1
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Kamada Y, Ohnishi Y, Nakashima C, Fujii A, Terakawa M, Hamano I, Nakayamada U, Katoh S, Hirata N, Tateishi H, Fukuda R, Takahashi H, Lukacs GL, Okiyoneda T. HERC3 facilitates ERAD of select membrane proteins by recognizing membrane-spanning domains. J Cell Biol 2024; 223:e202308003. [PMID: 38722278 PMCID: PMC11082371 DOI: 10.1083/jcb.202308003] [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: 08/01/2023] [Revised: 02/22/2024] [Accepted: 03/18/2024] [Indexed: 05/12/2024] Open
Abstract
Aberrant proteins located in the endoplasmic reticulum (ER) undergo rapid ubiquitination by multiple ubiquitin (Ub) E3 ligases and are retrotranslocated to the cytosol as part of the ER-associated degradation (ERAD). Despite several ERAD branches involving different Ub E3 ligases, the molecular machinery responsible for these ERAD branches in mammalian cells remains not fully understood. Through a series of multiplex knockdown/knockout experiments with real-time kinetic measurements, we demonstrate that HERC3 operates independently of the ER-embedded ubiquitin ligases RNF5 and RNF185 (RNF5/185) to mediate the retrotranslocation and ERAD of misfolded CFTR. While RNF5/185 participates in the ERAD process of both misfolded ABCB1 and CFTR, HERC3 uniquely promotes CFTR ERAD. In vitro assay revealed that HERC3 directly interacts with the exposed membrane-spanning domains (MSDs) of CFTR but not with the MSDs embedded in liposomes. Therefore, HERC3 could play a role in the quality control of MSDs in the cytoplasm and might be crucial for the ERAD pathway of select membrane proteins.
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Affiliation(s)
- Yuka Kamada
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Yuko Ohnishi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Chikako Nakashima
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Aika Fujii
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Mana Terakawa
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Ikuto Hamano
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Uta Nakayamada
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Saori Katoh
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Noriaki Hirata
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Hazuki Tateishi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Ryosuke Fukuda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Hirotaka Takahashi
- Division of Cell-Free Sciences, Proteo-Science Center (PROS), Ehime University, Matsuyama, Japan
| | - Gergely L. Lukacs
- Department of Physiology, McGill University, Montréal, Canada
- Department of Biochemistry, McGill University, Montréal, Canada
| | - Tsukasa Okiyoneda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
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2
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Baroni D, Scarano N, Ludovico A, Brandas C, Parodi A, Lunaccio D, Fossa P, Moran O, Cichero E, Millo E. In Silico and In Vitro Evaluation of the Mechanism of Action of Three VX809-Based Hybrid Derivatives as Correctors of the F508del CFTR Protein. Pharmaceuticals (Basel) 2023; 16:1702. [PMID: 38139828 PMCID: PMC10748060 DOI: 10.3390/ph16121702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Cystic fibrosis (CF), the most common autosomal recessive fatal genetic disease in the Caucasian population, is caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR), an anion channel that regulates salt and water transport across a variety of secretory epithelia. Deletion of phenylalanine at position 508, F508del, the most common CF-causing mutation, destabilises the CFTR protein, causing folding and trafficking defects that lead to a dramatic reduction in its functional expression. Small molecules called correctors have been developed to rescue processing-defective F508del CFTR. We have combined in silico and in vitro approaches to investigate the mechanism of action and potential as CFTR correctors of three hybrid derivatives (2a, 7a, and 7m) obtained by merging the amino-arylthiazole core with the benzodioxole carboxamide moiety characterising the corrector lumacaftor. Molecular modelling analyses suggested that the three hybrids interact with a putative region located at the MSD1/NBD1 interface. Biochemical analyses confirmed these results, showing that the three molecules affect the expression and stability of the F508del NBD1. Finally, the YFP assay was used to evaluate the influence of the three hybrid derivatives on F508del CFTR function, assessing that their effect is additive to that of the correctors VX661 and VX445. Our study shows that the development and testing of optimised compounds targeting different structural and functional defects of mutant CFTR is the best strategy to provide more effective correctors that could be used alone or in combination as a valuable therapeutic option to treat an even larger cohort of people affected by CF.
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Affiliation(s)
- Debora Baroni
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Via De Marini, 6, 16149 Genova, Italy; (A.L.); (O.M.)
| | - Naomi Scarano
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genova, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (P.F.)
| | - Alessandra Ludovico
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Via De Marini, 6, 16149 Genova, Italy; (A.L.); (O.M.)
| | - Chiara Brandas
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Via De Marini, 6, 16149 Genova, Italy; (A.L.); (O.M.)
| | - Alice Parodi
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genova, Italy; (A.P.); (D.L.); (E.M.)
| | - Dario Lunaccio
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genova, Italy; (A.P.); (D.L.); (E.M.)
| | - Paola Fossa
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genova, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (P.F.)
| | - Oscar Moran
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Via De Marini, 6, 16149 Genova, Italy; (A.L.); (O.M.)
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genova, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (P.F.)
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genova, Italy; (A.P.); (D.L.); (E.M.)
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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, 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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4
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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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5
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Zacarias S, Batista MSP, Ramalho SS, Victor BL, Farinha CM. Rescue of Rare CFTR Trafficking Mutants Highlights a Structural Location-Dependent Pattern for Correction. Int J Mol Sci 2023; 24:ijms24043211. [PMID: 36834620 PMCID: PMC9961391 DOI: 10.3390/ijms24043211] [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: 11/17/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Cystic Fibrosis (CF) is a genetic disease caused by mutations in the gene encoding the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) channel. Currently, more than 2100 variants have been identified in the gene, with a large number being very rare. The approval of modulators that act on mutant CFTR protein, correcting its molecular defect and thus alleviating the burden of the disease, revolutionized the field of CF. However, these drugs do not apply to all patients with CF, especially those with rare mutations-for which there is a lack of knowledge on the molecular mechanisms of the disease and the response to modulators. In this work, we evaluated the impact of several rare putative class II mutations on the expression, processing, and response of CFTR to modulators. Novel cell models consisting of bronchial epithelial cell lines expressing CFTR with 14 rare variants were created. The variants studied are localized at Transmembrane Domain 1 (TMD1) or very close to the signature motif of Nucleotide Binding Domain 1 (NBD1). Our data show that all mutations analyzed significantly decrease CFTR processing and while TMD1 mutations respond to modulators, those localized in NBD1 do not. Molecular modeling calculations confirm that the mutations in NBD1 induce greater destabilization of CFTR structure than those in TMD1. Furthermore, the structural proximity of TMD1 mutants to the reported binding site of CFTR modulators such as VX-809 and VX-661, make them more efficient in stabilizing the CFTR mutants analyzed. Overall, our data suggest a pattern for mutation location and impact in response to modulators that correlates with the global effect of the mutations on CFTR structure.
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6
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Fiedorczuk K, Chen J. Molecular structures reveal synergistic rescue of Δ508 CFTR by Trikafta modulators. Science 2022; 378:284-290. [PMID: 36264792 PMCID: PMC9912939 DOI: 10.1126/science.ade2216] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The predominant mutation causing cystic fibrosis, a deletion of phenylalanine 508 (Δ508) in the cystic fibrosis transmembrane conductance regulator (CFTR), leads to severe defects in CFTR biogenesis and function. The advanced therapy Trikafta combines the folding corrector tezacaftor (VX-661), the channel potentiator ivacaftor (VX-770), and the dual-function modulator elexacaftor (VX-445). However, it is unclear how elexacaftor exerts its effects, in part because the structure of Δ508 CFTR is unknown. Here, we present cryo-electron microscopy structures of Δ508 CFTR in the absence and presence of CFTR modulators. When used alone, elexacaftor partially rectified interdomain assembly defects in Δ508 CFTR, but when combined with a type I corrector, did so fully. These data illustrate how the different modulators in Trikafta synergistically rescue Δ508 CFTR structure and function.
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Affiliation(s)
- Karol Fiedorczuk
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Jue Chen
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY 10065, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA,Corresponding author.
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7
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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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8
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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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9
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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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10
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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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11
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Lopes-Pacheco M, Pedemonte N, Veit G. Discovery of CFTR modulators for the treatment of cystic fibrosis. Expert Opin Drug Discov 2021; 16:897-913. [PMID: 33823716 DOI: 10.1080/17460441.2021.1912732] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a life-threatening inherited disease caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR) protein, an anion channel expressed at the apical membrane of secretory epithelia. CF leads to multiorgan dysfunction with progressive deterioration of lung function being the major cause of untimely death. Conventional CF therapies target only symptoms and consequences downstream of the primary genetic defect and the current life expectancy and quality of life of these individuals are still very limited. AREA COVERED CFTR modulator drugs are novel-specialized therapies that enhance or even restore functional expression of CFTR mutants and have been approved for clinical use for individuals with specific CF genotypes. This review summarizes classical approaches used for the pre-clinical development of CFTR correctors and potentiators as well as emerging strategies aiming to accelerate modulator development and expand theratyping efforts. EXPERT OPINION Highly effective CFTR modulator drugs are expected to deeply modify the disease course for the majority of individuals with CF. A multitude of experimental approaches have been established to accelerate the development of novel modulators. CF patient-derived specimens are valuable cell models to predict therapeutic effectiveness of existing (and novel) modulators in a precision medicine approach.
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Affiliation(s)
| | | | - Guido Veit
- Department of Physiology, McGill University, Montréal, Canada
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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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Adivitiya, Kaushik MS, Chakraborty S, Veleri S, Kateriya S. Mucociliary Respiratory Epithelium Integrity in Molecular Defense and Susceptibility to Pulmonary Viral Infections. BIOLOGY 2021; 10:95. [PMID: 33572760 PMCID: PMC7911113 DOI: 10.3390/biology10020095] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/08/2023]
Abstract
Mucociliary defense, mediated by the ciliated and goblet cells, is fundamental to respiratory fitness. The concerted action of ciliary movement on the respiratory epithelial surface and the pathogen entrapment function of mucus help to maintain healthy airways. Consequently, genetic or acquired defects in lung defense elicit respiratory diseases and secondary microbial infections that inflict damage on pulmonary function and may even be fatal. Individuals living with chronic and acute respiratory diseases are more susceptible to develop severe coronavirus disease-19 (COVID-19) illness and hence should be proficiently managed. In light of the prevailing pandemic, we review the current understanding of the respiratory system and its molecular components with a major focus on the pathophysiology arising due to collapsed respiratory epithelium integrity such as abnormal ciliary movement, cilia loss and dysfunction, ciliated cell destruction, and changes in mucus rheology. The review includes protein interaction networks of coronavirus infection-manifested implications on the molecular machinery that regulates mucociliary clearance. We also provide an insight into the alteration of the transcriptional networks of genes in the nasopharynx associated with the mucociliary clearance apparatus in humans upon infection by severe acute respiratory syndrome coronavirus-2.
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Affiliation(s)
- Adivitiya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Manish Singh Kaushik
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Soura Chakraborty
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Shobi Veleri
- Drug Safety Division, ICMR-National Institute of Nutrition, Hyderabad 500007, India;
| | - Suneel Kateriya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
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14
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Discovery of novel VX-809 hybrid derivatives as F508del-CFTR correctors by molecular modeling, chemical synthesis and biological assays. Eur J Med Chem 2020; 208:112833. [DOI: 10.1016/j.ejmech.2020.112833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 11/21/2022]
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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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Beswick E, Amich J, Gago S. Factoring in the Complexity of the Cystic Fibrosis Lung to Understand Aspergillus fumigatus and Pseudomonas aeruginosa Interactions. Pathogens 2020; 9:pathogens9080639. [PMID: 32781694 PMCID: PMC7460534 DOI: 10.3390/pathogens9080639] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/25/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Pseudomonas aeruginosa has long been established as the most prevalent respiratory pathogen in Cystic Fibrosis (CF) patients, with opportunistic infection causing profound morbidity and mortality. Recently, Aspergillus fumigatus has also been recognised as a key contributor to CF lung deterioration, being consistently associated with decreased lung function and worsened prognosis in these patients. As clinical evidence for the common occurrence of combined infection with these two pathogens increases, research into the mechanism and consequences of their interaction is becoming more relevant. Clinical evidence suggests a synergistic effect of combined infection, which translates into a poorer prognosis for the patients. In vitro results from the laboratory have identified a variety of possible synergistic and antagonistic interactions between A. fumigatus and P. aeruginosa. Here, we present a comprehensive overview of the complex environment of the CF lung and discuss how it needs to be considered to determine the exact molecular interactions that A. fumigatus and P. aeruginosa undergo during combined infection and their effects on the host.
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Affiliation(s)
- Emily Beswick
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
- Academic Unit of Medical Education, Medical School, University of Sheffield, Beech Hill Road, Broomhall, Sheffield S10 2TG, UK;
| | - Jorge Amich
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
- Correspondence: (J.A.); (S.G.)
| | - Sara Gago
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
- Correspondence: (J.A.); (S.G.)
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17
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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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18
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Recent Strategic Advances in CFTR Drug Discovery: An Overview. Int J Mol Sci 2020; 21:ijms21072407. [PMID: 32244346 PMCID: PMC7177952 DOI: 10.3390/ijms21072407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR)-rescuing drugs have already transformed cystic fibrosis (CF) from a fatal disease to a treatable chronic condition. However, new-generation drugs able to bind CFTR with higher specificity/affinity and to exert stronger therapeutic benefits and fewer side effects are still awaited. Computational methods and biosensors have become indispensable tools in the process of drug discovery for many important human pathologies. Instead, they have been used only piecemeal in CF so far, calling for their appropriate integration with well-tried CF biochemical and cell-based models to speed up the discovery of new CFTR-rescuing drugs. This review will give an overview of the available structures and computational models of CFTR and of the biosensors, biochemical and cell-based assays already used in CF-oriented studies. It will also give the reader some insights about how to integrate these tools as to improve the efficiency of the drug discovery process targeted to CFTR.
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19
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Farkas B, Tordai H, Padányi R, Tordai A, Gera J, Paragi G, Hegedűs T. Discovering the chloride pathway in the CFTR channel. Cell Mol Life Sci 2020; 77:765-778. [PMID: 31327045 PMCID: PMC7039865 DOI: 10.1007/s00018-019-03211-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/22/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022]
Abstract
Cystic fibrosis (CF), a lethal monogenic disease, is caused by pathogenic variants of the CFTR chloride channel. The majority of CF mutations affect protein folding and stability leading overall to diminished apical anion conductance of epithelial cells. The recently published cryo-EM structures of full-length human and zebrafish CFTR provide a good model to gain insight into structure-function relationships of CFTR variants. Although, some of the structures were determined in the phosphorylated and ATP-bound active state, none of the static structures showed an open pathway for chloride permeation. Therefore, we performed molecular dynamics simulations to generate a conformational ensemble of the protein and used channel detecting algorithms to identify conformations with an opened channel. Our simulations indicate a main intracellular entry at TM4/6, a secondary pore at TM10/12, and a bottleneck region involving numerous amino acids from TM1, TM6, and TM12 in accordance with experiments. Since chloride ions entered the pathway in our equilibrium simulations, but did not traverse the bottleneck region, we performed metadynamics simulations, which revealed two possible exits. One of the chloride ions exits includes hydrophobic lipid tails that may explain the lipid-dependency of CFTR function. In summary, our in silico study provides a detailed description of a potential chloride channel pathway based on a recent cryo-EM structure and may help to understand the gating of the CFTR chloride channel, thus contributing to novel strategies to rescue dysfunctional mutants.
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Affiliation(s)
- Bianka Farkas
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- Faculty of Information Technology, Pázmány Péter Catholic University, Budapest, Hungary
| | - Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Rita Padányi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Attila Tordai
- Department of Pathophysiology, Semmelweis University, Budapest, Hungary
| | - János Gera
- Department of Medical Chemistry, University of Szeged, Szeged, Hungary
| | - Gábor Paragi
- MTA-SZTE Biomimetic System Research Group, Hungarian Academy of Sciences, Szeged, Hungary
- Institute of Physics, University of Pécs, Pecs, Hungary
| | - Tamás Hegedűs
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
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20
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Abreu B, Lopes EF, Oliveira ASF, Soares CM. F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis. Proteins 2019; 88:113-126. [PMID: 31298435 DOI: 10.1002/prot.25776] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/17/2019] [Accepted: 07/06/2019] [Indexed: 12/20/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) channel is an ion channel responsible for chloride transport in epithelia and it belongs to the class of ABC transporters. The deletion of phenylalanine 508 (F508del) in CFTR is the most common mutation responsible for cystic fibrosis. Little is known about the effect of the mutation in the isolated nucleotide binding domains (NBDs), on dimer dynamics, ATP hydrolysis and even on nucleotide binding. Using molecular dynamics simulations of the human CFTR NBD dimer, we showed that F508del increases, in the prehydrolysis state, the inter-motif distance in both ATP binding sites (ABP) when ATP is bound. Additionally, a decrease in the number of catalytically competent conformations was observed in the presence of F508del. We used the subtraction technique to study the first 300 ps after ATP hydrolysis in the catalytic competent site and found that the F508del dimer evidences lower conformational changes than the wild type. Using longer simulation times, the magnitude of the conformational changes in both forms increases. Nonetheless, the F508del dimer shows lower C-α RMS values in comparison to the wild-type, on the F508del loop, on the residues surrounding the catalytic site and the portion of NBD2 adjacent to ABP1. These results provide evidence that F508del interferes with the NBD dynamics before and after ATP hydrolysis. These findings shed a new light on the effect of F508del on NBD dynamics and reveal a novel mechanism for the influence of F508del on CFTR.
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Affiliation(s)
- Bárbara Abreu
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Emanuel F Lopes
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - A S F Oliveira
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal.,School of Biochemistry & Center for Computational Chemistry, University of Bristol, Bristol, UK
| | - Cláudio M Soares
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
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21
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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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22
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Bergbower EAS, Sabirzhanova I, Boinot C, Guggino WB, Cebotaru L. Restoration of F508-del Function by Transcomplementation: The Partners Meet in the Endoplasmic Reticulum. Cell Physiol Biochem 2019; 52:1267-1279. [PMID: 31026390 DOI: 10.33594/000000089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/23/2019] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND/AIMS Because of the small size of adeno-associated virus, AAV, the cystic fibrosis conductance regulator, CFTR, cDNA is too large to fit within AAV and must be truncated. We report here on two truncated versions of CFTR, which, when inserted into AAV1 and used to infect airway cells, rescue F508-del CFTR via transcomplementation. The purpose of this study is to shed light on where in the cell transcomplementation occurs and how it results in close association between the endogenous F508-del and truncated CFTR. METHODS We treated CF airway cells (CFBE41o-) with AAV2/1 (AAV2 inverted terminal repeats/AAV1 capsid) containing truncated forms of CFTR, ∆264 and ∆27-264 CFTR, who can restore the function of F508-del by transcomplementation. We addressed the aims of the study using a combination of confocal microscopy and short circuit currents measurements. For the latter, CF bronchial epithelial cells (CFBE) were grown on permeable supports. RESULTS We show that both F508del and the truncation mutants colocalize in the ER and that both the rescued F508-del and the transcomplementing mutants reach the plasma membrane together. There was significant fluorescence resonance energy transfer (FRET) between F508-del and the transcomplementing mutants within the endoplasmic reticulum (ER), suggesting that transcomplementation occurs through a bimolecular interaction. We found that transcomplementation could increase the Isc in CFBE41o- cells stably expressing additional wt-CFTR or F508-del and in parental CFBE41o- cells expressing endogenous levels of F508-del. CONCLUSION We conclude that the functional rescue of F508-del by transcomplementation occurs via a bimolecular interaction that most likely begins in the ER and continues at the plasma membrane. These results come at an opportune time for developing a gene therapy for CF and offer new treatment options for a wide range of CF patients.
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Affiliation(s)
| | - Inna Sabirzhanova
- Departments of Medicine and Physiology, Johns Hopkins University, Baltimore, USA
| | - Clément Boinot
- Departments of Medicine and Physiology, Johns Hopkins University, Baltimore, USA
| | - William B Guggino
- Departments of Medicine and Physiology, Johns Hopkins University, Baltimore, USA
| | - Liudmila Cebotaru
- Departments of Medicine and Physiology, Johns Hopkins University, Baltimore, USA,
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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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Differential Scanning Fluorimetry and Hydrogen Deuterium Exchange Mass Spectrometry to Monitor the Conformational Dynamics of NBD1 in Cystic Fibrosis. Methods Mol Biol 2019; 1873:53-67. [PMID: 30341603 DOI: 10.1007/978-1-4939-8820-4_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cystic fibrosis (CF) is one of the most common, lethal autosomal recessive diseases in Caucasians with a life expectancy of 37-47 years. The CF transmembrane conductance regulator (CFTR) is a plasma membrane ion channel, confined to apical membrane of epithelia, and ensures transepithelial water and solute movement across secretory epithelia in several organs. Numerous CF mutations, including the most prevalent deletion of F508 (ΔF508) in the nucleotide binding domain 1 (NBD1) leads to CFTR global misfolding and premature intracellular degradation at the endoplasmic reticulum (ER). To better understand the misfolding mechanism caused by CF-causing point mutations in the NBD1, which is poorly understood, differential scanning fluorimetry (DSF) and hydrogen deuterium exchange coupled with mass spectrometry (HDX-MS) are the choice of techniques. These established methods can measure the conformational dynamics of the NBD1 globally and at peptide resolution level by monitoring backbone amide HDX, respectively, and will be instrumental to evaluate the mechanism of action of CF mutations and folding correctors that rescue CFTR folding defects via stabilizing the mutant NBD1.
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25
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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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26
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Gong X, Liao Y, Ahner A, Larsen MB, Wang X, Bertrand CA, Frizzell RA. Different SUMO paralogues determine the fate of wild-type and mutant CFTRs: biogenesis versus degradation. Mol Biol Cell 2018; 30:4-16. [PMID: 30403549 PMCID: PMC6337916 DOI: 10.1091/mbc.e18-04-0252] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A pathway for cystic fibrosis transmembrane conductance regulator (CFTR) degradation is initiated by Hsp27, which cooperates with Ubc9 and binds to the common F508del mutant to modify it with SUMO-2/3. These SUMO paralogues form polychains, which are recognized by the ubiquitin ligase, RNF4, for proteosomal degradation. Here, protein array analysis identified the SUMO E3, protein inhibitor of activated STAT 4 (PIAS4), which increased wild-type (WT) and F508del CFTR biogenesis in CFBE airway cells. PIAS4 increased immature CFTR threefold and doubled expression of mature CFTR, detected by biochemical and functional assays. In cycloheximide chase assays, PIAS4 slowed immature F508del degradation threefold and stabilized mature WT CFTR at the plasma membrance. PIAS4 knockdown reduced WT and F508del CFTR expression by 40–50%, suggesting a physiological role in CFTR biogenesis. PIAS4 modified F508del CFTR with SUMO-1 in vivo and reduced its conjugation to SUMO-2/3. These SUMO paralogue-specific effects of PIAS4 were reproduced in vitro using purified F508del nucleotide-binding domain 1 and SUMOylation reaction components. PIAS4 reduced endogenous ubiquitin conjugation to F508del CFTR by ∼50% and blocked the impact of RNF4 on mutant CFTR disposal. These findings indicate that different SUMO paralogues determine the fates of WT and mutant CFTRs, and they suggest that a paralogue switch during biogenesis can direct these proteins to different outcomes: biogenesis versus degradation.
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Affiliation(s)
- Xiaoyan Gong
- Departments of Pediatrics and Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224
| | - Yong Liao
- Departments of Pediatrics and Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224
| | - Annette Ahner
- Departments of Pediatrics and Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224
| | - Mads Breum Larsen
- Departments of Pediatrics and Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224
| | - Xiaohui Wang
- Departments of Pediatrics and Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224
| | - Carol A Bertrand
- Departments of Pediatrics and Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224
| | - Raymond A Frizzell
- Departments of Pediatrics and Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224
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27
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The structural basis of cystic fibrosis. Biochem Soc Trans 2018; 46:1093-1098. [PMID: 30154098 DOI: 10.1042/bst20180296] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 12/18/2022]
Abstract
CFTR (ABCC7) is a phospho-regulated chloride channel that is found in the apical membranes of epithelial cells, is gated by ATP and the activity of the protein is crucial in the homeostasis of the extracellular liquid layer in many organs [Annu. Rev. Biochem. (2008) 77, 701-726; Science (1989) 245, 1066-1073]. Mutations in CFTR cause the inherited disease cystic fibrosis (CF), the most common inherited condition in humans of European descent [Science (1989) 245, 1066-1073; Pflugers Arch. (2007) 453, 555-567]. The structural basis of CF will be discussed in this article.
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28
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Hou ZS, Ulloa-Aguirre A, Tao YX. Pharmacoperone drugs: targeting misfolded proteins causing lysosomal storage-, ion channels-, and G protein-coupled receptors-associated conformational disorders. Expert Rev Clin Pharmacol 2018; 11:611-624. [DOI: 10.1080/17512433.2018.1480367] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Zhi-Shuai Hou
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | - Alfredo Ulloa-Aguirre
- Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM) and Instituto Nacional de Ciencias Médicas y Nutrición SZ, Mexico City, Mexico
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
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29
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Hwang TC, Yeh JT, Zhang J, Yu YC, Yeh HI, Destefano S. Structural mechanisms of CFTR function and dysfunction. J Gen Physiol 2018; 150:539-570. [PMID: 29581173 PMCID: PMC5881446 DOI: 10.1085/jgp.201711946] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/05/2018] [Indexed: 12/18/2022] Open
Abstract
Hwang et al. integrate new structural insights with prior functional studies to reveal the functional anatomy of CFTR chloride channels. Cystic fibrosis (CF) transmembrane conductance regulator (CFTR) chloride channel plays a critical role in regulating transepithelial movement of water and electrolyte in exocrine tissues. Malfunction of the channel because of mutations of the cftr gene results in CF, the most prevalent lethal genetic disease among Caucasians. Recently, the publication of atomic structures of CFTR in two distinct conformations provides, for the first time, a clear overview of the protein. However, given the highly dynamic nature of the interactions among CFTR’s various domains, better understanding of the functional significance of these structures requires an integration of these new structural insights with previously established biochemical/biophysical studies, which is the goal of this review.
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Affiliation(s)
- Tzyh-Chang Hwang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO .,Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO.,Department of Biological Engineering, University of Missouri, Columbia, MO
| | - Jiunn-Tyng Yeh
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO
| | - Jingyao Zhang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO.,Department of Biological Engineering, University of Missouri, Columbia, MO
| | - Ying-Chun Yu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO.,Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO
| | - Han-I Yeh
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO.,Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO
| | - Samantha Destefano
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO.,Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO
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30
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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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31
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Odera M, Furuta T, Sohma Y, Sakurai M. Molecular dynamics simulation study on the structural instability of the most common cystic fibrosis-associated mutant ΔF508-CFTR. Biophys Physicobiol 2018; 15:33-44. [PMID: 29607278 PMCID: PMC5873040 DOI: 10.2142/biophysico.15.0_33] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/28/2017] [Indexed: 02/03/2023] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel that belongs to the ATP binding cassette protein superfamily. Deletion of phenylalanine at position 508 (ΔF508) is the most common CF-associated mutation and is present in nearly 90% of CF patients. Currently, atomistic level studies are insufficient for understanding the mechanism by which the deletion of a single amino acid causes greatly reduced folding as well as trafficking and gating defects. To clarify this mechanism, we first constructed an atomic model of the inward-facing ΔF508-CFTR and performed allatom molecular dynamics (MD) simulations of the protein in a membrane environment. All of the computational methodologies used are based on those developed in our previous study for wild-type CFTR. Two important findings were obtained. First, consistent with several previous computational results, the deletion of F508 causes a disruption of a hydrophobic cluster located at the interface between the nucleotide binding domain 1 (NBD1) and intracellular loop 4 (ICL4). This exerts unfavorable influences on the correlated motion between ICLs and transmembrane domains (TMDs), likely resulting in gating defects. Second, the F508 deletion affected the NBD1-NBD2 interface via allosteric communication originating from the correlated motion between NBDs and ICLs. As a result, several unusual inter-residue interactions are caused at the NBD1-NBD2 interface. In other words, their correct dimerization is impaired. This study provided insight into the atomic-level details of structural and dynamics changes caused by the ΔF508 mutation and thus provides good insight for drug design.
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Affiliation(s)
- Mitsuhiko Odera
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Yoshiro Sohma
- Department of Pharmaceutical Sciences, Graduate School of Pharmacy and Center for Medical Science, International University of Health and Welfare, Ohtawara, Tochigi 324-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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32
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Structural effects of extracellular loop mutations in CFTR helical hairpins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1092-1098. [PMID: 29307731 DOI: 10.1016/j.bbamem.2018.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/29/2017] [Accepted: 01/02/2018] [Indexed: 01/06/2023]
Abstract
Missense mutations constitute 40% of 2000 cystic fibrosis-phenotypic mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) database, yet the precise mechanism as to how a point mutation can render the entire 1480-residue CFTR protein dysfunctional is not well-understood. Here we investigate the structural effects of two CF-phenotypic mutations - glutamic acid to glycine at position 217 (E217G) and glutamine to arginine at position 220 (Q220R) - in the extracellular (ECL2) loop region of human CFTR using helical hairpin constructs derived from transmembrane (TM) helices 3 and 4 of the first membrane domain. We systematically replaced the wild type (WT) residues E217 and Q220 with the subset of missense mutations that could arise through a single nucleotide change in their respective codons. Circular dichroism spectra of E217G revealed that a significant increase in helicity vs. WT arises in the membrane-mimetic environment of sodium dodecylsulfate (SDS) micelles, while this mutant showed a similar gel shift to WT on SDS-PAGE gels. In contrast, the CF-mutant Q220R showed similar helicity but an increased gel shift vs. WT. These structural variations are compared with the maturation levels of the corresponding mutant full-length CFTRs, which we found are reduced to approx. 50% for E217G and 30% for Q220R vs. WT. The overall results with CFTR hairpins illustrate the range of impacts that single mutations can evoke in intramolecular protein-protein and/or protein-lipid interactions - and the levels to which corresponding mutations in full-length CFTR may be flagged by quality control mechanisms during biosynthesis.
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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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34
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Premchandar A, Kupniewska A, Bonna A, Faure G, Fraczyk T, Roldan A, Hoffmann B, Faria da Cunha M, Herrmann H, Lukacs GL, Edelman A, Dadlez M. New insights into interactions between the nucleotide-binding domain of CFTR and keratin 8. Protein Sci 2017; 26:343-354. [PMID: 27870250 DOI: 10.1002/pro.3086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/16/2016] [Accepted: 11/16/2016] [Indexed: 01/14/2023]
Abstract
The intermediate filament protein keratin 8 (K8) interacts with the nucleotide-binding domain 1 (NBD1) of the cystic fibrosis (CF) transmembrane regulator (CFTR) with phenylalanine 508 deletion (ΔF508), and this interaction hampers the biogenesis of functional ΔF508-CFTR and its insertion into the plasma membrane. Interruption of this interaction may constitute a new therapeutic target for CF patients bearing the ΔF508 mutation. Here, we aimed to determine the binding surface between these two proteins, to facilitate the design of the interaction inhibitors. To identify the NBD1 fragments perturbed by the ΔF508 mutation, we used hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) on recombinant wild-type (wt) NBD1 and ΔF508-NBD1 of CFTR. We then performed the same analysis in the presence of a peptide from the K8 head domain, and extended this investigation using bioinformatics procedures and surface plasmon resonance, which revealed regions affected by the peptide binding in both wt-NBD1 and ΔF508-NBD1. Finally, we performed HDX-MS analysis of the NBD1 molecules and full-length K8, revealing hydrogen-bonding network changes accompanying complex formation. In conclusion, we have localized a region in the head segment of K8 that participates in its binding to NBD1. Our data also confirm the stronger binding of K8 to ΔF508-NBD1, which is supported by an additional binding site located in the vicinity of the ΔF508 mutation in NBD1.
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Affiliation(s)
| | - Anna Kupniewska
- INSERM U1151, team Canalopathies épithéliales : la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Arkadiusz Bonna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Poland.,Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Grazyna Faure
- Unité Récepteurs-Canaux; Institut Pasteur, CNRS, URA 2182, Paris, F-75015, France
| | - Tomasz Fraczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Poland
| | - Ariel Roldan
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Brice Hoffmann
- IMPMC, Sorbonne Universités, UPMC Université Paris 06, UMR CNRS 7590, Museum National d'Histoire Naturelle, IRD UMR 206, IUC, Paris Cedex 05, 75005, France
| | - Mélanie Faria da Cunha
- INSERM U1151, team Canalopathies épithéliales : la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Harald Herrmann
- Department of Molecular Genetics, German Cancer Research Center, Heidelberg, D-69120, Germany.,Institute of Neuropathology, University Hospital Erlangen, D-91054, Erlangen, Germany
| | - Gergely L Lukacs
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Aleksander Edelman
- INSERM U1151, team Canalopathies épithéliales : la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Poland
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35
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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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36
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Zhang Z, Chen J. Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator. Cell 2017; 167:1586-1597.e9. [PMID: 27912062 DOI: 10.1016/j.cell.2016.11.014] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 10/28/2016] [Accepted: 11/04/2016] [Indexed: 02/07/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from the ATP-binding cassette (ABC) transporter family. In this study, we determined the structure of zebrafish CFTR in the absence of ATP by electron cryo-microscopy to 3.7 Å resolution. Human and zebrafish CFTR share 55% sequence identity, and 42 of the 46 cystic-fibrosis-causing missense mutational sites are identical. In CFTR, we observe a large anion conduction pathway lined by numerous positively charged residues. A single gate near the extracellular surface closes the channel. The regulatory domain, dephosphorylated, is located in the intracellular opening between the two nucleotide-binding domains (NBDs), preventing NBD dimerization and channel opening. The structure also reveals why many cystic-fibrosis-causing mutations would lead to defects either in folding, ion conduction, or gating and suggests new avenues for therapeutic intervention.
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Affiliation(s)
- Zhe Zhang
- The Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA
| | - Jue Chen
- The Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.
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37
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Alvarez CP, Stagljar M, Muhandiram DR, Kanelis V. Hyperinsulinism-Causing Mutations Cause Multiple Molecular Defects in SUR1 NBD1. Biochemistry 2017; 56:2400-2416. [PMID: 28346775 DOI: 10.1021/acs.biochem.6b00681] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sulfonylurea receptor 1 (SUR1) protein forms the regulatory subunit in ATP sensitive K+ (KATP) channels in the pancreas. SUR proteins are members of the ATP binding cassette (ABC) superfamily of proteins. Binding and hydrolysis of MgATP at the SUR nucleotide binding domains (NBDs) lead to channel opening. Pancreatic KATP channels play an important role in insulin secretion. SUR1 mutations that result in increased levels of channel opening ultimately inhibit insulin secretion and lead to neonatal diabetes. In contrast, SUR1 mutations that disrupt trafficking and/or decrease gating of KATP channels cause congenital hyperinsulinism, where oversecretion of insulin occurs even in the presence of low glucose levels. Here, we present data on the effects of specific congenital hyperinsulinism-causing mutations (G716V, R842G, and K890T) located in different regions of the first nucleotide binding domain (NBD1). Nuclear magnetic resonance (NMR) and fluorescence data indicate that the K890T mutation affects residues throughout NBD1, including residues that bind MgATP, NBD2, and coupling helices. The mutations also decrease the MgATP binding affinity of NBD1. Size exclusion and NMR data indicate that the G716V and R842G mutations cause aggregation of NBD1 in vitro, possibly because of destabilization of the domain. These data describe structural characterization of SUR1 NBD1 and shed light on the underlying molecular basis of mutations that cause congenital hyperinsulinism.
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Affiliation(s)
- Claudia P Alvarez
- Department of Chemical and Physical Sciences, University of Toronto Mississauga , 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6.,Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario, Canada M5S 3H6
| | - Marijana Stagljar
- Department of Chemical and Physical Sciences, University of Toronto Mississauga , 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6.,Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario, Canada M5S 3H6.,Department of Cell and Systems Biology, University of Toronto , 25 Harbord Street, Toronto, Ontario, Canada M5S 3G5
| | - D Ranjith Muhandiram
- Department of Molecular Genetics, University of Toronto , 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Voula Kanelis
- Department of Chemical and Physical Sciences, University of Toronto Mississauga , 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6.,Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario, Canada M5S 3H6.,Department of Cell and Systems Biology, University of Toronto , 25 Harbord Street, Toronto, Ontario, Canada M5S 3G5
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38
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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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39
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Farinha CM, Canato S. From the endoplasmic reticulum to the plasma membrane: mechanisms of CFTR folding and trafficking. Cell Mol Life Sci 2017; 74:39-55. [PMID: 27699454 PMCID: PMC11107782 DOI: 10.1007/s00018-016-2387-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [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: 01/10/2023]
Abstract
CFTR biogenesis starts with its co-translational insertion into the membrane of endoplasmic reticulum and folding of the cytosolic domains, towards the acquisition of a fully folded compact native structure. Efficiency of this process is assessed by the ER quality control system that allows the exit of folded proteins but targets unfolded/misfolded CFTR to degradation. If allowed to leave the ER, CFTR is modified at the Golgi and reaches the post-Golgi compartments to be delivered to the plasma membrane where it functions as a cAMP- and phosphorylation-regulated chloride/bicarbonate channel. CFTR residence at the membrane is a balance of membrane delivery, endocytosis, and recycling. Several adaptors, motor, and scaffold proteins contribute to the regulation of CFTR stability and are involved in continuously assessing its structure through peripheral quality control systems. Regulation of CFTR biogenesis and traffic (and its dysregulation by mutations, such as the most common F508del) determine its overall activity and thus contribute to the fine modulation of chloride secretion and hydration of epithelial surfaces. This review covers old and recent knowledge on CFTR folding and trafficking from its synthesis to the regulation of its stability at the plasma membrane and highlights how several of these steps can be modulated to promote the rescue of mutant CFTR.
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Affiliation(s)
- Carlos M Farinha
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
| | - Sara Canato
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
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40
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Moran O. The biophysics, biochemistry and physiology of CFTR. Cell Mol Life Sci 2017; 74:1-2. [PMID: 27704173 PMCID: PMC11107758 DOI: 10.1007/s00018-016-2384-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Oscar Moran
- Istituto di Biofisica, CNR, Via De Marini, 6, 16149, Genoa, Italy.
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41
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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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42
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Cystic fibrosis lung environment and Pseudomonas aeruginosa infection. BMC Pulm Med 2016; 16:174. [PMID: 27919253 PMCID: PMC5139081 DOI: 10.1186/s12890-016-0339-5] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/24/2016] [Indexed: 12/20/2022] Open
Abstract
Background The airways of patients with cystic fibrosis (CF) are highly complex, subject to various environmental conditions as well as a distinct microbiota. Pseudomonas aeruginosa is recognized as one of the most important pulmonary pathogens and the predominant cause of morbidity and mortality in CF. A multifarious interplay between the host, pathogens, microbiota, and the environment shapes the course of the disease. There have been several excellent reviews detailing CF pathology, Pseudomonas and the role of environment in CF but only a few reviews connect these entities with regards to influence on the overall course of the disease. A holistic understanding of contributing factors is pertinent to inform new research and therapeutics. Discussion In this article, we discuss the deterministic alterations in lung physiology as a result of CF. We also revisit the impact of those changes on the microbiota, with special emphasis on P. aeruginosa and the influence of other non-genetic factors on CF. Substantial past and current research on various genetic and non-genetic aspects of cystic fibrosis has been reviewed to assess the effect of different factors on CF pulmonary infection. A thorough review of contributing factors in CF and the alterations in lung physiology indicate that CF lung infection is multi-factorial with no isolated cause that should be solely targeted to control disease progression. A combinatorial approach may be required to ensure better disease outcomes. Conclusion CF lung infection is a complex disease and requires a broad multidisciplinary approach to improve CF disease outcomes. A holistic understanding of the underlying mechanisms and non-genetic contributing factors in CF is central to development of new and targeted therapeutic strategies.
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43
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Faure G, Bakouh N, Lourdel S, Odolczyk N, Premchandar A, Servel N, Hatton A, Ostrowski MK, Xu H, Saul FA, Moquereau C, Bitam S, Pranke I, Planelles G, Teulon J, Herrmann H, Roldan A, Zielenkiewicz P, Dadlez M, Lukacs GL, Sermet-Gaudelus I, Ollero M, Corringer PJ, Edelman A. Rattlesnake Phospholipase A2 Increases CFTR-Chloride Channel Current and Corrects ∆F508CFTR Dysfunction: Impact in Cystic Fibrosis. J Mol Biol 2016; 428:2898-915. [PMID: 27241308 DOI: 10.1016/j.jmb.2016.05.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 01/26/2023]
Abstract
Deletion of Phe508 in the nucleotide binding domain (∆F508-NBD1) of the cystic fibrosis transmembrane regulator (CFTR; a cyclic AMP-regulated chloride channel) is the most frequent mutation associated with cystic fibrosis. This mutation affects the maturation and gating of CFTR protein. The search for new high-affinity ligands of CFTR acting as dual modulators (correctors/activators) presents a major challenge in the pharmacology of cystic fibrosis. Snake venoms are a rich source of natural multifunctional proteins, potential binders of ion channels. In this study, we identified the CB subunit of crotoxin from Crotalus durissus terrificus as a new ligand and allosteric modulator of CFTR. We showed that CB interacts with NBD1 of both wild type and ∆F508CFTR and increases their chloride channel currents. The potentiating effect of CB on CFTR activity was demonstrated using electrophysiological techniques in Xenopus laevis oocytes, in CFTR-HeLa cells, and ex vivo in mouse colon tissue. The correcting effect of CB was shown by functional rescue of CFTR activity after 24-h ΔF508CFTR treatments with CB. Moreover, the presence of fully glycosylated CFTR was observed. Molecular docking allowed us to propose a model of the complex involving of the ABCβ and F1-like ATP-binding subdomains of ΔF508-NBD1. Hydrogen-deuterium exchange analysis confirmed stabilization in these regions, also showing allosteric stabilization in two other distal regions. Surface plasmon resonance competition studies showed that CB disrupts the ∆F508CFTR-cytokeratin 8 complex, allowing for the escape of ∆F508CFTR from degradation. Therefore CB, as a dual modulator of ΔF508CFTR, constitutes a template for the development of new anti-CF agents.
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Affiliation(s)
- Grazyna Faure
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France.
| | - Naziha Bakouh
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Stéphane Lourdel
- UPMC Université Paris 06, UMRS 872, Laboratoire de génomique, physiologie et physiopathologie rénales, Paris, France
| | - Norbert Odolczyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Aiswarya Premchandar
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Nathalie Servel
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Aurélie Hatton
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Maciej K Ostrowski
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France
| | - Haijin Xu
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France
| | - Frederick A Saul
- Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR 3528, Paris, France
| | - Christelle Moquereau
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Sara Bitam
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Iwona Pranke
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Gabrielle Planelles
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Jacques Teulon
- UPMC Université Paris 06, UMRS 872, Laboratoire de génomique, physiologie et physiopathologie rénales, Paris, France
| | - Harald Herrmann
- Department of Molecular Genetics, German Cancer Research Center, D-69120 Heidelberg, Germany; Institute of Neuropathology, University Hospital Erlangen, D-91054 Erlangen, Germany
| | - Ariel Roldan
- Department of Physiology, McGill University, Montreal, Canada
| | - Piotr Zielenkiewicz
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Michal Dadlez
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | | | - Isabelle Sermet-Gaudelus
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Mario Ollero
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Pierre-Jean Corringer
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France
| | - Aleksander Edelman
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
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44
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Gakhal AK, Jensen TJ, Bozoky Z, Roldan A, Lukacs GL, Forman-Kay J, Riordan JR, Sidhu SS. Development and characterization of synthetic antibodies binding to the cystic fibrosis conductance regulator. MAbs 2016; 8:1167-76. [PMID: 27185291 DOI: 10.1080/19420862.2016.1186320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel in the apical surface of epithelial cells in the airway and gastrointestinal tract, and mutation of CFTR is the underlying cause of cystic fibrosis. However, the precise molecular details of the structure and function of CFTR in native and disease states remains elusive and cystic fibrosis researchers are hindered by a lack of high specificity, high affinity binding reagents for use in structural and biological studies. Here, we describe a panel of synthetic antigen-binding fragments (Fabs) isolated from a phage-displayed library that are specific for intracellular domains of CFTR that include the nucleotide-binding domains (NBD1 and NBD2), the R-region, and the regulatory insertion loop of NBD1. Binding assays performed under conditions that promote the native fold of the protein demonstrated that all Fabs recognized full-length CFTR. However, only the NBD1-specific Fab recognized denatured CFTR by western blot, suggesting a conformational epitope requirement for the other Fabs. Surface plasmon resonance experiments showed that the R-region Fab binds with high affinity to both the phosphorylated and unphosphorylated R-region. In addition, NMR analysis of bound versus unbound R-region revealed a distinct conformational effect upon Fab binding. We further defined residues involved with antibody recognition using an overlapping peptide array. In summary, we describe methodology complementary to previous hybridoma-based efforts to develop antibody reagents to CFTR, and introduce a synthetic antibody panel to aid structural and biological studies.
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Affiliation(s)
- Amandeep K Gakhal
- a Donnelly Center for Cellular and Biomolecular Research , University of Toronto , Toronto , Ontario , Canada
| | - Timothy J Jensen
- b Department of Biochemistry and Biophysics , Cystic Fibrosis Treatment and Research Center, University of North Carolina , Chapel Hill , NC , USA
| | - Zoltan Bozoky
- c Program in Molecular Structure & Function , The Hospital for Sick Children , Toronto , ON , Canada.,d Department of Biochemistry , University of Toronto, Toronto , ON , Canada
| | - Ariel Roldan
- e Department of Physiology and Biochemistry , McGill University , Montreal , QC , Canada
| | - Gergely L Lukacs
- e Department of Physiology and Biochemistry , McGill University , Montreal , QC , Canada
| | - Julie Forman-Kay
- c Program in Molecular Structure & Function , The Hospital for Sick Children , Toronto , ON , Canada.,d Department of Biochemistry , University of Toronto, Toronto , ON , Canada
| | - John R Riordan
- b Department of Biochemistry and Biophysics , Cystic Fibrosis Treatment and Research Center, University of North Carolina , Chapel Hill , NC , USA
| | - Sachdev S Sidhu
- a Donnelly Center for Cellular and Biomolecular Research , University of Toronto , Toronto , Ontario , Canada
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45
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Pollock NL, Satriano L, Zegarra-Moran O, Ford RC, Moran O. Structure of wild type and mutant F508del CFTR: A small-angle X-ray scattering study of the protein–detergent complexes. J Struct Biol 2016; 194:102-11. [DOI: 10.1016/j.jsb.2016.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
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46
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Hall JD, Wang H, Byrnes LJ, Shanker S, Wang K, Efremov IV, Chong PA, Forman-Kay JD, Aulabaugh AE. Binding screen for cystic fibrosis transmembrane conductance regulator correctors finds new chemical matter and yields insights into cystic fibrosis therapeutic strategy. Protein Sci 2016; 25:360-73. [PMID: 26444971 DOI: 10.1002/pro.2821] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/01/2015] [Indexed: 11/08/2022]
Abstract
The most common mutation in cystic fibrosis (CF) patients is deletion of F508 (ΔF508) in the first nucleotide binding domain (NBD1) of the CF transmembrane conductance regulator (CFTR). ΔF508 causes a decrease in the trafficking of CFTR to the cell surface and reduces the thermal stability of isolated NBD1; it is well established that both of these effects can be rescued by additional revertant mutations in NBD1. The current paradigm in CF small molecule drug discovery is that, like revertant mutations, a path may exist to ΔF508 CFTR correction through a small molecule chaperone binding to NBD1. We, therefore, set out to find small molecule binders of NBD1 and test whether it is possible to develop these molecules into potent binders that increase CFTR trafficking in CF-patient-derived human bronchial epithelial cells. Several fragments were identified that bind NBD1 at either the CFFT-001 site or the BIA site. However, repeated attempts to improve the affinity of these fragments resulted in only modest gains. Although these results cannot prove that there is no possibility of finding a high-affinity small molecule binder of NBD1, they are discouraging and lead us to hypothesize that the nature of these two binding sites, and isolated NBD1 itself, may not contain the features needed to build high-affinity interactions. Future work in this area may, therefore, require constructs including other domains of CFTR in addition to NBD1, if high-affinity small molecule binding is to be achieved.
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Affiliation(s)
- Justin D Hall
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
| | - Hong Wang
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
| | - Laura J Byrnes
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
| | - Suman Shanker
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
| | - Kelong Wang
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
| | - Ivan V Efremov
- Worldwide Medicinal Chemistry, , Pfizer, Cambridge, Massachusetts, 02140
| | - P Andrew Chong
- Molecular Structure and Function Program, Hospital for Sick Kids, Toronto, Ontario, M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Julie D Forman-Kay
- Molecular Structure and Function Program, Hospital for Sick Kids, Toronto, Ontario, M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ann E Aulabaugh
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut, 06340
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47
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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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48
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Ehrhardt A, Chung WJ, Pyle LC, Wang W, Nowotarski K, Mulvihill CM, Ramjeesingh M, Hong J, Velu SE, Lewis HA, Atwell S, Aller S, Bear CE, Lukacs GL, Kirk KL, Sorscher EJ. Channel Gating Regulation by the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) First Cytosolic Loop. J Biol Chem 2015; 291:1854-1865. [PMID: 26627831 DOI: 10.1074/jbc.m115.704809] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 11/06/2022] Open
Abstract
In this study, we present data indicating a robust and specific domain interaction between the cystic fibrosis transmembrane conductance regulator (CFTR) first cytosolic loop (CL1) and nucleotide binding domain 1 (NBD1) that allows ion transport to proceed in a regulated fashion. We used co-precipitation and ELISA to establish the molecular contact and showed that binding kinetics were not altered by the common clinical mutation F508del. Both intrinsic ATPase activity and CFTR channel gating were inhibited severely by CL1 peptide, suggesting that NBD1/CL1 binding is a crucial requirement for ATP hydrolysis and channel function. In addition to cystic fibrosis, CFTR dysregulation has been implicated in the pathogenesis of prevalent diseases such as chronic obstructive pulmonary disease, acquired rhinosinusitis, pancreatitis, and lethal secretory diarrhea (e.g. cholera). On the basis of clinical relevance of the CFTR as a therapeutic target, a cell-free drug screen was established to identify modulators of NBD1/CL1 channel activity independent of F508del CFTR and pharmacologic rescue. Our findings support a targetable mechanism of CFTR regulation in which conformational changes in the NBDs cause reorientation of transmembrane domains via interactions with CL1 and result in channel gating.
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Affiliation(s)
- Annette Ehrhardt
- From the Gregory Fleming James Cystic Fibrosis Research Center and; the Department of Pediatrics, Emory University, Atlanta, Georgia 30322
| | - W Joon Chung
- From the Gregory Fleming James Cystic Fibrosis Research Center and; Departments of Neurobiology
| | - Louise C Pyle
- From the Gregory Fleming James Cystic Fibrosis Research Center and
| | - Wei Wang
- Cellular, Integrative, and Developmental Biology
| | | | - Cory M Mulvihill
- the Hospital for Sick Children Research Institute, Toronto M5G 1X8, Canada
| | | | - Jeong Hong
- From the Gregory Fleming James Cystic Fibrosis Research Center and; Cellular, Integrative, and Developmental Biology
| | - Sadanandan E Velu
- Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Hal A Lewis
- Bristol-Myers Squibb, Princeton, New Jersey 08543
| | | | - Steve Aller
- From the Gregory Fleming James Cystic Fibrosis Research Center and; Pharmacology, and
| | - Christine E Bear
- the Hospital for Sick Children Research Institute, Toronto M5G 1X8, Canada,; the Departments of Biochemistry and; Physiology, University of Toronto, Toronto M5G 1X8, Canada, and
| | - Gergely L Lukacs
- the Department of Physiology, McGill University, Montreal H3G 1Y6, Canada
| | - Kevin L Kirk
- From the Gregory Fleming James Cystic Fibrosis Research Center and; Cellular, Integrative, and Developmental Biology
| | - Eric J Sorscher
- the Department of Pediatrics, Emory University, Atlanta, Georgia 30322,.
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49
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Gong X, Ahner A, Roldan A, Lukacs GL, Thibodeau PH, Frizzell RA. Non-native Conformers of Cystic Fibrosis Transmembrane Conductance Regulator NBD1 Are Recognized by Hsp27 and Conjugated to SUMO-2 for Degradation. J Biol Chem 2015; 291:2004-2017. [PMID: 26627832 DOI: 10.1074/jbc.m115.685628] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Indexed: 12/24/2022] Open
Abstract
A newly identified pathway for selective degradation of the common mutant of the cystic fibrosis transmembrane conductance regulator (CFTR), F508del, is initiated by binding of the small heat shock protein, Hsp27. Hsp27 collaborates with Ubc9, the E2 enzyme for protein SUMOylation, to selectively degrade F508del CFTR via the SUMO-targeted ubiquitin E3 ligase, RNF4 (RING finger protein 4) (1). Here, we ask what properties of CFTR are sensed by the Hsp27-Ubc9 pathway by examining the ability of NBD1 (locus of the F508del mutation) to mimic the disposal of full-length (FL) CFTR. Similar to FL CFTR, F508del NBD1 expression was reduced 50-60% by Hsp27; it interacted preferentially with the mutant and was modified primarily by SUMO-2. Mutation of the consensus SUMOylation site, Lys(447), obviated Hsp27-mediated F508del NBD1 SUMOylation and degradation. As for FL CFTR and NBD1 in vivo, SUMO modification using purified components in vitro was greater for F508del NBD1 versus WT and for the SUMO-2 paralog. Several findings indicated that Hsp27-Ubc9 targets the SUMOylation of a transitional, non-native conformation of F508del NBD1: (a) its modification decreased as [ATP] increased, reflecting stabilization of the nucleotide-binding domain by ligand binding; (b) a temperature-induced increase in intrinsic fluorescence, which reflects formation of a transitional NBD1 conformation, was followed by its SUMO modification; and (c) introduction of solubilizing or revertant mutations to stabilize F508del NBD1 reduced its SUMO modification. These findings indicate that the Hsp27-Ubc9 pathway recognizes a non-native conformation of mutant NBD1, which leads to its SUMO-2 conjugation and degradation by the ubiquitin-proteasome system.
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Affiliation(s)
| | | | - Ariel Roldan
- the Department of Physiology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Gergely L Lukacs
- the Department of Physiology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Patrick H Thibodeau
- Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261 and
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50
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Bali V, Lazrak A, Guroji P, Fu L, Matalon S, Bebok Z. A synonymous codon change alters the drug sensitivity of ΔF508 cystic fibrosis transmembrane conductance regulator. FASEB J 2015; 30:201-13. [PMID: 26336913 DOI: 10.1096/fj.15-273714] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/31/2015] [Indexed: 11/11/2022]
Abstract
Synonymous mutations, such as I507-ATC→ATT, in deletion of Phe508 in cystic fibrosis transmembrane conductance regulator (ΔF508 CFTR), the most frequent disease-associated mutant of CFTR, may affect protein biogenesis, structure, and function and contribute to an altered disease phenotype. Small-molecule drugs are being developed to correct ΔF508 CFTR. To understand correction mechanisms and the consequences of synonymous mutations, we analyzed the effect of mechanistically distinct correctors, corrector 4a (C4) and lumacaftor (VX-809), on I507-ATT and I507-ATC ΔF508 CFTR biogenesis and function. C4 stabilized I507-ATT ΔF508 CFTR band B, but without considerable biochemical and functional correction. VX-809 biochemically corrected ∼10% of both of the variants, leading to stable, forskolin+3-isobutyl-1-methylxanthine (IBMX)-activated whole-cell currents in the presence of the corrector. Omitting VX-809 during whole-cell recordings led to a spontaneous decline of the currents, suggesting posttranslational stabilization by VX-809. Treatment of cells with the C4+VX-809 combination resulted in enhanced rescue and 2-fold higher forskolin+IBMX-activated currents of both I507-ATT and I507-ATC ΔF508 CFTR, compared with VX-809 treatment alone. The lack of an effect of C4 on I507-ATC ΔF508 CFTR, but its additive effect in combination with VX-809, implies that C4 acted on VX-809-modified I507-ATC ΔF508 CFTR. Our results suggest that binding of C4 and VX-809 to ΔF508 CFTR is conformation specific and provide evidence that synonymous mutations can alter the drug sensitivity of proteins.
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Affiliation(s)
- Vedrana Bali
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ahmed Lazrak
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Purushotham Guroji
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lianwu Fu
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sadis Matalon
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Zsuzsanna Bebok
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
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