichia coli cytoplasm. The sbmA homologue is found in a variety of bacteria, though the physiological role of the protein is hitherto unknown. In this work, we carried out a functional and structural analysis to determine which amino acids are critical for the transport properties of SbmA. We created a set of 15 site-directed sbmA mutants in which single conserved amino acids were replaced by glycine residues. Our work demonstrated that strains carrying the site-directed mutants V102G, F219G, and E276G had a null phenotype for SbmA transport functions. In contrast, strains carrying the single point mutants W19G, W53G, F60G, S69G, N155G, R190, L233G, A344G, T255G, N308G, and R385G showed transport capacities indistinguishable from those of strains harboring a wild-type sbmA. The strain carrying the Y116G mutant exhibited mixed phenotypic characteristics. We also demonstrated that those sbmA mutants with severely impaired transport capacity showed a dominant negative phenotype. Electron microscopy data and in silico three-dimensional (3D) homology modeling support the idea that SbmA forms a homodimeric complex, closely resembling the membrane-spanning region of the ATP-binding cassette transporter family. Direct mapping of the sbmA single point mutants on the protein surface allowed us to explain the observed phenotypic differences in transport ability.
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44
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Wang W, El Hiani Y, Rubaiy HN, Linsdell P. Relative contribution of different transmembrane segments to the CFTR chloride channel pore. Pflugers Arch 2013; 466:477-90. [PMID: 23955087 DOI: 10.1007/s00424-013-1317-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/18/2013] [Accepted: 06/18/2013] [Indexed: 12/16/2022]
Abstract
The membrane-spanning part of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl(-) channel comprises 12 transmembrane (TM) α-helices, arranged in 2 symmetrical groups of 6. However, those TMs that line the channel pore are not completely defined. We used patch clamp recording to compare the accessibility of cysteine-reactive reagents to cysteines introduced into different TMs. Several residues in TM11 were accessible to extracellular and/or intracellular cysteine reactive reagents; however, no reactive cysteines were identified in TMs 5 or 11. Two accessible residues in TM11 (T1115C and S1118C) were found to be more readily modified from the extracellular solution in closed channels, but more readily modified from the intracellular solution in open channels, as previously reported for T338C in TM6. However, the effects of mutagenesis at S1118 (TM11) on a range of pore functional properties were relatively minor compared to the large effects of mutagenesis at T338 (TM6). Our results suggest that the CFTR pore is lined by TM11 but not by TM5 or TM7. Comparison with previous works therefore suggests that the pore is lined by TMs 1, 6, 11, and 12, suggesting that the structure of the open channel pore is asymmetric in terms of the contributions of different TMs. Although TMs 6 and 11 appear to undergo similar conformational changes during channel opening and closing, the influence of these two TMs on the functional properties of the narrowest region of the pore is clearly unequal.
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Affiliation(s)
- Wuyang Wang
- Department of Physiology and Biophysics, Dalhousie University, PO Box 15000 Halifax, Nova Scotia, B3H 4R2, Canada
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45
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Cheepala SB, Bao J, Nachagari D, Sun D, Wang Y, Zhong TP, Zhong T, Naren AP, Zheng J, Schuetz JD. Crucial role for phylogenetically conserved cytoplasmic loop 3 in ABCC4 protein expression. J Biol Chem 2013; 288:22207-18. [PMID: 23766510 DOI: 10.1074/jbc.m113.476218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The ABC transporter ABCC4 is recognized as an ATP-dependent exporter of endogenous substances as well as an increasing variety of anionic chemotherapeutics. A loss-of-function variant of zebrafish Abcc4 was identified with a single amino acid substitution in the cytoplasmic loop T804M. Because this substituted amino acid is highly conserved among ABCC4 orthologs and is located in cytoplasmic loop 3 (CL3), we investigated the impact of this mutation on human and zebrafish Abcc4 expression. We demonstrate that zebrafish Abcc4 T804M or human ABCC4 T796M exhibit substantially reduced expression, coupled with impaired plasma membrane localization. To understand the molecular basis for the localization defect, we developed a homology model of zebrafish Abcc4. The homology model suggested that the bulky methionine substitution disrupted side-chain contacts. Molecular dynamic simulations of a fragment of human or zebrafish CL3 containing a methionine substitution indicated altered helicity coupled with reduced thermal stability. Trifluoroethanol challenge coupled with circular dichroism revealed that the methionine substitution disrupted the ability of this fragment of CL3 to readily form an α-helix. Furthermore, expression and plasma membrane localization of these mutant ABCC4/Abcc4 proteins are mostly rescued by growing cells at subphysiological temperatures. Because the cystic fibrosis transmembrane conductance regulator (ABCC7) is closely related to ABCC4, we extended this by engineering certain pathogenic CFTR-CL3 mutations, and we showed they destabilized human and zebrafish ABCC4. Altogether, our studies provide the first evidence for a conserved domain in CL3 of ABCC4 that is crucial in ensuring its proper plasma membrane localization.
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Affiliation(s)
- Satish B Cheepala
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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46
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Hunt JF, Wang C, Ford RC. Cystic fibrosis transmembrane conductance regulator (ABCC7) structure. Cold Spring Harb Perspect Med 2013; 3:a009514. [PMID: 23378596 DOI: 10.1101/cshperspect.a009514] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Structural studies of the cystic fibrosis transmembrane conductance regulator (CFTR) are reviewed. Like many membrane proteins, full-length CFTR has proven to be difficult to express and purify, hence much of the structural data available is for the more tractable, independently expressed soluble domains. Therefore, this chapter covers structural data for individual CFTR domains in addition to the sparser data available for the full-length protein. To set the context for these studies, we will start by reviewing structural information on model proteins from the ATP-binding cassette (ABC) transporter superfamily, to which CFTR belongs.
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Affiliation(s)
- John F Hunt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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Akin Y, Demir D, Görgişen G, Lüleci G, Alper OM, Watanabe CS, Sahiner IF, Usta MF. Novel and rare CFTR gene mutations in Turkish patients with congenital aplasia of vas deferens. Andrologia 2012; 46:198-9. [PMID: 23240968 DOI: 10.1111/and.12053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Y Akin
- Department of Urology, Erzincan University School of Medicine, Erzincan, Turkey.
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Modzel M, Stefanowicz P, Szewczuk Z. Hydrogen scrambling in non-covalent complexes of peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:2739-2744. [PMID: 23124664 DOI: 10.1002/rcm.6396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE Mass spectrometry analysis combined with hydrogen-deuterium exchange (HDX-MS) is arising as a tool for quick analysis of native protein conformation. However, during collision-induced dissociation (CID) the spatial distribution of deuterium is not always conserved. It is therefore important to find out how hydrogen scrambling occurs--this study concentrates on the possibility of scrambling between amino acid residues spatially close together, but not connected by covalent bonds. METHODS Peptides used in this study were synthesized by Fmoc strategy. Deuteration occurred in ammonia formate solution in D(2)O. Non-covalent complexes consisting of a deuterated and a non-deuterated peptide were analyzed by electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FT-ICR-MS) with quadrupole mass filter. Low-energy CID was used for complex dissociation. RESULTS The complexes were isolated on a quadrupole and subjected to CID to cause dissociation. The deuterium distribution before and after the dissociation of a non-covalent complex to its components was measured. The study revealed that no significant scrambling occurred between the constituents of the complexes--the degree of scrambling did not exceed 10%. CONCLUSIONS The results obtained for the complexes should be similar to those for protein parts spatially close together--hydrogen scrambling between them should be negligible. The knowledge that almost all the scrambling occurs along peptide chains gives a better insight into the mechanism of HDX inside a protein.
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Affiliation(s)
- Maciej Modzel
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, Wroclaw, Poland
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Robertson JWF, Kasianowicz JJ, Banerjee S. Analytical Approaches for Studying Transporters, Channels and Porins. Chem Rev 2012; 112:6227-49. [DOI: 10.1021/cr300317z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph W. F. Robertson
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - John J. Kasianowicz
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - Soojay Banerjee
- National
Institute of Neurological
Disorders and Stroke, Bethesda, Maryland 20824, United States
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Pedemonte N, Galietta LJV. Pharmacological Correctors of Mutant CFTR Mistrafficking. Front Pharmacol 2012; 3:175. [PMID: 23060795 PMCID: PMC3464431 DOI: 10.3389/fphar.2012.00175] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/14/2012] [Indexed: 12/31/2022] Open
Abstract
The lack of phenylalanine 508 (ΔF508 mutation) in the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) Cl− channel represents the most frequent cause of CF, a genetic disease affecting multiple organs such as lung, pancreas, and liver. ΔF508 causes instability and misfolding of CFTR protein leading to early degradation in the endoplasmic reticulum and accelerated removal from the plasma membrane. Pharmacological correctors of mutant CFTR protein have been identified by high-throughput screening of large chemical libraries, by in silico docking of virtual compounds on CFTR structure models, or by using compounds that affect the whole proteome (e.g., histone deacetylase inhibitors) or a single CFTR-interacting protein. The presence of multiple defects of the CFTR protein caused by the ΔF508 mutation and the redundancy of quality control mechanisms detecting ΔF508-CFTR as a defective protein impose a ceiling to the maximal effect that a single compound (corrector) may obtain. Therefore, treatment of patients with the most frequent CF mutation may require the optimized combination of two drugs having additive or synergic effects.
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