1
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van der Sluijs P, Hoelen H, Schmidt A, Braakman I. The Folding Pathway of ABC Transporter CFTR: Effective and Robust. J Mol Biol 2024; 436:168591. [PMID: 38677493 DOI: 10.1016/j.jmb.2024.168591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024]
Abstract
De novo protein folding into a native three-dimensional structure is indispensable for biological function, is instructed by its amino acid sequence, and occurs along a vectorial trajectory. The human proteome contains thousands of membrane-spanning proteins, whose biosynthesis begins on endoplasmic reticulum-associated ribosomes. Nearly half of all membrane proteins traverse the membrane more than once, including therapeutically important protein families such as solute carriers, G-protein-coupled receptors, and ABC transporters. These mediate a variety of functions like signal transduction and solute transport and are often of vital importance for cell function and tissue homeostasis. Missense mutations in multispan membrane proteins can lead to misfolding and cause disease; an example is the ABC transporter Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). Even though our understanding of multispan membrane-protein folding still is rather rudimental, the cumulative knowledge of 20 years of basic research on CFTR folding has led to development of drugs that modulate the misfolded protein. This has provided the prospect of a life without CF to the vast majority of patients. In this review we describe our understanding of the folding pathway of CFTR in cells, which is modular and tolerates many defects, making it effective and robust. We address how modulator drugs affect folding and function of CFTR, and distinguish protein stability from its folding process. Since the domain architecture of (mammalian) ABC transporters are highly conserved, we anticipate that the insights we discuss here for folding of CFTR may lay the groundwork for understanding the general rules of ABC-transporter folding.
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Affiliation(s)
- Peter van der Sluijs
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
| | - Hanneke Hoelen
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; Present address: GenDx, Yalelaan 48, 3584 CM Utrecht, The Netherlands
| | - Andre Schmidt
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; 3D-Pharmxchange, Tilburg, the Netherlands
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
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2
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Soya N, Xu H, Roldan A, Yang Z, Ye H, Jiang F, Premchandar A, Veit G, Cole SPC, Kappes J, Hegedüs T, Lukacs GL. Folding correctors can restore CFTR posttranslational folding landscape by allosteric domain-domain coupling. Nat Commun 2023; 14:6868. [PMID: 37891162 PMCID: PMC10611759 DOI: 10.1038/s41467-023-42586-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The folding/misfolding and pharmacological rescue of multidomain ATP-binding cassette (ABC) C-subfamily transporters, essential for organismal health, remain incompletely understood. The ABCC transporters core consists of two nucleotide binding domains (NBD1,2) and transmembrane domains (TMD1,2). Using molecular dynamic simulations, biochemical and hydrogen deuterium exchange approaches, we show that the mutational uncoupling or stabilization of NBD1-TMD1/2 interfaces can compromise or facilitate the CFTR(ABCC7)-, MRP1(ABCC1)-, and ABCC6-transporters posttranslational coupled domain-folding in the endoplasmic reticulum. Allosteric or orthosteric binding of VX-809 and/or VX-445 folding correctors to TMD1/2 can rescue kinetically trapped CFTR posttranslational folding intermediates of cystic fibrosis (CF) mutants of NBD1 or TMD1 by global rewiring inter-domain allosteric-networks. We propose that dynamic allosteric domain-domain communications not only regulate ABCC-transporters function but are indispensable to tune the folding landscape of their posttranslational intermediates. These allosteric networks can be compromised by CF-mutations, and reinstated by correctors, offering a framework for mechanistic understanding of ABCC-transporters (mis)folding.
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Affiliation(s)
- Naoto Soya
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Haijin Xu
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Ariel Roldan
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Zhengrong Yang
- Heersink School of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Haoxin Ye
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Fan Jiang
- Heersink School of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Aiswarya Premchandar
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Guido Veit
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Susan P C Cole
- Division of Cancer Biology and Genetics, Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Kingston, ON, Canada
| | - John Kappes
- Heersink School of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Tamás Hegedüs
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085, Budapest, Hungary
- ELKH-SE Biophysical Virology Research Group, Eötvös Loránd Research Network, Budapest, Hungary
| | - Gergely L Lukacs
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada.
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3
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Soya N, Xu H, Roldan A, Yang Z, Ye H, Jiang F, Premchandar A, Veit G, Cole SPC, Kappes J, Hegedus T, Lukacs GL. Folding correctors can restore CFTR posttranslational folding landscape by allosteric domain-domain coupling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563107. [PMID: 37905074 PMCID: PMC10614980 DOI: 10.1101/2023.10.19.563107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The folding/misfolding and pharmacological rescue of multidomain ATP-binding cassette (ABC) C-subfamily transporters, essential for organismal health, remain incompletely understood. The ABCC transporters core consists of two nucleotide binding domains (NBD1,2) and transmembrane domains (TMD1,2). Using molecular dynamic simulations, biochemical and hydrogen deuterium exchange approaches, we show that the mutational uncoupling or stabilization of NBD1-TMD1/2 interfaces can compromise or facilitate the CFTR(ABCC7)-, MRP1(ABCC1)-, and ABCC6-transporters posttranslational coupled domain-folding in the endoplasmic reticulum. Allosteric or orthosteric binding of VX-809 and/or VX-445 folding correctors to TMD1/2 can rescue kinetically trapped CFTR post-translational folding intermediates of cystic fibrosis (CF) mutants of NBD1 or TMD1 by global rewiring inter-domain allosteric-networks. We propose that dynamic allosteric domain-domain communications not only regulate ABCC-transporters function but are indispensable to tune the folding landscape of their post-translational intermediates. These allosteric networks can be compromised by CF-mutations, and reinstated by correctors, offering a framework for mechanistic understanding of ABCC-transporters (mis)folding. One-Sentence Summary Allosteric interdomain communication and its modulation are critical determinants of ABCC-transporters post-translational conformational biogenesis, misfolding, and pharmacological rescue.
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4
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McDonald EF, Meiler J, Plate L. CFTR Folding: From Structure and Proteostasis to Cystic Fibrosis Personalized Medicine. ACS Chem Biol 2023; 18:2128-2143. [PMID: 37730207 PMCID: PMC10595991 DOI: 10.1021/acschembio.3c00310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/02/2023] [Indexed: 09/22/2023]
Abstract
Cystic fibrosis (CF) is a lethal genetic disease caused by mutations in the chloride ion channel cystic fibrosis transmembrane conductance regulator (CFTR). Class-II mutants of CFTR lack intermolecular interactions important for CFTR structural stability and lead to misfolding. Misfolded CFTR is detected by a diverse suite of proteostasis factors that preferentially bind and route mutant CFTR toward premature degradation, resulting in reduced plasma membrane CFTR levels and impaired chloride ion conductance associated with CF. CF treatment has been vastly improved over the past decade by the availability of small molecules called correctors. Correctors directly bind CFTR, stabilize its structure by conferring thermodynamically favorable interactions that compensate for mutations, and thereby lead to downstream folding fidelity. However, each of over 100 Class-II CF causing mutations causes unique structural defects and shows a unique response to drug treatment, described as theratype. Understanding CFTR structural defects, the proteostasis factors evaluating those defects, and the stabilizing effects of CFTR correctors will illuminate a path toward personalized medicine for CF. Here, we review recent advances in our understanding of CFTR folding, focusing on structure, corrector binding sites, the mechanisms of proteostasis factors that evaluate CFTR, and the implications for CF personalized medicine.
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Affiliation(s)
- Eli Fritz McDonald
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Jens Meiler
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Institute
for Drug Discovery, Leipzig University, Leipzig, SAC 04103, Germany
| | - Lars Plate
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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5
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Wang G. Network Basis for the Heat-Adapted Structural Thermostability of Bacterial Class II Fructose Bisphosphate Aldolase. ACS OMEGA 2023; 8:17731-17739. [PMID: 37251155 PMCID: PMC10210171 DOI: 10.1021/acsomega.3c00473] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 05/31/2023]
Abstract
The sufficient structural thermostability of a biological macromolecule is an overriding need for green nanoreactors and nanofactories to secure high activity. However, little is still known about what specific structural motif is responsible for it. Here, graph theory was employed to examine if the temperature-dependent noncovalent interactions and metal bridges, as identified in the structures of Escherichia coli class II fructose 1,6-bisphosphate aldolase, could shape a systematic fluidic grid-like mesh network with topological grids to regulate the structural thermostability of the wild-type construct and its evolved variants in each generation upon decyclization. The results indicated that the biggest grids may govern the temperature thresholds for their tertiary structural perturbations but without affecting the catalytic activities. Moreover, lower grid-based systematic thermal instability may facilitate structural thermostability, but a highly independent thermostable grid may still be required to serve as a critical anchor to secure the stereospecific thermoactivity. Its end melting temperature thresholds, together with the start ones of the biggest grids in the evolved variants, may confer high temperature sensitivity against thermal inactivation. Collectively, this computational study may have widespread significance in advancing our complete understanding and biotechnology of the thermoadaptive mechanism of the structural thermostability of a biological macromolecule.
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Baatallah N, Elbahnsi A, Chevalier B, Castanier S, Mornon JP, Pranke I, Edelman A, Sermet-Gaudelus I, Callebaut I, Hinzpeter A. Acting on the CFTR Membrane-Spanning Domains Interface Rescues Some Misfolded Mutants. Int J Mol Sci 2022; 23:ijms232416225. [PMID: 36555865 PMCID: PMC9780841 DOI: 10.3390/ijms232416225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
ABC transporters are large membrane proteins sharing a complex architecture, which comprises two nucleotide-binding domains (NBDs) and two membrane-spanning domains (MSDs). These domains are susceptible to mutations affecting their folding and assembly. In the CFTR (ABCC7) protein, a groove has been highlighted in the MSD1 at the level of the membrane inner leaflet, containing both multiple mutations affecting folding and a binding site for pharmaco-chaperones that stabilize this region. This groove is also present in ABCB proteins, however it is covered by a short elbow helix, while in ABCC proteins it remains unprotected, due to a lower position of the elbow helix in the presence of the ABCC-specific lasso motif. Here, we identified a MSD1 second-site mutation located in the vicinity of the CFTR MSD1 groove that partially rescued the folding defect of cystic fibrosis causing mutations located within MSD1, while having no effect on the most frequent mutation, F508del, located within NBD1. A model of the mutated protein 3D structure suggests additional interaction between MSD1 and MSD2, strengthening the assembly at the level of the MSD intracellular loops. Altogether, these results provide insightful information in understanding key features of the folding and function of the CFTR protein in particular, and more generally, of type IV ABC transporters.
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Affiliation(s)
- Nesrine Baatallah
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Ahmad Elbahnsi
- Sorbonne Université, Muséum National d’Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Benoit Chevalier
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Solène Castanier
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Jean-Paul Mornon
- Sorbonne Université, Muséum National d’Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Iwona Pranke
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Aleksander Edelman
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Isabelle Sermet-Gaudelus
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d’Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
- Correspondence: (I.C.); (A.H.)
| | - Alexandre Hinzpeter
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
- Correspondence: (I.C.); (A.H.)
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7
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Anglès F, Wang C, Balch WE. Spatial covariance analysis reveals the residue-by-residue thermodynamic contribution of variation to the CFTR fold. Commun Biol 2022; 5:356. [PMID: 35418593 PMCID: PMC9008016 DOI: 10.1038/s42003-022-03302-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/21/2022] [Indexed: 12/21/2022] Open
Abstract
Although the impact of genome variation on the thermodynamic properties of function on the protein fold has been studied in vitro, it remains a challenge to assign these relationships across the entire polypeptide sequence in vivo. Using the Gaussian process regression based principle of Spatial CoVariance, we globally assign on a residue-by-residue basis the biological thermodynamic properties that contribute to the functional fold of CFTR in the cell. We demonstrate the existence of a thermodynamically sensitive region of the CFTR fold involving the interface between NBD1 and ICL4 that contributes to its export from endoplasmic reticulum. At the cell surface a new set of residues contribute uniquely to the management of channel function. These results support a general ‘quality assurance’ view of global protein fold management as an SCV principle describing the differential pre- and post-ER residue interactions contributing to compartmentalization of the energetics of the protein fold for function. Our results set the stage for future analyses of the quality systems managing protein sequence-to-function-to-structure broadly encompassing genome design leading to protein function in complex cellular relationships responsible for diversity and fitness in biology in response to the environment. Spatial covariance analysis shows how each residue in the critical fold region of chloride channel CFTR, defective in cystic fibrosis patients, contributes to CFTR’s export from the endoplasmic reticulum and function in the cell.
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Affiliation(s)
- Frédéric Anglès
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Chao Wang
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - William E Balch
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA.
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8
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McDonald EF, Woods H, Smith ST, Kim M, Schoeder CT, Plate L, Meiler J. Structural Comparative Modeling of Multi-Domain F508del CFTR. Biomolecules 2022; 12:biom12030471. [PMID: 35327663 PMCID: PMC8946492 DOI: 10.3390/biom12030471] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/07/2022] Open
Abstract
Cystic fibrosis (CF) is a rare genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an epithelial anion channel expressed in several vital organs. Absence of functional CFTR results in imbalanced osmotic equilibrium and subsequent mucus build up in the lungs-which increases the risk of infection and eventually causes death. CFTR is an ATP-binding cassette (ABC) transporter family protein composed of two transmembrane domains (TMDs), two nucleotide binding domains (NBDs), and an unstructured regulatory domain. The most prevalent patient mutation is the deletion of F508 (F508del), making F508del CFTR the primary target for current FDA approved CF therapies. However, no experimental multi-domain F508del CFTR structure has been determined and few studies have modeled F508del using multi-domain WT CFTR structures. Here, we used cryo-EM density data and Rosetta comparative modeling (RosettaCM) to compare a F508del model with published experimental data on CFTR NBD1 thermodynamics. We then apply this modeling method to generate multi-domain WT and F508del CFTR structural models. These models demonstrate the destabilizing effects of F508del on NBD1 and the NBD1/TMD interface in both the inactive and active conformation of CFTR. Furthermore, we modeled F508del/R1070W and F508del bound to the CFTR corrector VX-809. Our models reveal the stabilizing effects of VX-809 on multi-domain models of F508del CFTR and pave the way for rational design of additional drugs that target F508del CFTR for treatment of CF.
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Affiliation(s)
- Eli Fritz McDonald
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (E.F.M.); (C.T.S.); (L.P.)
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; (H.W.); (S.T.S.)
| | - Hope Woods
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; (H.W.); (S.T.S.)
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37235, USA;
| | - Shannon T. Smith
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; (H.W.); (S.T.S.)
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37235, USA;
| | - Minsoo Kim
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37235, USA;
| | - Clara T. Schoeder
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (E.F.M.); (C.T.S.); (L.P.)
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; (H.W.); (S.T.S.)
- Leipzig Medical School, Leipzig University, 04109 Leipzig, Germany
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (E.F.M.); (C.T.S.); (L.P.)
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (E.F.M.); (C.T.S.); (L.P.)
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; (H.W.); (S.T.S.)
- Leipzig Medical School, Leipzig University, 04109 Leipzig, Germany
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA
- Institute for Drug Discovery, Leipzig University, 04109 Leipzig, Germany
- Correspondence: ; Tel.: +1-(615)-936-2211
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9
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Yeh HI, Yu YC, Kuo PL, Tsai CK, Huang HT, Hwang TC. Functional stability of CFTR depends on tight binding of ATP at its degenerate ATP-binding site. J Physiol 2021; 599:4625-4642. [PMID: 34411298 DOI: 10.1113/jp281933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/13/2021] [Indexed: 01/28/2023] Open
Abstract
Opening of the cystic fibrosis transmembrane conductance regulator (CFTR) channel is coupled to the motion of its two nucleotide-binding domains: they form a heterodimer sandwiching two functionally distinct ATP-binding sites (sites 1 and 2). While active ATP hydrolysis in site 2 triggers rapid channel closure, the functional role of stable ATP binding in the catalysis-incompetent (or degenerate) site 1, a feature conserved in many other ATP-binding cassette (ABC) transporter proteins, remains elusive. Here, we found that CFTR loses its prompt responsiveness to ATP after the channel is devoid of ATP for tens to hundreds of seconds. Mutants with weakened ATP binding in site 1 and the most prevalent disease-causing mutation, F508del, are more vulnerable to ATP depletion. In contrast, strengthening ligand binding in site 1 with N6 -(2-phenylethyl)-ATP, a high-affinity ATP analogue, or abolishing ATP hydrolysis in site 2 by the mutation D1370N, helps sustain a durable function of the otherwise unstable mutant channels. Thus, tight binding of ATP in the degenerate ATP-binding site is crucial to the functional stability of CFTR. Small molecules targeting site 1 may bear therapeutic potential to overcome the membrane instability of F508del-CFTR. KEY POINTS: During evolution, many ATP-binding cassette transporters - including the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel, whose dysfunction causes cystic fibrosis (CF) - lose the ability to hydrolyse ATP in one of the two ATP-binding sites. Here we show that tight ATP binding at this degenerate site in CFTR is central for maintaining the stable, robust function of normal CFTR. We also demonstrate that membrane instability of the most common CF-causing mutant, F508del-CFTR, can be rescued by strengthening ATP binding at CFTR's degenerate site. Our data thus explain an evolutionary puzzle and offer a potential therapeutic strategy for CF.
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Affiliation(s)
- Han-I Yeh
- Dalton Cardiovascular Research Center and Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO, 65211, USA.,Department of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ying-Chun Yu
- Dalton Cardiovascular Research Center and Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Pei-Lun Kuo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chun-Kuang Tsai
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsin-Tuan Huang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tzyh-Chang Hwang
- Dalton Cardiovascular Research Center and Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO, 65211, USA.,Department of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
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10
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Scholl D, Sigoillot M, Overtus M, Martinez RC, Martens C, Wang Y, Pardon E, Laeremans T, Garcia-Pino A, Steyaert J, Sheppard DN, Hendrix J, Govaerts C. A topological switch in CFTR modulates channel activity and sensitivity to unfolding. Nat Chem Biol 2021; 17:989-997. [PMID: 34341587 DOI: 10.1038/s41589-021-00844-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/28/2021] [Indexed: 12/25/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) anion channel is essential to maintain fluid homeostasis in key organs. Functional impairment of CFTR due to mutations in the cftr gene leads to cystic fibrosis. Here, we show that the first nucleotide-binding domain (NBD1) of CFTR can spontaneously adopt an alternate conformation that departs from the canonical NBD fold previously observed. Crystallography reveals that this conformation involves a topological reorganization of NBD1. Single-molecule fluorescence resonance energy transfer microscopy shows that the equilibrium between the conformations is regulated by adenosine triphosphate binding. However, under destabilizing conditions, such as the disease-causing mutation F508del, this conformational flexibility enables unfolding of the β-subdomain. Our data indicate that, in wild-type CFTR, this conformational transition of NBD1 regulates channel function, but, in the presence of the F508del mutation, it allows domain misfolding and subsequent protein degradation. Our work provides a framework to design conformation-specific therapeutics to prevent noxious transitions.
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Affiliation(s)
- Daniel Scholl
- SFMB, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Marie Overtus
- SFMB, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Chloé Martens
- SFMB, Université Libre de Bruxelles, Brussels, Belgium
| | - Yiting Wang
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Els Pardon
- VIB-VUB center for Structural Biology, VIB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Toon Laeremans
- VIB-VUB center for Structural Biology, VIB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Jan Steyaert
- VIB-VUB center for Structural Biology, VIB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium.,Molecular Imaging and Photonics, Chemistry Department, KU Leuven, Leuven, Belgium
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11
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Bahia MS, Khazanov N, Zhou Q, Yang Z, Wang C, Hong JS, Rab A, Sorscher EJ, Brouillette CG, Hunt JF, Senderowitz H. Stability Prediction for Mutations in the Cytosolic Domains of Cystic Fibrosis Transmembrane Conductance Regulator. J Chem Inf Model 2021; 61:1762-1777. [PMID: 33720715 DOI: 10.1021/acs.jcim.0c01207] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cystic Fibrosis (CF) is caused by mutations to the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) chloride channel. CFTR is composed of two membrane spanning domains, two cytosolic nucleotide-binding domains (NBD1 and NBD2) and a largely unstructured R-domain. Multiple CF-causing mutations reside in the NBDs and some are known to compromise the stability of these domains. The ability to predict the effect of mutations on the stability of the cytosolic domains of CFTR and to shed light on the mechanisms by which they exert their effect is therefore important in CF research. With this in mind, we have predicted the effect on domain stability of 59 mutations in NBD1 and NBD2 using 15 different algorithms and evaluated their performances via comparison to experimental data using several metrics including the correct classification rate (CCR), and the squared Pearson correlation (R2) and Spearman's correlation (ρ) calculated between the experimental ΔTm values and the computationally predicted ΔΔG values. Overall, the best results were obtained with FoldX and Rosetta. For NBD1 (35 mutations), FoldX provided R2 and ρ values of 0.64 and -0.71, respectively, with an 86% correct classification rate (CCR). For NBD2 (24 mutations), FoldX R2, ρ, and CCR were 0.51, -0.73, and 75%, respectively. Application of the Rosetta high-resolution protocol (Rosetta_hrp) to NBD1 yielded R2, ρ, and CCR of 0.64, -0.75, and 69%, respectively, and for NBD2 yielded R2, ρ, and CCR of 0.29, -0.27, and 50%, respectively. The corresponding numbers for the Rosetta's low-resolution protocol (Rosetta_lrp) were R2 = 0.47, ρ = -0.69, and CCR = 69% for NBD1 and R2 = 0.27, ρ = -0.24, and CCR = 63% for NBD2. For NBD1, both algorithms suggest that destabilizing mutations suffer from destabilizing vdW clashes, whereas stabilizing mutations benefit from favorable H-bond interactions. Two triple consensus approaches based on FoldX, Rosetta_lpr, and Rosetta_hpr were attempted using either "majority-voting" or "all-voting". The all-voting consensus outperformed the individual predictors, albeit on a smaller data set. In summary, our results suggest that the effect of mutations on the stability of CFTR's NBDs could be largely predicted. Since NBDs are common to all ABC transporters, these results may find use in predicting the effect and mechanism of the action of multiple disease-causing mutations in other proteins.
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Affiliation(s)
| | - Netaly Khazanov
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Qingxian Zhou
- School of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Zhengrong Yang
- School of Medicine, Division of Hematology & Oncology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Chi Wang
- 702 Fairchild Center, MC3423, Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Jeong S Hong
- Department of Paediatrics, Emory University School of Medicine, Atlanta, Georgia 30303, United States
| | - Andras Rab
- Department of Paediatrics, Emory University School of Medicine, Atlanta, Georgia 30303, United States
| | - Eric J Sorscher
- Department of Paediatrics, Emory University School of Medicine, Atlanta, Georgia 30303, United States
| | - Christie G Brouillette
- Department of Biochemistry & Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - John F Hunt
- 702 Fairchild Center, MC3423, Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Hanoch Senderowitz
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
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12
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Bitam S, Elbahnsi A, Creste G, Pranke I, Chevalier B, Berhal F, Hoffmann B, Servel N, Baatalah N, Tondelier D, Hatton A, Moquereau C, Faria Da Cunha M, Pastor A, Lepissier A, Hinzpeter A, Mornon JP, Prestat G, Edelman A, Callebaut I, Gravier-Pelletier C, Sermet-Gaudelus I. New insights into structure and function of bis-phosphinic acid derivatives and implications for CFTR modulation. Sci Rep 2021; 11:6842. [PMID: 33767236 PMCID: PMC7994384 DOI: 10.1038/s41598-021-83240-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 01/18/2021] [Indexed: 01/31/2023] Open
Abstract
C407 is a compound that corrects the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein carrying the p.Phe508del (F508del) mutation. We investigated the corrector effect of c407 and its derivatives on F508del-CFTR protein. Molecular docking and dynamics simulations combined with site-directed mutagenesis suggested that c407 stabilizes the F508del-Nucleotide Binding Domain 1 (NBD1) during the co-translational folding process by occupying the position of the p.Phe1068 side chain located at the fourth intracellular loop (ICL4). After CFTR domains assembly, c407 occupies the position of the missing p.Phe508 side chain. C407 alone or in combination with the F508del-CFTR corrector VX-809, increased CFTR activity in cell lines but not in primary respiratory cells carrying the F508del mutation. A structure-based approach resulted in the synthesis of an extended c407 analog G1, designed to improve the interaction with ICL4. G1 significantly increased CFTR activity and response to VX-809 in primary nasal cells of F508del homozygous patients. Our data demonstrate that in-silico optimized c407 derivative G1 acts by a mechanism different from the reference VX-809 corrector and provide insights into its possible molecular mode of action. These results pave the way for novel strategies aiming to optimize the flawed ICL4-NBD1 interface.
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Affiliation(s)
- Sara Bitam
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Ahmad Elbahnsi
- Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, 75005, Paris, France
| | - Geordie Creste
- UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (LCBPT), Université de Paris, 75006, Paris, France
| | - Iwona Pranke
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Benoit Chevalier
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Farouk Berhal
- UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (LCBPT), Université de Paris, 75006, Paris, France
| | - Brice Hoffmann
- Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, 75005, Paris, France
| | - Nathalie Servel
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Nesrine Baatalah
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Danielle Tondelier
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Aurelie Hatton
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Christelle Moquereau
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Mélanie Faria Da Cunha
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Alexandra Pastor
- UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (LCBPT), Université de Paris, 75006, Paris, France
| | - Agathe Lepissier
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Alexandre Hinzpeter
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Jean-Paul Mornon
- Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, 75005, Paris, France
| | - Guillaume Prestat
- UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (LCBPT), Université de Paris, 75006, Paris, France
| | - Aleksander Edelman
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France
| | - Isabelle Callebaut
- Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, 75005, Paris, France
| | - Christine Gravier-Pelletier
- UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (LCBPT), Université de Paris, 75006, Paris, France
| | - Isabelle Sermet-Gaudelus
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 75015, Paris, France.
- Centre de Référence Maladies Rares Mucoviscidose et Maladies du CFTR, European Reference Network for Rare Respiratory Diseases, Hôpital Necker Enfants Malades, 75015, Paris, France.
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13
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Abstract
Allosteric regulation in proteins is fundamental to many important biological processes. Allostery has been employed to control protein functions by regulating protein activity. Engineered allosteric regulation allows controlling protein activity in subsecond time scale and has a broad range of applications, from dissecting spatiotemporal dynamics in biochemical cascades to applications in biotechnology and medicine. Here, we review the concept of allostery in proteins and various approaches to identify allosteric sites and pathways. We then provide an overview of strategies and tools used in allosteric protein regulation and their utility in biological applications. We highlight various classes of proteins, where regulation is achieved through allostery. Finally, we analyze the current problems, critical challenges, and future prospective in achieving allosteric regulation in proteins.
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Affiliation(s)
| | - Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
- Departments of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
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14
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Prins S, Langron E, Hastings C, Hill EJ, Stefan AC, Griffin LD, Vergani P. Fluorescence assay for simultaneous quantification of CFTR ion-channel function and plasma membrane proximity. J Biol Chem 2020; 295:16529-16544. [PMID: 32934006 PMCID: PMC7864054 DOI: 10.1074/jbc.ra120.014061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/21/2020] [Indexed: 11/21/2022] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a plasma membrane anion channel that plays a key role in controlling transepithelial fluid movement. Excessive activation results in intestinal fluid loss during secretory diarrheas, whereas CFTR mutations underlie cystic fibrosis (CF). Anion permeability depends both on how well CFTR channels work (permeation/gating) and on how many are present at the membrane. Recently, treatments with two drug classes targeting CFTR-one boosting ion-channel function (potentiators) and the other increasing plasma membrane density (correctors)-have provided significant health benefits to CF patients. Here, we present an image-based fluorescence assay that can rapidly and simultaneously estimate both CFTR ion-channel function and the protein's proximity to the membrane. We monitor F508del-CFTR, the most common CF-causing variant, and confirm rescue by low temperature, CFTR-targeting drugs and second-site revertant mutation R1070W. In addition, we characterize a panel of 62 CF-causing mutations. Our measurements correlate well with published data (electrophysiology and biochemistry), further confirming validity of the assay. Finally, we profile effects of acute treatment with approved potentiator drug VX-770 on the rare-mutation panel. Mapping the potentiation profile on CFTR structures raises mechanistic hypotheses on drug action, suggesting that VX-770 might allow an open-channel conformation with an alternative arrangement of domain interfaces. The assay is a valuable tool for investigation of CFTR molecular mechanisms, allowing accurate inferences on gating/permeation. In addition, by providing a two-dimensional characterization of the CFTR protein, it could better inform development of single-drug and precision therapies addressing the root cause of CF disease.
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Affiliation(s)
- Stella Prins
- Department of Neuroscience, Physiology, and Pharmacology, University College London, London, United Kingdom
| | - Emily Langron
- Department of Neuroscience, Physiology, and Pharmacology, University College London, London, United Kingdom
| | - Cato Hastings
- CoMPLEX, University College London, London, United Kingdom
| | - Emily J Hill
- Department of Neuroscience, Physiology, and Pharmacology, University College London, London, United Kingdom
| | - Andra C Stefan
- Natural Sciences, University College London, London, United Kingdom
| | | | - Paola Vergani
- Department of Neuroscience, Physiology, and Pharmacology, University College London, London, United Kingdom.
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15
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Shishido H, Yoon JS, Yang Z, Skach WR. CFTR trafficking mutations disrupt cotranslational protein folding by targeting biosynthetic intermediates. Nat Commun 2020; 11:4258. [PMID: 32848127 PMCID: PMC7450043 DOI: 10.1038/s41467-020-18101-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/04/2020] [Indexed: 02/03/2023] Open
Abstract
Protein misfolding causes a wide spectrum of human disease, and therapies that target misfolding are transforming the clinical care of cystic fibrosis. Despite this success, however, very little is known about how disease-causing mutations affect the de novo folding landscape. Here we show that inherited, disease-causing mutations located within the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) have distinct effects on nascent polypeptides. Two of these mutations (A455E and L558S) delay compaction of the nascent NBD1 during a critical window of synthesis. The observed folding defect is highly dependent on nascent chain length as well as its attachment to the ribosome. Moreover, restoration of the NBD1 cotranslational folding defect by second site suppressor mutations also partially restores folding of full-length CFTR. These findings demonstrate that nascent folding intermediates can play an important role in disease pathogenesis and thus provide potential targets for pharmacological correction.
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Affiliation(s)
- Hideki Shishido
- CFFT Lab, Cystic Fibrosis Foundation, 44 Hartwell Ave, Lexington, MA, 02421, USA
| | - Jae Seok Yoon
- CFFT Lab, Cystic Fibrosis Foundation, 44 Hartwell Ave, Lexington, MA, 02421, USA
| | - Zhongying Yang
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd, Portland, OR, 97239, USA
| | - William R Skach
- Cystic Fibrosis Foundation, 4550 Montgomery Ave., Suite 1100N, Bethesda, MD, 20814, USA.
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16
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Uliyakina I, Botelho HM, da Paula AC, Afonso S, Lobo MJ, Felício V, Farinha CM, Amaral MD. Full Rescue of F508del-CFTR Processing and Function by CFTR Modulators Can Be Achieved by Removal of Two Regulatory Regions. Int J Mol Sci 2020; 21:ijms21124524. [PMID: 32630527 PMCID: PMC7350234 DOI: 10.3390/ijms21124524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
Cystic Fibrosis (CF) is caused by mutations in the CF Transmembrane conductance Regulator (CFTR), the only ATP-binding cassette (ABC) transporter functioning as a channel. Unique to CFTR is a regulatory domain which includes a highly conformationally dynamic region—the regulatory extension (RE). The first nucleotide-binding domain of CFTR contains another dynamic region—regulatory insertion (RI). Removal of RI rescues the trafficking defect of CFTR with F508del, the most common CF-causing mutation. Here we aimed to assess the impact of RE removal (with/without RI or genetic revertants) on F508del-CFTR trafficking and how CFTR modulator drugs VX-809/lumacaftor and VX-770/ivacaftor rescue these variants. We generated cell lines expressing ΔRE and ΔRI CFTR (with/without genetic revertants) and assessed CFTR expression, stability, plasma membrane levels, and channel activity. Our data demonstrated that ΔRI significantly enhanced rescue of F508del-CFTR by VX-809. While the presence of the RI seems to be precluding full rescue of F508del-CFTR processing by VX-809, this region appears essential to rescue its function by VX-770, suggesting some contradictory role in rescue of F508del-CFTR by these two modulators. This negative impact of RI removal on VX-770-stimulated currents on F508del-CFTR can be compensated by deletion of the RE which also leads to the stabilization of this mutant. Despite both regions being conformationally dynamic, RI precludes F508del-CFTR processing while RE affects mostly its stability and channel opening.
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17
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Ivey G, Youker RT. Disease-relevant mutations alter amino acid co-evolution networks in the second nucleotide binding domain of CFTR. PLoS One 2020; 15:e0227668. [PMID: 31978131 PMCID: PMC6980524 DOI: 10.1371/journal.pone.0227668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 12/25/2019] [Indexed: 01/23/2023] Open
Abstract
Cystic Fibrosis (CF) is an inherited disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel. Mutations in CFTR cause impaired chloride ion transport in the epithelial tissues of patients leading to cardiopulmonary decline and pancreatic insufficiency in the most severely affected patients. CFTR is composed of twelve membrane-spanning domains, two nucleotide-binding domains (NBDs), and a regulatory domain. The most common mutation in CFTR is a deletion of phenylalanine at position 508 (ΔF508) in NBD1. Previous research has primarily concentrated on the structure and dynamics of the NBD1 domain; However numerous pathological mutations have also been found in the lesser-studied NBD2 domain. We have investigated the amino acid co-evolved network of interactions in NBD2, and the changes that occur in that network upon the introduction of CF and CF-related mutations (S1251N(T), S1235R, D1270N, N1303K(T)). Extensive coupling between the α- and β-subdomains were identified with residues in, or near Walker A, Walker B, H-loop and C-loop motifs. Alterations in the predicted residue network varied from moderate for the S1251T perturbation to more severe for N1303T. The S1235R and D1270N networks varied greatly compared to the wildtype, but these CF mutations only affect ion transport preference and do not severely disrupt CFTR function, suggesting dynamic flexibility in the network of interactions in NBD2. Our results also suggest that inappropriate interactions between the β-subdomain and Q-loop could be detrimental. We also identified mutations predicted to stabilize the NBD2 residue network upon introduction of the CF and CF-related mutations, and these predicted mutations are scored as benign by the MUTPRED2 algorithm. Our results suggest the level of disruption of the co-evolution predictions of the amino acid networks in NBD2 does not have a straightforward correlation with the severity of the CF phenotypes observed.
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Affiliation(s)
- Gabrianne Ivey
- Kyder Christian Academy, Franklin, North Carolina, United States of America
- Southwestern Community College, Sylva, North Carolina, United States of America
| | - Robert T. Youker
- Department of Biology, Western Carolina University, Cullowhee, North Carolina, United States of America
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18
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Towards next generation therapies for cystic fibrosis: Folding, function and pharmacology of CFTR. J Cyst Fibros 2020; 19 Suppl 1:S25-S32. [PMID: 31902693 PMCID: PMC7052731 DOI: 10.1016/j.jcf.2019.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/19/2022]
Abstract
The treatment of cystic fibrosis (CF) has been transformed by orally-bioavailable small molecule modulators of the cystic fibrosis transmembrane conductance regulator (CFTR), which restore function to CF mutants. However, CFTR modulators are not available to all people with CF and better modulators are required to prevent disease progression. Here, we review selectively recent advances in CFTR folding, function and pharmacology. We highlight ensemble and single-molecule studies of CFTR folding, which provide new insight into CFTR assembly, its perturbation by CF mutations and rescue by CFTR modulators. We discuss species-dependent differences in the action of the F508del-CFTR mutation on CFTR expression, stability and function, which might influence pharmacological studies of CFTR modulators in CF animal models. Finally, we illuminate the identification of combinations of two CFTR potentiators (termed co-potentiators), which restore therapeutically-relevant levels of CFTR activity to rare CF mutations. Thus, mechanistic studies of CFTR folding, function and pharmacology inform the development of highly effective CFTR modulators.
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19
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Laselva O, Erwood S, Du K, Ivakine Z, Bear CE. Activity of lumacaftor is not conserved in zebrafish Cftr bearing the major cystic fibrosis-causing mutation. FASEB Bioadv 2019; 1:661-670. [PMID: 32123813 PMCID: PMC6996396 DOI: 10.1096/fba.2019-00039] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/02/2019] [Accepted: 08/30/2019] [Indexed: 12/11/2022] Open
Abstract
F508del-cystic fibrosis transmembrane conductance regulator (CFTR) is the major mutant responsible for cystic fibrosis (CF). ORKAMBI®, approved for patients bearing this mutant, contains lumacaftor (VX-809) that partially corrects F508del-CFTR's processing defect and ivacaftor (VX-770) that potentiates its defective channel activity. Unfortunately, the clinical efficacy of ORKAMBI® is modest, highlighting the need to understand how the small molecules work so that superior compounds can be developed. Because, human CFTR (hCFTR) and zebrafish Cftr (zCftr) are structurally conserved as determined in recent cryo-EM structural models, we hypothesized that the consequences of the major mutation and small molecule modulators would be similar for the two species of protein. As expected, like the F508del mutation in hCFTR, the homologous mutation in zCftr (F507del) is misprocessed, yet not as severely as the human mutant and this defect was restored by low-temperature (27°C) culture conditions. After rescue to the cell surface, F507del-zCftr exhibited regulated channel activity that was potentiated by ivacaftor. Surprisingly, lumacaftor failed to rescue misprocessing of the F507del-zCftr at either 37 or 27°C suggesting that future comparative studies with F508del-hCFTR would provide insight into its structure: function relationships. Interestingly, the robust rescue of F508del-zCftr at 27°C and availability of methods for in vivo screening in zebrafish present the opportunity to define the cellular pathways underlying rescue.
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Affiliation(s)
- Onofrio Laselva
- Programme in Molecular MedicineHospital for Sick ChildrenTorontoCanada
- Department of PhysiologyUniversity of TorontoTorontoCanada
| | - Steven Erwood
- Programme in Genetics and Genome BiologyHospital for Sick ChildrenTorontoCanada
| | - Kai Du
- Programme in Molecular MedicineHospital for Sick ChildrenTorontoCanada
| | - Zhenya Ivakine
- Programme in Genetics and Genome BiologyHospital for Sick ChildrenTorontoCanada
| | - Christine E. Bear
- Programme in Molecular MedicineHospital for Sick ChildrenTorontoCanada
- Department of PhysiologyUniversity of TorontoTorontoCanada
- Department of BiochemistryUniversity of TorontoTorontoCanada
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20
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Sigoillot M, Overtus M, Grodecka M, Scholl D, Garcia-Pino A, Laeremans T, He L, Pardon E, Hildebrandt E, Urbatsch I, Steyaert J, Riordan JR, Govaerts C. Domain-interface dynamics of CFTR revealed by stabilizing nanobodies. Nat Commun 2019; 10:2636. [PMID: 31201318 PMCID: PMC6572788 DOI: 10.1038/s41467-019-10714-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 05/21/2019] [Indexed: 01/17/2023] Open
Abstract
The leading cause of cystic fibrosis (CF) is the deletion of phenylalanine 508 (F508del) in the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR). The mutation affects the thermodynamic stability of the domain and the integrity of the interface between NBD1 and the transmembrane domain leading to its clearance by the quality control system. Here, we develop nanobodies targeting NBD1 of human CFTR and demonstrate their ability to stabilize both isolated NBD1 and full-length protein. Crystal structures of NBD1-nanobody complexes provide an atomic description of the epitopes and reveal the molecular basis for stabilization. Furthermore, our data uncover a conformation of CFTR, involving detachment of NBD1 from the transmembrane domain, which contrast with the compact assembly observed in cryo-EM structures. This unexpected interface rearrangement is likely to have major relevance for CF pathogenesis but also for the normal function of CFTR and other ABC proteins.
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Affiliation(s)
- Maud Sigoillot
- SFMB, Université Libre de Bruxelles (ULB), CP206/02, Boulevard du Triomphe, building BC, B-1050, Brussels, Belgium
| | - Marie Overtus
- SFMB, Université Libre de Bruxelles (ULB), CP206/02, Boulevard du Triomphe, building BC, B-1050, Brussels, Belgium
| | - Magdalena Grodecka
- SFMB, Université Libre de Bruxelles (ULB), CP206/02, Boulevard du Triomphe, building BC, B-1050, Brussels, Belgium
| | - Daniel Scholl
- SFMB, Université Libre de Bruxelles (ULB), CP206/02, Boulevard du Triomphe, building BC, B-1050, Brussels, Belgium
| | - Abel Garcia-Pino
- Laboratoire de Microbiologie Moléculaire et Cellulaire, ULB CP300, rue des Professeurs Jeener et Brachet 12, B-6041, Charleroi, Belgium
| | - Toon Laeremans
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium.,VIB-VUB center for Structural Biology, VIB, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Lihua He
- Department of Biochemistry and Biophysics and Cystic Fibrosis Center, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium.,VIB-VUB center for Structural Biology, VIB, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Ellen Hildebrandt
- Department of Cell Biology and Biochemistry and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street, Stop 6540, Lubbock, TX, 79430, USA
| | - Ina Urbatsch
- Department of Cell Biology and Biochemistry and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street, Stop 6540, Lubbock, TX, 79430, USA
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium.,VIB-VUB center for Structural Biology, VIB, Pleinlaan 2, B-1050, Brussels, Belgium
| | - John R Riordan
- Department of Biochemistry and Biophysics and Cystic Fibrosis Center, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Cedric Govaerts
- SFMB, Université Libre de Bruxelles (ULB), CP206/02, Boulevard du Triomphe, building BC, B-1050, Brussels, Belgium.
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21
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Bose SJ, Bijvelds MJC, Wang Y, Liu J, Cai Z, Bot AGM, de Jonge HR, Sheppard DN. Differential thermostability and response to cystic fibrosis transmembrane conductance regulator potentiators of human and mouse F508del-CFTR. Am J Physiol Lung Cell Mol Physiol 2019; 317:L71-L86. [PMID: 30969810 PMCID: PMC6689747 DOI: 10.1152/ajplung.00034.2019] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cross-species comparative studies have highlighted differences between human and mouse cystic fibrosis transmembrane conductance regulator (CFTR), the epithelial Cl- channel defective in cystic fibrosis (CF). Here, we compare the impact of the most common CF mutation F508del on the function of human and mouse CFTR heterologously expressed in mammalian cells and their response to CFTR modulators using the iodide efflux and patch-clamp techniques. Once delivered to the plasma membrane, human F508del-CFTR exhibited a severe gating defect characterized by infrequent channel openings and was thermally unstable, deactivating within minutes at 37°C. By contrast, the F508del mutation was without effect on the gating pattern of mouse CFTR, and channel activity demonstrated thermostability at 37°C. Strikingly, at all concentrations tested, the clinically approved CFTR potentiator ivacaftor was without effect on the mouse F508del-CFTR Cl- channel. Moreover, eight CFTR potentiators, including ivacaftor, failed to generate CFTR-mediated iodide efflux from CHO cells expressing mouse F508del-CFTR. However, they all produced CFTR-mediated iodide efflux with human F508del-CFTR-expressing CHO cells, while fifteen CFTR correctors rescued the plasma membrane expression of both human and mouse F508del-CFTR. Interestingly, the CFTR potentiator genistein enhanced CFTR-mediated iodide efflux from CHO cells expressing either human or mouse F508del-CFTR, whereas it only potentiated human F508del-CFTR Cl- channels in cell-free membrane patches, suggesting that its action on mouse F508del-CFTR is indirect. Thus, the F508del mutation has distinct effects on human and mouse CFTR Cl- channels.
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Affiliation(s)
- Samuel J Bose
- School of Physiology, Pharmacology and Neuroscience, University of Bristol , Bristol , United Kingdom
| | - Marcel J C Bijvelds
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center , Rotterdam , The Netherlands
| | - Yiting Wang
- School of Physiology, Pharmacology and Neuroscience, University of Bristol , Bristol , United Kingdom
| | - Jia Liu
- School of Physiology, Pharmacology and Neuroscience, University of Bristol , Bristol , United Kingdom
| | - Zhiwei Cai
- School of Physiology, Pharmacology and Neuroscience, University of Bristol , Bristol , United Kingdom
| | - Alice G M Bot
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center , Rotterdam , The Netherlands
| | - Hugo R de Jonge
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center , Rotterdam , The Netherlands
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol , Bristol , United Kingdom
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22
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Patel W, Moore PJ, Sassano MF, Lopes-Pacheco M, Aleksandrov AA, Amaral MD, Tarran R, Gray MA. Increases in cytosolic Ca 2+ induce dynamin- and calcineurin-dependent internalisation of CFTR. Cell Mol Life Sci 2019; 76:977-994. [PMID: 30547226 PMCID: PMC6394554 DOI: 10.1007/s00018-018-2989-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/12/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-regulated, apical anion channel that regulates ion and fluid transport in many epithelia including the airways. We have previously shown that cigarette smoke (CS) exposure to airway epithelia causes a reduction in plasma membrane CFTR expression which correlated with a decrease in airway surface hydration. The effect of CS on CFTR was dependent on an increase in cytosolic Ca2+. However, the underlying mechanism for this Ca2+-dependent, internalisation of CFTR is unknown. To gain a better understanding of the effect of Ca2+ on CFTR, we performed whole cell current recordings to study the temporal effect of raising cytosolic Ca2+ on CFTR function. We show that an increase in cytosolic Ca2+ induced a time-dependent reduction in whole cell CFTR conductance, which was paralleled by a loss of cell surface CFTR expression, as measured by confocal and widefield fluorescence microscopy. The decrease in CFTR conductance and cell surface expression were both dynamin-dependent. Single channel reconstitution studies showed that raising cytosolic Ca2+ per se had no direct effect on CFTR. In fact, the loss of CFTR plasma membrane activity correlated with activation of calcineurin, a Ca2+-dependent phosphatase, suggesting that dephosphorylation of CFTR was linked to the loss of surface expression. In support of this, the calcineurin inhibitor, cyclosporin A, prevented the Ca2+-induced decrease in cell surface CFTR. These results provide a hitherto unrecognised role for cytosolic Ca2+ in modulating the residency of CFTR at the plasma membrane through a dynamin- and calcineurin-dependent mechanism.
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Affiliation(s)
- Waseema Patel
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick J Moore
- Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Flori Sassano
- Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miquéias Lopes-Pacheco
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Andrei A Aleksandrov
- Department of Biochemistry and Biophysics, Cystic Fibrosis Research and Treatment Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Margarida D Amaral
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Robert Tarran
- Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, Cystic Fibrosis Research and Treatment Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael A Gray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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23
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Chen X, Zhu S, Zhenin M, Xu W, Bose SJ, Wong MPF, Leung GPH, Senderowitz H, Chen JH. A defective flexible loop contributes to the processing and gating defects of the predominant cystic fibrosis-causing mutation. FASEB J 2019; 33:5126-5142. [PMID: 30668920 DOI: 10.1096/fj.201801218rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
People with the genetic disease cystic fibrosis (CF) often carry a deletion mutation ΔF508 on the gene encoding the CF transmembrane conductance regulator (CFTR) Cl- channel. This mutation greatly reduces the CFTR maturation process and slows the channel opening rate. Here, we investigate whether residues near F508 contribute to these defects in ΔF508-CFTR. Most deletion mutations, but not alanine substitutions, of individual residues from positions 503 to 513 impaired CFTR maturation. Interestingly, only protein processing of ΔY512-CFTR, like that of ΔF508-CFTR, was greatly improved by low-temperature culture at 27°C or small-molecule corrector C18. The 2 mutant Cl- channels were equally slow to open, suggesting that they may share common structural flaws. Studies on the H3-H4 loop that links residues F508 and Y512 demonstrate that G509A/V510G mutations, moving G509 1 position backward in the loop, markedly enhanced ΔF508-CFTR maturation and opening rate while promoting protein stability and persistence of the H3 helix in ΔF508 nucleotide-binding domain 1. Moreover, V510A/S511A mutations noticeably increased ΔY512-CFTR maturation at 27°C and its opening rate. Thus, loop abnormalities may contribute to ΔF508- and ΔY512-CFTR defects. Importantly, correcting defects from G509 displacement in ΔF508-CFTR may offer a new avenue for drug discovery and CF treatments.-Chen, X., Zhu, S., Zhenin, M., Xu, W., Bose, S. J., Wong, M. P.-F., Leung, G. P. H., Senderowitz, H., Chen, J.-H. A defective flexible loop contributes to the processing and gating defects of the predominant cystic fibrosis-causing mutation.
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Affiliation(s)
- Xinying Chen
- School of Biomedical Sciences, University of Hong Kong, Hong Kong.,The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
| | - Siyu Zhu
- School of Biomedical Sciences, University of Hong Kong, Hong Kong.,The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
| | - Michael Zhenin
- Department of Chemistry, Bar Ilan University, Ramat-Gan, Israel
| | - Weiyi Xu
- School of Biomedical Sciences, University of Hong Kong, Hong Kong.,The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
| | - Samuel J Bose
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Bristol, United Kingdom; and
| | - Molly Pik-Fan Wong
- School of Biomedical Sciences, University of Hong Kong, Hong Kong.,The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
| | - George P H Leung
- Department of Pharmacology and Pharmacy, University of Hong Kong, Hong Kong, China
| | | | - Jeng-Haur Chen
- School of Biomedical Sciences, University of Hong Kong, Hong Kong.,The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
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24
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Wang C, Aleksandrov AA, Yang Z, Forouhar F, Proctor EA, Kota P, An J, Kaplan A, Khazanov N, Boël G, Stockwell BR, Senderowitz H, Dokholyan NV, Riordan JR, Brouillette CG, Hunt JF. Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator. J Biol Chem 2018; 293:17685-17704. [PMID: 29903914 PMCID: PMC6240863 DOI: 10.1074/jbc.ra117.000819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/31/2018] [Indexed: 01/07/2023] Open
Abstract
Many disease-causing mutations impair protein stability. Here, we explore a thermodynamic strategy to correct the disease-causing F508del mutation in the human cystic fibrosis transmembrane conductance regulator (hCFTR). F508del destabilizes nucleotide-binding domain 1 (hNBD1) in hCFTR relative to an aggregation-prone intermediate. We developed a fluorescence self-quenching assay for compounds that prevent aggregation of hNBD1 by stabilizing its native conformation. Unexpectedly, we found that dTTP and nucleotide analogs with exocyclic methyl groups bind to hNBD1 more strongly than ATP and preserve electrophysiological function of full-length F508del-hCFTR channels at temperatures up to 37 °C. Furthermore, nucleotides that increase open-channel probability, which reflects stabilization of an interdomain interface to hNBD1, thermally protect full-length F508del-hCFTR even when they do not stabilize isolated hNBD1. Therefore, stabilization of hNBD1 itself or of one of its interdomain interfaces by a small molecule indirectly offsets the destabilizing effect of the F508del mutation on full-length hCFTR. These results indicate that high-affinity binding of a small molecule to a remote site can correct a disease-causing mutation. We propose that the strategies described here should be applicable to identifying small molecules to help manage other human diseases caused by mutations that destabilize native protein conformation.
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Affiliation(s)
- Chi Wang
- From the Departments of Biological Sciences and
| | - Andrei A. Aleksandrov
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Zhengrong Yang
- the Department of Chemistry, University of Alabama, Birmingham, Alabama 35294, and
| | | | - Elizabeth A. Proctor
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Pradeep Kota
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jianli An
- the Department of Chemistry, University of Alabama, Birmingham, Alabama 35294, and
| | - Anna Kaplan
- From the Departments of Biological Sciences and
| | - Netaly Khazanov
- the Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | - Brent R. Stockwell
- From the Departments of Biological Sciences and ,Chemistry, Columbia University, New York, New York 10027
| | - Hanoch Senderowitz
- the Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Nikolay V. Dokholyan
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - John R. Riordan
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - John F. Hunt
- From the Departments of Biological Sciences and , To whom correspondence should be addressed. Tel.:
212-854-5443; Fax:
212-865-8246; E-mail:
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25
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Wang Y, Cai Z, Gosling M, Sheppard DN. Potentiation of the cystic fibrosis transmembrane conductance regulator Cl− channel by ivacaftor is temperature independent. Am J Physiol Lung Cell Mol Physiol 2018; 315:L846-L857. [DOI: 10.1152/ajplung.00235.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ivacaftor is the first drug to target directly defects in the cystic fibrosis transmembrane conductance regulator (CFTR), which causes cystic fibrosis (CF). To understand better how ivacaftor potentiates CFTR channel gating, here we investigated the effects of temperature on its action. As a control, we studied the benzimidazolone UCCF-853, which potentiates CFTR by a different mechanism. Using the patch-clamp technique and cells expressing recombinant CFTR, we studied the single-channel behavior of wild-type and F508del-CFTR, the most common CF mutation. Raising the temperature of the intracellular solution from 23 to 37°C increased the frequency but reduced the duration of wild-type and F508del-CFTR channel openings. Although the open probability ( Po) of wild-type CFTR increased progressively as temperature was elevated, the relationship between Po and temperature for F508del-CFTR was bell-shaped with a maximum Po at ~30°C. For wild-type CFTR and to a greatly reduced extent F508del-CFTR, the temperature dependence of channel gating was asymmetric with the opening rate demonstrating greater temperature sensitivity than the closing rate. At all temperatures tested, ivacaftor and UCCF-853 potentiated wild-type and F508del-CFTR. Strikingly, ivacaftor but not UCCF-853 abolished the asymmetric temperature dependence of CFTR channel gating. At all temperatures tested, Po values of wild-type CFTR in the presence of ivacaftor were approximately double those of F508del-CFTR, which were equivalent to or greater than those of wild-type CFTR at 37°C in the absence of the drug. We conclude that the principal effect of ivacaftor is to promote channel opening to abolish the temperature dependence of CFTR channel gating.
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Affiliation(s)
- Yiting Wang
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
| | - Zhiwei Cai
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
| | - Martin Gosling
- Enterprise Therapeutics, Sussex Innovation Centre, University of Sussex, Science Park Square, Brighton, United Kingdom
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - David N. Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
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26
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Fay JF, Aleksandrov LA, Jensen TJ, Cui LL, Kousouros JN, He L, Aleksandrov AA, Gingerich DS, Riordan JR, Chen JZ. Cryo-EM Visualization of an Active High Open Probability CFTR Anion Channel. Biochemistry 2018; 57:6234-6246. [PMID: 30281975 DOI: 10.1021/acs.biochem.8b00763] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) anion channel, crucial to epithelial salt and water homeostasis, and defective due to mutations in its gene in patients with cystic fibrosis, is a unique member of the large family of ATP-binding cassette transport proteins. Regulation of CFTR channel activity is stringently controlled by phosphorylation and nucleotide binding. Structural changes that underlie transitions between active and inactive functional states are not yet fully understood. Indeed the first 3D structures of dephosphorylated, ATP-free, and phosphorylated ATP-bound states were only recently reported. Here we have determined the structure of inactive and active states of a thermally stabilized CFTR, the latter with a very high channel open probability, confirmed after reconstitution into proteoliposomes. These structures, obtained at nominal resolution of 4.3 and 6.6 Å, reveal a unique repositioning of the transmembrane helices and regulatory domain density that provide insights into the structural transition between active and inactive functional states of CFTR. Moreover, we observe an extracellular vestibule that may provide anion access to the pore due to the conformation of transmembrane helices 7 and 8 that differs from the previous orthologue CFTR structures. In conclusion, our work contributes detailed structural information on an active, open state of the CFTR anion channel.
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Affiliation(s)
- Jonathan F Fay
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Luba A Aleksandrov
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Timothy J Jensen
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Liying L Cui
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Joseph N Kousouros
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Lihua He
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Andrei A Aleksandrov
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Drew S Gingerich
- Oregon Health & Science University , Portland , Oregon 97239 , United States
| | - John R Riordan
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - James Z Chen
- Oregon Health & Science University , Portland , Oregon 97239 , United States
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27
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Sites associated with Kalydeco binding on human Cystic Fibrosis Transmembrane Conductance Regulator revealed by Hydrogen/Deuterium Exchange. Sci Rep 2018; 8:4664. [PMID: 29549268 PMCID: PMC5856801 DOI: 10.1038/s41598-018-22959-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
Cystic Fibrosis (CF) is caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). Mutations associated with CF cause loss-of-function in CFTR leading to salt imbalance in epithelial tissues. Kalydeco (also called VX-770 or ivacaftor) was approved for CF treatment in 2012 but little is known regarding the compound’s interactions with CFTR including the site of binding or mechanisms of action. In this study we use hydrogen/deuterium exchange (HDX) coupled with mass spectrometry to assess the conformational dynamics of a thermostabilized form of CFTR in apo and ligand-bound states. We observe HDX protection at a known binding site for AMPPNP and significant protection for several regions of CFTR in the presence of Kalydeco. The ligand-induced changes of CFTR in the presence of Kalydeco suggest a potential binding site.
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28
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Shobair M, Popov KI, Dang YL, He H, Stutts MJ, Dokholyan NV. Mapping allosteric linkage to channel gating by extracellular domains in the human epithelial sodium channel. J Biol Chem 2018; 293:3675-3684. [PMID: 29358325 DOI: 10.1074/jbc.ra117.000604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/08/2018] [Indexed: 11/06/2022] Open
Abstract
The epithelial sodium channel (ENaC) mediates sodium absorption in lung, kidney, and colon epithelia. Channels in the ENaC/degenerin family possess an extracellular region that senses physicochemical changes in the extracellular milieu and allosterically regulates the channel opening. Proteolytic cleavage activates the ENaC opening, by the removal of specific segments in the finger domains of the α- and γ ENaC-subunits. Cleavage causes perturbations in the extracellular region that propagate to the channel gate. However, it is not known how the channel structure mediates the propagation of activation signals through the extracellular sensing domains. Here, to identify the structure-function determinants that mediate allosteric ENaC activation, we performed MD simulations, thiol modification of residues substituted by cysteine, and voltage-clamp electrophysiology recordings. Our simulations of an ENaC heterotetramer, α1βα2γ, in the proteolytically cleaved and uncleaved states revealed structural pathways in the α-subunit that are responsible for ENaC proteolytic activation. To validate these findings, we performed site-directed mutagenesis to introduce cysteine substitutions in the extracellular domains of the α-, β-, and γ ENaC-subunits. Insertion of a cysteine at the α-subunit Glu557 site, predicted to stabilize a closed state of ENaC, inhibited ENaC basal activity and retarded the kinetics of proteolytic activation by 2-fold. Our results suggest that the lower palm domain of αENaC is essential for ENaC activation. In conclusion, our integrated computational and experimental approach suggests key structure-function determinants for ENaC proteolytic activation and points toward a mechanistic model for the allosteric communication in the extracellular domains of the ENaC/degenerin family channels.
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Affiliation(s)
- Mahmoud Shobair
- From the Program in Molecular and Cellular Biophysics.,Curriculum in Bioinformatics and Computational Biology.,Department of Biochemistry and Biophysics, and.,Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | | | - Yan L Dang
- Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Hong He
- Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - M Jackson Stutts
- Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Nikolay V Dokholyan
- From the Program in Molecular and Cellular Biophysics, .,Curriculum in Bioinformatics and Computational Biology.,Department of Biochemistry and Biophysics, and.,Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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29
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Yang Z, Hildebrandt E, Jiang F, Aleksandrov AA, Khazanov N, Zhou Q, An J, Mezzell AT, Xavier BM, Ding H, Riordan JR, Senderowitz H, Kappes JC, Brouillette CG, Urbatsch IL. Structural stability of purified human CFTR is systematically improved by mutations in nucleotide binding domain 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1193-1204. [PMID: 29425673 DOI: 10.1016/j.bbamem.2018.02.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/19/2018] [Accepted: 02/05/2018] [Indexed: 12/17/2022]
Abstract
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is an ABC transporter containing two transmembrane domains forming a chloride ion channel, and two nucleotide binding domains (NBD1 and NBD2). CFTR has presented a formidable challenge to obtain monodisperse, biophysically stable protein. Here we report a comprehensive study comparing effects of single and multiple NBD1 mutations on stability of both the NBD1 domain alone and on purified full length human CFTR. Single mutations S492P, A534P, I539T acted additively, and when combined with M470V, S495P, and R555K cumulatively yielded an NBD1 with highly improved structural stability. Strategic combinations of these mutations strongly stabilized the domain to attain a calorimetric Tm > 70 °C. Replica exchange molecular dynamics simulations on the most stable 6SS-NBD1 variant implicated fluctuations, electrostatic interactions and side chain packing as potential contributors to improved stability. Progressive stabilization of NBD1 directly correlated with enhanced structural stability of full-length CFTR protein. Thermal unfolding of the stabilized CFTR mutants, monitored by changes in intrinsic fluorescence, demonstrated that Tm could be shifted as high as 67.4 °C in 6SS-CFTR, more than 20 °C higher than wild-type. H1402S, an NBD2 mutation, conferred CFTR with additional thermal stability, possibly by stabilizing an NBD-dimerized conformation. CFTR variants with NBD1-stabilizing mutations were expressed at the cell surface in mammalian cells, exhibited ATPase and channel activity, and retained these functions to higher temperatures. The capability to produce enzymatically active CFTR with improved structural stability amenable to biophysical and structural studies will advance mechanistic investigations and future cystic fibrosis drug development.
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Affiliation(s)
- Zhengrong Yang
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ellen Hildebrandt
- Department of Cell Biology and Biochemistry, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street, Stop 6540, Lubbock, TX 79430, USA
| | - Fan Jiang
- Department of Medicine, University of Alabama at Birmingham, 701 19th Street South, Birmingham, AL 35294-0007, USA
| | - Andrei A Aleksandrov
- Department of Biochemistry and Biophysics and Cystic Fibrosis Treatment and Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Netaly Khazanov
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Qingxian Zhou
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jianli An
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew T Mezzell
- Department of Medicine, University of Alabama at Birmingham, 701 19th Street South, Birmingham, AL 35294-0007, USA
| | - Bala M Xavier
- Department of Cell Biology and Biochemistry, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street, Stop 6540, Lubbock, TX 79430, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, 701 19th Street South, Birmingham, AL 35294-0007, USA
| | - John R Riordan
- Department of Biochemistry and Biophysics and Cystic Fibrosis Treatment and Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hanoch Senderowitz
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - John C Kappes
- Department of Medicine, University of Alabama at Birmingham, 701 19th Street South, Birmingham, AL 35294-0007, USA; Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL 35233, USA
| | | | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street, Stop 6540, Lubbock, TX 79430, USA.
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30
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31
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Xavier BM, Hildebrandt E, Jiang F, Ding H, Kappes JC, Urbatsch IL. Substitution of Yor1p NBD1 residues improves the thermal stability of Human Cystic Fibrosis Transmembrane Conductance Regulator. Protein Eng Des Sel 2017; 30:729-741. [PMID: 29053845 PMCID: PMC5914393 DOI: 10.1093/protein/gzx054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/08/2017] [Accepted: 09/15/2017] [Indexed: 01/05/2023] Open
Abstract
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a plasma membrane chloride channel protein that regulates vertebrate fluid homeostasis. The inefficiency of wild type human CFTR protein folding/trafficking is exacerbated by genetic mutations that can cause protein misfolding in the endoplasmic reticulum (ER) and subsequent degradation. This project investigates small changes in protein sequence that can alter the thermal stability of the large multi-domain CFTR protein. We target a conserved 70-residue α-subdomain located in the first nucleotide-binding domain that hosts the common misfolding mutation ∆F508. To investigate substitutions that can stabilize this domain, we constructed chimeras between human CFTR and its closest yeast homolog Yor1p. The α-subdomain of Yor1p was replaced with that of CFTR in Saccharomyces cerevisiae. Cellular localization of green fluorescence protein-tagged Yor1p-CFTR chimeras was analyzed by fluorescence microscopy and quantitative multispectral imaging flow cytometry, steady-state protein levels were compared by SDS-PAGE and protein function probed by a phenotypic oligomycin resistance assay. The chimeras exhibited ER retention in yeast characteristic of defective protein folding/processing. Substitution of seven CFTR α-subdomain residues that are highly conserved in Yor1p and other transporters but differ in CFTR (S495P/R516K/F533L/A534P/K536G/I539T/R553K) improved Yor1p-CFTR chimera localization to the yeast plasma membrane. When introduced into human CFTR expressed in mammalian cells, the same substitutions improve the purified protein thermal stability. This stabilized human CFTR protein will be directly useful for structural and biophysical studies that have been limited by the thermal sensitivity of wild type CFTR. The insights into critical structural residues within CFTR could facilitate development of effective therapeutics for CF-causing mutations.
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Affiliation(s)
- B M Xavier
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - E Hildebrandt
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - F Jiang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - H Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - J C Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Veterans Affairs Medical Center, Research Service, Birmingham, AL 35294, USA
| | - I L Urbatsch
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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Krishnan V, Maddox JW, Rodriguez T, Gleason E. A role for the cystic fibrosis transmembrane conductance regulator in the nitric oxide-dependent release of Cl - from acidic organelles in amacrine cells. J Neurophysiol 2017; 118:2842-2852. [PMID: 28835528 DOI: 10.1152/jn.00511.2017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/21/2017] [Accepted: 08/21/2017] [Indexed: 12/16/2022] Open
Abstract
γ-Amino butyric acid (GABA) and glycine typically mediate synaptic inhibition because their ligand-gated ion channels support the influx of Cl- However, the electrochemical gradient for Cl- across the postsynaptic plasma membrane determines the voltage response of the postsynaptic cell. Typically, low cytosolic Cl- levels support inhibition, whereas higher levels of cytosolic Cl- can suppress inhibition or promote depolarization. We previously reported that nitric oxide (NO) releases Cl- from acidic organelles and transiently elevates cytosolic Cl-, making the response to GABA and glycine excitatory. In this study, we test the hypothesis that the cystic fibrosis transmembrane conductance regulator (CFTR) is involved in the NO-dependent efflux of organellar Cl- We first establish the mRNA and protein expression of CFTR in our model system, cultured chick retinal amacrine cells. Using whole cell voltage-clamp recordings of currents through GABA-gated Cl- channels, we examine the effects of pharmacological inhibition of CFTR on the NO-dependent release of internal Cl- To interfere with the expression of CFTR, we used clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 genome editing. We find that both pharmacological inhibition and CRISPR/Cas9-mediated knockdown of CFTR block the ability of NO to release Cl- from internal stores. These results demonstrate that CFTR is required for the NO-dependent efflux of Cl- from acidic organelles.NEW & NOTEWORTHY Although CFTR function has been studied extensively in the context of epithelia, relatively little is known about its function in neurons. We show that CFTR is involved in an NO-dependent release of Cl- from acidic organelles. This internal function of CFTR is particularly relevant to neuronal physiology because postsynaptic cytosolic Cl- levels determine the outcome of GABA- and glycinergic synaptic signaling. Thus the CFTR may play a role in regulating synaptic transmission.
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Affiliation(s)
- Vijai Krishnan
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - J Wesley Maddox
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Tyler Rodriguez
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Evanna Gleason
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
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Musgaard M, Paramo T, Domicevica L, Andersen OJ, Biggin PC. Insights into channel dysfunction from modelling and molecular dynamics simulations. Neuropharmacology 2017; 132:20-30. [PMID: 28669899 DOI: 10.1016/j.neuropharm.2017.06.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 06/06/2017] [Accepted: 06/28/2017] [Indexed: 11/20/2022]
Abstract
Developments in structural biology mean that the number of different ion channel structures has increased significantly in recent years. Structures of ion channels enable us to rationalize how mutations may lead to channelopathies. However, determining the structures of ion channels is still not trivial, especially as they necessarily exist in many distinct functional states. Therefore, the use of computational modelling can provide complementary information that can refine working hypotheses of both wild type and mutant ion channels. The simplest but still powerful tool is homology modelling. Many structures are available now that can provide suitable templates for many different types of ion channels, allowing a full three-dimensional interpretation of mutational effects. These structural models, and indeed the structures themselves obtained by X-ray crystallography, and more recently cryo-electron microscopy, can be subjected to molecular dynamics simulations, either as a tool to help explore the conformational dynamics in detail or simply as a means to refine the models further. Here we review how these approaches have been used to improve our understanding of how diseases might be linked to specific mutations in ion channel proteins. This article is part of the Special Issue entitled 'Channelopathies.'
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Affiliation(s)
- Maria Musgaard
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Teresa Paramo
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Laura Domicevica
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Ole Juul Andersen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
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34
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Molecular Structure of the Human CFTR Ion Channel. Cell 2017; 169:85-95.e8. [PMID: 28340353 DOI: 10.1016/j.cell.2017.02.024] [Citation(s) in RCA: 346] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/09/2017] [Accepted: 02/14/2017] [Indexed: 01/13/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is an ATP-binding cassette (ABC) transporter that uniquely functions as an ion channel. Here, we present a 3.9 Å structure of dephosphorylated human CFTR without nucleotides, determined by electron cryomicroscopy (cryo-EM). Close resemblance of this human CFTR structure to zebrafish CFTR under identical conditions reinforces its relevance for understanding CFTR function. The human CFTR structure reveals a previously unresolved helix belonging to the R domain docked inside the intracellular vestibule, precluding channel opening. By analyzing the sigmoid time course of CFTR current activation, we propose that PKA phosphorylation of the R domain is enabled by its infrequent spontaneous disengagement, which also explains residual ATPase and gating activity of dephosphorylated CFTR. From comparison with MRP1, a feature distinguishing CFTR from all other ABC transporters is the helix-loop transition in transmembrane helix 8, which likely forms the structural basis for CFTR's channel function.
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Hudson RP, Dawson JE, Chong PA, Yang Z, Millen L, Thomas PJ, Brouillette CG, Forman-Kay JD. Direct Binding of the Corrector VX-809 to Human CFTR NBD1: Evidence of an Allosteric Coupling between the Binding Site and the NBD1:CL4 Interface. Mol Pharmacol 2017; 92:124-135. [PMID: 28546419 DOI: 10.1124/mol.117.108373] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/17/2017] [Indexed: 01/06/2023] Open
Abstract
Understanding the mechanism of action of modulator compounds for the cystic fibrosis transmembrane conductance regulator (CFTR) is key for the optimization of therapeutics as well as obtaining insights into the molecular mechanisms of CFTR function. We demonstrate the direct binding of VX-809 to the first nucleotide-binding domain (NBD1) of human CFTR. Disruption of the interaction between C-terminal helices and the NBD1 core upon VX-809 binding is observed from chemical shift changes in the NMR spectra of residues in the helices and on the surface of β-strands S3, S9, and S10. Binding to VX-809 leads to a significant negative shift in NBD1 thermal melting temperature (Tm), pointing to direct VX-809 interaction shifting the NBD1 conformational equilibrium. An inter-residue correlation analysis of the chemical shift changes provides evidence of allosteric coupling between the direct binding site and the NBD1:CL4 interface, thus enabling effects on the interface in the absence of direct binding in that location. These NMR binding data and the negative Tm shifts are very similar to those previously reported by us for binding of the dual corrector-potentiator CFFT-001 to NBD1 (Hudson et al., 2012), suggesting that the two compounds may share some aspects of their mechanisms of action. Although previous studies have shown an important role for VX-809 in modulating the conformation of the first membrane spanning domain (Aleksandrov et al., 2012; Ren et al., 2013), this additional mode of VX-809 binding provides insight into conformational dynamics and allostery within CFTR.
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Affiliation(s)
- Rhea P Hudson
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Jennifer E Dawson
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - P Andrew Chong
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Zhengrong Yang
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Linda Millen
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Philip J Thomas
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Christie G Brouillette
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Julie D Forman-Kay
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.).
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36
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Jones PM, George AM. How Intrinsic Dynamics Mediates the Allosteric Mechanism in the ABC Transporter Nucleotide Binding Domain Dimer. J Chem Theory Comput 2017; 13:1712-1722. [PMID: 28240893 DOI: 10.1021/acs.jctc.6b00839] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A protein's architecture facilitates specific motions-intrinsic dynamic modes-that are employed to effect function. Here we used molecular dynamics (MD) simulations to investigate the dynamics of the MJ0796 ABC transporter nucleotide-binding domain (NBD). ABC transporter NBDs form a rotationally symmetric dimer whereby two equivalent active sites are formed at their interface; in complex with a dimer of transmembrane domains they hydrolyze ATP to energize translocation of substrates across cellular membranes. Our data suggest the ABC NBD's ensemble of functional states can be understood predominately in terms of conformational changes between its major subdomains, occurring along two orthogonal dynamic modes. The data show that ligands and oligomeric interactions modulate the equilibrium conformation of the NBD with respect to these motions, suggesting that allostery is achieved by affecting the energetic profile along these two modes. The observed dynamics and allostery integrate consonantly and logically within a mechanistic framework for the ABC NBD dimer, which is supported by a large body of experimental and theoretical data, providing a higher resolution view of the enzyme's dynamic cycle. Our study shows how valuable mechanistic inferences can be derived from accessible short-time scale MD simulations of an enzyme's substructures.
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Affiliation(s)
- Peter M Jones
- School of Life Sciences, University of Technology Sydney , P.O. Box 123, Broadway, New South Wales 2007, Australia
| | - Anthony M George
- School of Life Sciences, University of Technology Sydney , P.O. Box 123, Broadway, New South Wales 2007, Australia
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37
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Meng X, Wang Y, Wang X, Wrennall JA, Rimington TL, Li H, Cai Z, Ford RC, Sheppard DN. Two Small Molecules Restore Stability to a Subpopulation of the Cystic Fibrosis Transmembrane Conductance Regulator with the Predominant Disease-causing Mutation. J Biol Chem 2017; 292:3706-3719. [PMID: 28087700 PMCID: PMC5339754 DOI: 10.1074/jbc.m116.751537] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 01/12/2017] [Indexed: 12/17/2022] Open
Abstract
Cystic fibrosis (CF) is caused by mutations that disrupt the plasma membrane expression, stability, and function of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channel. Two small molecules, the CFTR corrector lumacaftor and the potentiator ivacaftor, are now used clinically to treat CF, although some studies suggest that they have counteracting effects on CFTR stability. Here, we investigated the impact of these compounds on the instability of F508del-CFTR, the most common CF mutation. To study individual CFTR Cl- channels, we performed single-channel recording, whereas to assess entire CFTR populations, we used purified CFTR proteins and macroscopic CFTR Cl- currents. At 37 °C, low temperature-rescued F508del-CFTR more rapidly lost function in cell-free membrane patches and showed altered channel gating and current flow through open channels. Compared with purified wild-type CFTR, the full-length F508del-CFTR was about 10 °C less thermostable. Lumacaftor partially stabilized purified full-length F508del-CFTR and slightly delayed deactivation of individual F508del-CFTR Cl- channels. By contrast, ivacaftor further destabilized full-length F508del-CFTR and accelerated channel deactivation. Chronic (prolonged) co-incubation of F508del-CFTR-expressing cells with lumacaftor and ivacaftor deactivated macroscopic F508del-CFTR Cl- currents. However, at the single-channel level, chronic co-incubation greatly increased F508del-CFTR channel activity and temporal stability in most, but not all, cell-free membrane patches. We conclude that chronic lumacaftor and ivacaftor co-treatment restores stability in a small subpopulation of F508del-CFTR Cl- channels but that the majority remain destabilized. A fuller understanding of these effects and the characterization of the small F508del-CFTR subpopulation might be crucial for CF therapy development.
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Affiliation(s)
- Xin Meng
- From the Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PL, United Kingdom and
| | - Yiting Wang
- the School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Xiaomeng Wang
- From the Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PL, United Kingdom and
| | - Joe A Wrennall
- the School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Tracy L Rimington
- From the Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PL, United Kingdom and
| | - Hongyu Li
- the School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Zhiwei Cai
- the School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Robert C Ford
- From the Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PL, United Kingdom and
| | - David N Sheppard
- the School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
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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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39
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Abstract
The anion channel cystic fibrosis transmembrane conductance regulator (CFTR) is a unique ATP-binding cassette (ABC) transporter. CFTR plays a pivotal role in transepithelial ion transport as its dysfunction in the genetic disease cystic fibrosis (CF) dramatically demonstrates. Phylogenetic analysis suggests that CFTR first appeared in aquatic vertebrates fulfilling important roles in osmosensing and organ development. Here, we review selectively, knowledge of CFTR structure, function and pharmacology, gleaned from cross-species comparative studies of recombinant CFTR proteins, including CFTR chimeras. The data argue that subtle changes in CFTR structure can affect strongly channel function and the action of CF mutations.
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40
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Abstract
Allosteric transition, defined as conformational changes induced by ligand binding, is one of the fundamental properties of proteins. Allostery has been observed and characterized in many proteins, and has been recently utilized to control protein function via regulation of protein activity. Here, we review the physical and evolutionary origin of protein allostery, as well as its importance to protein regulation, drug discovery, and biological processes in living systems. We describe recently developed approaches to identify allosteric pathways, connected sets of pairwise interactions that are responsible for propagation of conformational change from the ligand-binding site to a distal functional site. We then present experimental and computational protein engineering approaches for control of protein function by modulation of allosteric sites. As an example of application of these approaches, we describe a synergistic computational and experimental approach to rescue the cystic-fibrosis-associated protein cystic fibrosis transmembrane conductance regulator, which upon deletion of a single residue misfolds and causes disease. This example demonstrates the power of allosteric manipulation in proteins to both elucidate mechanisms of molecular function and to develop therapeutic strategies that rescue those functions. Allosteric control of proteins provides a tool to shine a light on the complex cascades of cellular processes and facilitate unprecedented interrogation of biological systems.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
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41
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Estácio SG, Martiniano HFMC, Faísca PFN. Thermal unfolding simulations of NBD1 domain variants reveal structural motifs associated with the impaired folding of F508del-CFTR. MOLECULAR BIOSYSTEMS 2016; 12:2834-48. [DOI: 10.1039/c6mb00193a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The deletion of phenylalanine 508 reshapes the conformational space of the NBD1 domain that populates unique intermediate states that provide insights into the molecular events that underlie the impaired folding of F508del-NBD1.
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Affiliation(s)
- Sílvia G. Estácio
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - Hugo F. M. C. Martiniano
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - Patrícia F. N. Faísca
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
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42
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Zhenin M, Noy E, Senderowitz H. REMD Simulations Reveal the Dynamic Profile and Mechanism of Action of Deleterious, Rescuing, and Stabilizing Perturbations to NBD1 from CFTR. J Chem Inf Model 2015; 55:2349-64. [PMID: 26418372 DOI: 10.1021/acs.jcim.5b00312] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cystic Fibrosis (CF) is a lethal, genetic disease caused by mutations to the CFTR chloride channel. The most common CF causing mutation is the deletion of F508 from the first Nucleotide Binding Domain (F508del-NBD1). This mutation leads to a thermally unstable domain and a misfolded, nonfunctioning CFTR. Replica Exchange MD simulations were used to simulate seven NBD1 constructs including wt and F508del-NBD1 both alone and in the presence of known rescuing mutations as well as F508del-NBD1 in complex with a known small (ligand) stabilizer. Analyzing the resulting trajectories suggests that differences in the biochemical properties of the constructs result from local and coupled differences in their dynamic profiles. A comparative analysis of these profiles as well as of the resulting trajectories reveals how the different perturbations exert their deleterious, rescuing, and stabilizing effects on NBD1. These simulations may therefore be useful for the design and mechanism-of-action analysis of new NBD1 stabilizers.
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Affiliation(s)
- Michael Zhenin
- Department of Chemistry, Bar Ilan University , Ramat-Gan 52900, Israel
| | - Efrat Noy
- Department of Chemistry, Bar Ilan University , Ramat-Gan 52900, Israel
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43
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Characterizing diverse orthologues of the cystic fibrosis transmembrane conductance regulator protein for structural studies. Biochem Soc Trans 2015; 43:894-900. [DOI: 10.1042/bst20150081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As an ion channel, the cystic fibrosis transmembrane conductance regulator (CFTR) protein occupies a unique niche within the ABC family. Orthologues of CFTR are extant throughout the animal kingdom from sharks to platypods to sheep, where the osmoregulatory function of the protein has been applied to differing lifestyles and diverse organ systems. In humans, loss-of-function mutations to CFTR cause the disease cystic fibrosis, which is a significant health burden in populations of white European descent. Orthologue screening has proved fruitful in the pursuit of high-resolution structural data for several membrane proteins, and we have applied some of the princples developed in previous studies to the expression and purification of CFTR. We have overexpressed this protein, along with evolutionarily diverse orthologues, in Saccharomyces cerevisiae and developed a purification to isolate it in quantities sufficient for structural and functional studies.
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44
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Solomon GM, Marshall SG, Ramsey BW, Rowe SM. Breakthrough therapies: Cystic fibrosis (CF) potentiators and correctors. Pediatr Pulmonol 2015; 50 Suppl 40:S3-S13. [PMID: 26097168 PMCID: PMC4620567 DOI: 10.1002/ppul.23240] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/29/2015] [Accepted: 06/03/2015] [Indexed: 12/28/2022]
Abstract
Cystic Fibrosis is caused by mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene resulting in abnormal protein function. Recent advances of targeted molecular therapies and high throughput screening have resulted in multiple drug therapies that target many important mutations in the CFTR protein. In this review, we provide the latest results and current progress of CFTR modulators for the treatment of cystic fibrosis, focusing on potentiators of CFTR channel gating and Phe508del processing correctors for the Phe508del CFTR mutation. Special emphasis is placed on the molecular basis underlying these new therapies and emerging results from the latest clinical trials. The future directions for augmenting the rescue of Phe508del with CFTR modulators are also emphasized.
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Affiliation(s)
- George M Solomon
- Department of Medicine and the Gregory Fleming James Cystic Fibrosis Research Center, Birmingham, Alabama
| | - Susan G Marshall
- Division of Pulmonary Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington
| | - Bonnie W Ramsey
- Division of Pulmonary Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington.,Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, Washington
| | - Steven M Rowe
- Department of Medicine and the Gregory Fleming James Cystic Fibrosis Research Center, Birmingham, Alabama.,Departments of Medicine, Pediatrics, Cell Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
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45
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Thermal stability of purified and reconstituted CFTR in a locked open channel conformation. Protein Expr Purif 2015; 116:159-66. [PMID: 26384709 DOI: 10.1016/j.pep.2015.09.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/11/2015] [Accepted: 09/14/2015] [Indexed: 11/20/2022]
Abstract
CFTR is unique among ABC transporters as the only one functioning as an ion channel and from a human health perspective because mutations in its gene cause cystic fibrosis. Although considerable advances have been made towards understanding CFTR's mechanism of action and the impact of mutations, the lack of a high-resolution 3D structure has hindered progress. The large multi-domain membrane glycoprotein is normally present at low copy number and when over expressed at high levels it aggregates strongly, limiting the production of stable mono-disperse preparations. While the reasons for the strong self-association are not fully understood, its relatively low thermal stability seems likely to be one. The major CF causing mutation, ΔF508, renders the protein very thermally unstable and therefore a great deal of attention has been paid to this property of CFTR. Multiple second site mutations of CFTR in NBD1 where F508 normally resides and small molecule binders of the domain increase the thermal stability of the mutant. These manipulations also stabilize the wild-type protein. Here we have applied ΔF508-stabilizing changes and other modifications to generate wild-type constructs that express at much higher levels in scaled-up suspension cultures of mammalian cells. After purification and reconstitution into liposomes these proteins are active in a locked-open conformation at temperatures as high as 50 °C and remain monodisperse at 4 °C in detergent or lipid for at least a week. The availability of adequate amounts of these and related stable active preparations of homogeneous CFTR will enable stalled structural and ligand binding studies to proceed.
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46
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Chong PA, Farber PJ, Vernon RM, Hudson RP, Mittermaier AK, Forman-Kay JD. Deletion of Phenylalanine 508 in the First Nucleotide-binding Domain of the Cystic Fibrosis Transmembrane Conductance Regulator Increases Conformational Exchange and Inhibits Dimerization. J Biol Chem 2015; 290:22862-78. [PMID: 26149808 DOI: 10.1074/jbc.m115.641134] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Indexed: 12/17/2022] Open
Abstract
Deletion of Phe-508 (F508del) in the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) results in destabilization of the domain, intramolecular interactions involving the domain, and the entire channel. The destabilization caused by F508del manifests itself in defective channel processing and channel gating defects. Here, we present NMR studies of the effect of F508del and the I539T stabilizing mutation on NBD1 dynamics, with a view to understanding these changes in stability. Qualitatively, F508del NMR spectra exhibit significantly more peak broadening than WT spectra due to the enhanced intermediate time scale (millisecond to microsecond) motions in the mutant. Unexpectedly, studies of fast (nanosecond to picosecond) motions revealed that F508del NBD1 tumbles more rapidly in solution than WT NBD1. Whereas F508del tumbles at a rate nearly consistent with the monomeric state, the WT protein tumbles significantly more slowly. Paramagnetic relaxation enhancement experiments confirm that NBD1 homodimerizes in solution in the expected head-to-tail orientation. NMR spectra of WT NBD1 reveal significant concentration-dependent chemical shift perturbations consistent with NBD1 dimerization. Chemical shift analysis suggests that the more rapid tumbling of F508del is the result of an impaired ability to dimerize. Based on previously published crystal structures and NMR spectra of various NBD1 mutants, we propose that deletion of Phe-508 affects Q-loop conformational sampling in a manner that inhibits dimerization. These results provide a potential mechanism for inhibition of channel opening by F508del and support the dimer interface as a target for cystic fibrosis therapeutics.
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Affiliation(s)
- P Andrew Chong
- From the Molecular Structure and Function Program, Hospital for Sick Children, and
| | - Patrick J Farber
- From the Molecular Structure and Function Program, Hospital for Sick Children, and
| | - Robert M Vernon
- From the Molecular Structure and Function Program, Hospital for Sick Children, and
| | - Rhea P Hudson
- From the Molecular Structure and Function Program, Hospital for Sick Children, and
| | | | - Julie D Forman-Kay
- From the Molecular Structure and Function Program, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1X8 and
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47
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Maiuri L, De Stefano D, Raia V, Kroemer G. The holy grail of cystic fibrosis research: pharmacological repair of the F508del-CFTR mutation. ANNALS OF TRANSLATIONAL MEDICINE 2015; 3:S24. [PMID: 26046070 DOI: 10.3978/j.issn.2305-5839.2015.02.32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 02/10/2015] [Indexed: 11/14/2022]
Affiliation(s)
- Luigi Maiuri
- 1 European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan, Italy ; 2 SCDU of Pediatrics, Department of Health Sciences, University of Piemonte Orientale, Novara, Italy ; 3 Regional Cystic Fibrosis Center; Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, Italy ; 4 Equipe 11 labellisee Ligue contre le Cancer; INSERM U1138; Centre de Recherche des Cordeliers, Paris, France ; 5 Universite Paris Descartes, Paris, France ; 6 Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France ; 7 Pole de Biologie, Hopital Européen Georges Pompidou, AP-HP, Paris, France
| | - Daniela De Stefano
- 1 European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan, Italy ; 2 SCDU of Pediatrics, Department of Health Sciences, University of Piemonte Orientale, Novara, Italy ; 3 Regional Cystic Fibrosis Center; Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, Italy ; 4 Equipe 11 labellisee Ligue contre le Cancer; INSERM U1138; Centre de Recherche des Cordeliers, Paris, France ; 5 Universite Paris Descartes, Paris, France ; 6 Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France ; 7 Pole de Biologie, Hopital Européen Georges Pompidou, AP-HP, Paris, France
| | - Valeria Raia
- 1 European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan, Italy ; 2 SCDU of Pediatrics, Department of Health Sciences, University of Piemonte Orientale, Novara, Italy ; 3 Regional Cystic Fibrosis Center; Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, Italy ; 4 Equipe 11 labellisee Ligue contre le Cancer; INSERM U1138; Centre de Recherche des Cordeliers, Paris, France ; 5 Universite Paris Descartes, Paris, France ; 6 Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France ; 7 Pole de Biologie, Hopital Européen Georges Pompidou, AP-HP, Paris, France
| | - Guido Kroemer
- 1 European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan, Italy ; 2 SCDU of Pediatrics, Department of Health Sciences, University of Piemonte Orientale, Novara, Italy ; 3 Regional Cystic Fibrosis Center; Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, Italy ; 4 Equipe 11 labellisee Ligue contre le Cancer; INSERM U1138; Centre de Recherche des Cordeliers, Paris, France ; 5 Universite Paris Descartes, Paris, France ; 6 Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France ; 7 Pole de Biologie, Hopital Européen Georges Pompidou, AP-HP, Paris, France
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48
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Kim SJ, Yoon JS, Shishido H, Yang Z, Rooney LA, Barral JM, Skach WR. Translational tuning optimizes nascent protein folding in cells. Science 2015; 348:444-8. [DOI: 10.1126/science.aaa3974] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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49
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Cholon DM, Quinney NL, Fulcher ML, Esther CR, Das J, Dokholyan NV, Randell SH, Boucher RC, Gentzsch M. Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis. Sci Transl Med 2015; 6:246ra96. [PMID: 25101886 DOI: 10.1126/scitranslmed.3008680] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR). Newly developed "correctors" such as lumacaftor (VX-809) that improve CFTR maturation and trafficking and "potentiators" such as ivacaftor (VX-770) that enhance channel activity may provide important advances in CF therapy. Although VX-770 has demonstrated substantial clinical efficacy in the small subset of patients with a mutation (G551D) that affects only channel activity, a single compound is not sufficient to treat patients with the more common CFTR mutation, ΔF508. Thus, patients with ΔF508 will likely require treatment with both correctors and potentiators to achieve clinical benefit. However, whereas the effectiveness of acute treatment with this drug combination has been demonstrated in vitro, the impact of chronic therapy has not been established. In studies of human primary airway epithelial cells, we found that both acute and chronic treatment with VX-770 improved CFTR function in cells with the G551D mutation, consistent with clinical studies. In contrast, chronic VX-770 administration caused a dose-dependent reversal of VX-809-mediated CFTR correction in ΔF508 homozygous cultures. This result reflected the destabilization of corrected ΔF508 CFTR by VX-770, markedly increasing its turnover rate. Chronic VX-770 treatment also reduced mature wild-type CFTR levels and function. These findings demonstrate that chronic treatment with CFTR potentiators and correctors may have unexpected effects that cannot be predicted from short-term studies. Combining these drugs to maximize rescue of ΔF508 CFTR may require changes in dosing and/or development of new potentiator compounds that do not interfere with CFTR stability.
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Affiliation(s)
- Deborah M Cholon
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nancy L Quinney
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - M Leslie Fulcher
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Charles R Esther
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Division of Pediatric Pulmonology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jhuma Das
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Scott H Randell
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Richard C Boucher
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Martina Gentzsch
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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50
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Cai Z, Palmai-Pallag T, Khuituan P, Mutolo MJ, Boinot C, Liu B, Scott-Ward TS, Callebaut I, Harris A, Sheppard DN. Impact of the F508del mutation on ovine CFTR, a Cl- channel with enhanced conductance and ATP-dependent gating. J Physiol 2015; 593:2427-46. [PMID: 25763566 DOI: 10.1113/jp270227] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/02/2015] [Indexed: 12/20/2022] Open
Abstract
KEY POINTS Malfunction of the cystic fibrosis transmembrane conductance regulator (CFTR), a gated pathway for chloride movement, causes the common life-shortening genetic disease cystic fibrosis (CF). Towards the development of a sheep model of CF, we have investigated the function of sheep CFTR. We found that sheep CFTR was noticeably more active than human CFTR, while the most common CF mutation, F508del, had reduced impact on sheep CFTR function. Our results demonstrate that subtle changes in protein structure have marked effects on CFTR function and the consequences of the CF mutation F508del. ABSTRACT Cross-species comparative studies are a powerful approach to understanding the epithelial Cl(-) channel cystic fibrosis transmembrane conductance regulator (CFTR), which is defective in the genetic disease cystic fibrosis (CF). Here, we investigate the single-channel behaviour of ovine CFTR and the impact of the most common CF mutation, F508del-CFTR, using excised inside-out membrane patches from transiently transfected CHO cells. Like human CFTR, ovine CFTR formed a weakly inwardly rectifying Cl(-) channel regulated by PKA-dependent phosphorylation, inhibited by the open-channel blocker glibenclamide. However, for three reasons, ovine CFTR was noticeably more active than human CFTR. First, single-channel conductance was increased. Second, open probability was augmented because the frequency and duration of channel openings were increased. Third, with enhanced affinity and efficacy, ATP more strongly stimulated ovine CFTR channel gating. Consistent with these data, the CFTR modulator phloxine B failed to potentiate ovine CFTR Cl(-) currents. Similar to its impact on human CFTR, the F508del mutation caused a temperature-sensitive folding defect, which disrupted ovine CFTR protein processing and reduced membrane stability. However, the F508del mutation had reduced impact on ovine CFTR channel gating in contrast to its marked effects on human CFTR. We conclude that ovine CFTR forms a regulated Cl(-) channel with enhanced conductance and ATP-dependent channel gating. This phylogenetic analysis of CFTR structure and function demonstrates that subtle changes in structure have pronounced effects on channel function and the consequences of the CF mutation F508del.
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Affiliation(s)
- Zhiwei Cai
- School of Physiology and Pharmacology, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Timea Palmai-Pallag
- Human Molecular Genetics Program, Lurie Children's Research Center and Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60614, USA.,Harris Laboratory, formerly at the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Pissared Khuituan
- School of Physiology and Pharmacology, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,Center of Calcium and Bone Research, Department of Physiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Michael J Mutolo
- Human Molecular Genetics Program, Lurie Children's Research Center and Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60614, USA
| | - Clément Boinot
- Institut de Physiologie et Biologie Cellulaires, Université de Poitiers, CNRS FRE 3511, 86022, Poitiers, France
| | - Beihui Liu
- School of Physiology and Pharmacology, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Toby S Scott-Ward
- School of Physiology and Pharmacology, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Isabelle Callebaut
- IMPMC, Sorbonne Universités - UPMC Univ Paris 06, UMR CNRS 7590, Museum National d'Histoire Naturelle, IRD UMR 206, IUC, 75005, Paris, France
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center and Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60614, USA
| | - David N Sheppard
- School of Physiology and Pharmacology, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
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