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Reporting Two Novel Mutations in Two Iranian Families with Cystic Fibrosis, Molecular and Bioinformatic Analysis. IRANIAN BIOMEDICAL JOURNAL 2022; 26:398-405. [PMID: 35468710 PMCID: PMC9763878 DOI: 10.52547/ibj.3713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Cystic fibrosis (CF) is the most common heredity disease among the Caucasian population. More than 350 known pathogenic variations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene (NM_000492.4) cause CF. Herein, we report the outcome of our investigation in two unrelated Iranian families with CF patients. Methods We conducted phenotypic examination, segregation, linkage analysis, and CFTR gene sequencing to define causative mutations. Results We found two novel mutations in the present study. The first one was a deletion causing frameshift, c.299delT p.(Leu100Profs*7), and the second one was a missense mutation, c.1857G>T, at nucleotide binding domain 1 of the CFTR protein. Haplotype segregation data supported our new mutation findings. Conclusion Findings of this study expand the spectrum of CFTR pathogenic variations and can improve prenatal diagnosis and genetic counseling for CF.
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Ivey G, Youker RT. Disease-relevant mutations alter amino acid co-evolution networks in the second nucleotide binding domain of CFTR. PLoS One 2020; 15:e0227668. [PMID: 31978131 PMCID: PMC6980524 DOI: 10.1371/journal.pone.0227668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 12/25/2019] [Indexed: 01/23/2023] Open
Abstract
Cystic Fibrosis (CF) is an inherited disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel. Mutations in CFTR cause impaired chloride ion transport in the epithelial tissues of patients leading to cardiopulmonary decline and pancreatic insufficiency in the most severely affected patients. CFTR is composed of twelve membrane-spanning domains, two nucleotide-binding domains (NBDs), and a regulatory domain. The most common mutation in CFTR is a deletion of phenylalanine at position 508 (ΔF508) in NBD1. Previous research has primarily concentrated on the structure and dynamics of the NBD1 domain; However numerous pathological mutations have also been found in the lesser-studied NBD2 domain. We have investigated the amino acid co-evolved network of interactions in NBD2, and the changes that occur in that network upon the introduction of CF and CF-related mutations (S1251N(T), S1235R, D1270N, N1303K(T)). Extensive coupling between the α- and β-subdomains were identified with residues in, or near Walker A, Walker B, H-loop and C-loop motifs. Alterations in the predicted residue network varied from moderate for the S1251T perturbation to more severe for N1303T. The S1235R and D1270N networks varied greatly compared to the wildtype, but these CF mutations only affect ion transport preference and do not severely disrupt CFTR function, suggesting dynamic flexibility in the network of interactions in NBD2. Our results also suggest that inappropriate interactions between the β-subdomain and Q-loop could be detrimental. We also identified mutations predicted to stabilize the NBD2 residue network upon introduction of the CF and CF-related mutations, and these predicted mutations are scored as benign by the MUTPRED2 algorithm. Our results suggest the level of disruption of the co-evolution predictions of the amino acid networks in NBD2 does not have a straightforward correlation with the severity of the CF phenotypes observed.
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Affiliation(s)
- Gabrianne Ivey
- Kyder Christian Academy, Franklin, North Carolina, United States of America
- Southwestern Community College, Sylva, North Carolina, United States of America
| | - Robert T. Youker
- Department of Biology, Western Carolina University, Cullowhee, North Carolina, United States of America
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Fay JF, Aleksandrov LA, Jensen TJ, Cui LL, Kousouros JN, He L, Aleksandrov AA, Gingerich DS, Riordan JR, Chen JZ. Cryo-EM Visualization of an Active High Open Probability CFTR Anion Channel. Biochemistry 2018; 57:6234-6246. [PMID: 30281975 DOI: 10.1021/acs.biochem.8b00763] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) anion channel, crucial to epithelial salt and water homeostasis, and defective due to mutations in its gene in patients with cystic fibrosis, is a unique member of the large family of ATP-binding cassette transport proteins. Regulation of CFTR channel activity is stringently controlled by phosphorylation and nucleotide binding. Structural changes that underlie transitions between active and inactive functional states are not yet fully understood. Indeed the first 3D structures of dephosphorylated, ATP-free, and phosphorylated ATP-bound states were only recently reported. Here we have determined the structure of inactive and active states of a thermally stabilized CFTR, the latter with a very high channel open probability, confirmed after reconstitution into proteoliposomes. These structures, obtained at nominal resolution of 4.3 and 6.6 Å, reveal a unique repositioning of the transmembrane helices and regulatory domain density that provide insights into the structural transition between active and inactive functional states of CFTR. Moreover, we observe an extracellular vestibule that may provide anion access to the pore due to the conformation of transmembrane helices 7 and 8 that differs from the previous orthologue CFTR structures. In conclusion, our work contributes detailed structural information on an active, open state of the CFTR anion channel.
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Affiliation(s)
- Jonathan F Fay
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Luba A Aleksandrov
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Timothy J Jensen
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Liying L Cui
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Joseph N Kousouros
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Lihua He
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Andrei A Aleksandrov
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - Drew S Gingerich
- Oregon Health & Science University , Portland , Oregon 97239 , United States
| | - John R Riordan
- University of North Carolina , Chapel Hill , North Carolina 27515 , United States
| | - James Z Chen
- Oregon Health & Science University , Portland , Oregon 97239 , United States
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Targeting Nucleotide Binding Domain of Multidrug Resistance-associated Protein-1 (MRP1) for the Reversal of Multi Drug Resistance in Cancer. Sci Rep 2018; 8:11973. [PMID: 30097643 PMCID: PMC6086895 DOI: 10.1038/s41598-018-30420-x] [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] [Received: 04/12/2018] [Accepted: 07/25/2018] [Indexed: 12/12/2022] Open
Abstract
Multidrug resistance (MDR) is the major cause, by which cancer cells expel the drugs out, developing a challenge against the current chemotherapeutic drugs regime. This mechanism is attributed to the over expression of ABC transporters like MRP1 on the surface of cells. Since nucleotide binding domains (NBD) of ABC transporters are the site of ATP binding and hydrolysis, thereby in this study we have targeted NBD1 of MRP1using molecular docking and molecular dynamic simulations (MDS). The compounds present in the FDA approved library were docked against NBD1 of the human multidrug resistance associated protein 1 (PDB ID: 2CBZ). For the docking studies, Standard Precision and Extra Precision methods were employed. After the EP docking studies, ligands showed an extremely low docking score that was indicative of very high binding affinity of the ligands to the NBD. Apart from the low docking score, another short listing criterion in simulation studies was the interaction of incoming ligand with the desired conserved residues of NDB involved in ATP binding and hydrolysis. Based on these measures, potassium citrate (DB09125) and technetium Tc-99m medronate (DB09138) were chosen and subjected to 100 ns simulation studies. From the MDS study we concluded that between these two compounds, potassium citrate is a better candidate for targeting MRP1.
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Dworakowska B, Nurowska E, Dołowy K. Hydrocortisone inhibition of wild-type and αD200Q nicotinic acetylcholine receptors. Chem Biol Drug Des 2018; 92:1610-1617. [DOI: 10.1111/cbdd.13325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/23/2018] [Accepted: 04/23/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Beata Dworakowska
- Department of Biophysics; Warsaw University of Life Sciences-SGGW; Warsaw Poland
| | - Ewa Nurowska
- Laboratory of Physiology and Pathophysiology; Centre for Preclinical Research and Technology (CePT); Medical University of Warsaw; Warsaw Poland
| | - Krzysztof Dołowy
- Department of Biophysics; Warsaw University of Life Sciences-SGGW; Warsaw Poland
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Micoud J, Chauvet S, Scheckenbach KEL, Alfaidy N, Chanson M, Benharouga M. Involvement of the heterodimeric interface region of the nucleotide binding domain-2 (NBD2) in the CFTR quaternary structure and membrane stability. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2420-31. [PMID: 26083625 DOI: 10.1016/j.bbamcr.2015.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 06/02/2015] [Accepted: 06/12/2015] [Indexed: 11/27/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is the only member of the ATP-binding cassette (ABC) superfamily that functions as a chloride channel. The predicted structure of CFTR protein contains two membrane-spanning domains (MSDs), each followed by a nucleotide binding domain (NBD1 and NBD2). The opening of the Cl- channel is directly linked to ATP-driven tight dimerization of CFTR's NBD1 and NBD2 domains. The presence of a heterodimeric interfaces (HI) region in NBD1 and NBD2 generated a head to tail orientation necessary for channel activity. This process was also suggested to promote important conformational changes in the associated transmembrane domains of CFTR, which may impact the CFTR plasma membrane stability. To better understand the role of the individual HI region in this process, we generated recombinant CFTR protein with suppressed HI-NBD1 and HI-NBD2. Our results indicate that HI-NBD2 deletion leads to the loss of the dimerization profile of CFTR that affect its plasma membrane stability. We conclude that, in addition to its role in Cl- transport, HI-NBD2 domain confers membrane stability of CFTR by consolidating its quaternary structure through interactions with HI-NBD1 region.
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Affiliation(s)
- Julien Micoud
- Centre National de la Recherche Scientifique (CNRS), LCBM-UMR 5249, Grenoble, France; Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France
| | - Sylvain Chauvet
- Centre National de la Recherche Scientifique (CNRS), LCBM-UMR 5249, Grenoble, France; Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France
| | | | - Nadia Alfaidy
- Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1036 Grenoble, France
| | - Marc Chanson
- Laboratory of Clinical Investigation III, Geneva University Hospitals and University of Geneva, 1211 Geneva, Switzerland
| | - Mohamed Benharouga
- Centre National de la Recherche Scientifique (CNRS), LCBM-UMR 5249, Grenoble, France; Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France.
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Hunt JF, Wang C, Ford RC. Cystic fibrosis transmembrane conductance regulator (ABCC7) structure. Cold Spring Harb Perspect Med 2013; 3:a009514. [PMID: 23378596 DOI: 10.1101/cshperspect.a009514] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Structural studies of the cystic fibrosis transmembrane conductance regulator (CFTR) are reviewed. Like many membrane proteins, full-length CFTR has proven to be difficult to express and purify, hence much of the structural data available is for the more tractable, independently expressed soluble domains. Therefore, this chapter covers structural data for individual CFTR domains in addition to the sparser data available for the full-length protein. To set the context for these studies, we will start by reviewing structural information on model proteins from the ATP-binding cassette (ABC) transporter superfamily, to which CFTR belongs.
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Affiliation(s)
- John F Hunt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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