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Kleinsasser B, Garreis F, Musialik M, Zahn I, Kral B, Kutlu Z, Sahin A, Paulsen F, Schicht M. Molecular detection of lacrimal apparatus and ocular surface - related ABC transporter genes. Ann Anat 2024; 255:152272. [PMID: 38697581 DOI: 10.1016/j.aanat.2024.152272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
The ocular system is in constant interaction with the environment and with numerous pathogens. The ATP-binding cassette (ABC) transporters represent one of the largest groups among the transmembrane proteins. Their relevance has been demonstrated for their defense function against biotic and abiotic stress factors, for metabolic processes in tumors and for their importance in the development of resistance to drugs. The aim of this study was to analyze which ABC transporters are expressed at the ocular surface and in the human lacrimal apparatus. Using RT-PCR, all ABC transporters known to date in humans were examined in tissue samples from human cornea, conjunctiva, meibomian glands and lacrimal glands. The RT-PCR analyses revealed the presence of all ABC transporters in the samples examined, although the results for some of the 48 transporters known in human and analyzed were different in the various tissues. The present results provide information on the expression of ABC transporters at the mRNA level on the ocular surface and in the lacrimal system. Their detection forms the basis for follow-up studies at the protein level, which will provide more information about their physiological significance at the ocular surface and in the lacrimal system and which may explain pathological effects such as drug resistance.
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Affiliation(s)
- Benedikt Kleinsasser
- Department of Functional and Clinical Anatomy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Fabian Garreis
- Department of Functional and Clinical Anatomy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Maximilian Musialik
- Department of Functional and Clinical Anatomy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ingrid Zahn
- Department of Functional and Clinical Anatomy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Barbara Kral
- Department of Functional and Clinical Anatomy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Zeynep Kutlu
- Koc University School of Medicine, Rumelifeneri Yolu, Istanbul 34450, Turkey
| | - Afsun Sahin
- Department of Ophthalmology, Koc University Medical School, Istanbul, Turkey
| | - Friedrich Paulsen
- Department of Functional and Clinical Anatomy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Martin Schicht
- Department of Functional and Clinical Anatomy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
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2
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Sheikhi N, Bahraminejad M, Saeedi M, Mirfazli SS. A review: FDA-approved fluorine-containing small molecules from 2015 to 2022. Eur J Med Chem 2023; 260:115758. [PMID: 37657268 DOI: 10.1016/j.ejmech.2023.115758] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
Fluorine-containing small molecules have occupied a special position in drug discovery research. The successful clinical use of fluorinated corticosteroids in the 1950s and fluoroquinolones in the 1980s led to an ever-increasing number of approved fluorinated compounds over the last 50 years. They have shown various biological properties such as antitumor, antimicrobial, and anti-inflammatory activities. Fluoro-pharmaceuticals have been considered a strong and practical tool in the rational drug design approach due to their benefits from potency and ADME (absorption, distribution, metabolism, and excretion) points of view. Herein, approved fluorinated drugs from 2015 to 2022 were reviewed.
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Affiliation(s)
- Negar Sheikhi
- Department of Medicinal Chemistry, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Bahraminejad
- Department of Medicinal Chemistry, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran
| | - Mina Saeedi
- Medicinal Plants Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Persian Medicine and Pharmacy Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Seyedeh Sara Mirfazli
- Department of Medicinal Chemistry, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran.
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3
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Lomunova MA, Gershovich PM. Gene Therapy for Cystic Fibrosis: Recent Advances and Future Prospects. Acta Naturae 2023; 15:20-31. [PMID: 37538805 PMCID: PMC10395777 DOI: 10.32607/actanaturae.11708] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/22/2023] [Indexed: 08/05/2023] Open
Abstract
Gene replacement therapies are novel therapeutic approaches that seek to tackle hereditary diseases caused by a congenital deficiency in a particular gene, when a functional copy of a gene can be delivered to the cells and tissues using various delivery systems. To do this, viral particles carrying a functional copy of the gene of interest and various nonviral gene delivery systems, including liposomes, nanoparticles, etc., can be used. In this review, we discuss the state of current knowledge regarding the molecular mechanisms and types of genetic mutations that lead to cystic fibrosis and highlight recent developments in gene therapy that can be leveraged to correct these mutations and to restore the physiological function of the carrier protein transporting sodium and chlorine ions in the airway epithelial cells. Restoration of carrier protein expression could lead to the normalization of ion and water transport across the membrane and induce a decrease in the viscosity of airway surface fluid, which is one of the pathological manifestations of this disease. This review also summarizes recently published preclinical and clinical data for various gene therapies to allow one to make some conclusions about future prospects for gene therapy in cystic fibrosis treatment.
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4
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Bieczynski F, Painefilú JC, Venturino A, Luquet CM. Expression and Function of ABC Proteins in Fish Intestine. Front Physiol 2021; 12:791834. [PMID: 34955897 PMCID: PMC8696203 DOI: 10.3389/fphys.2021.791834] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
In fish, the intestine is fundamental for digestion, nutrient absorption, and other functions like osmoregulation, acid-base balance, and excretion of some metabolic products. These functions require a large exchange surface area, which, in turn, favors the absorption of natural and anthropogenic foreign substances (xenobiotics) either dissolved in water or contained in the food. According to their chemical nature, nutrients, ions, and water may cross the intestine epithelium cells' apical and basolateral membranes by passive diffusion or through a wide array of transport proteins and also through endocytosis and exocytosis. In the same way, xenobiotics can cross this barrier by passive diffusion or taking advantage of proteins that transport physiological substrates. The entry of toxic substances is counterbalanced by an active efflux transport mediated by diverse membrane proteins, including the ATP binding cassette (ABC) proteins. Recent advances in structure, molecular properties, and functional studies have shed light on the importance of these proteins in cellular and organismal homeostasis. There is abundant literature on mammalian ABC proteins, while the studies on ABC functions in fish have mainly focused on the liver and, to a minor degree, on the kidney and other organs. Despite their critical importance in normal physiology and as a barrier to prevent xenobiotics incorporation, fish intestine's ABC transporters have received much less attention. All the ABC subfamilies are present in the fish intestine, although their functionality is still scarcely studied. For example, there are few studies of ABC-mediated transport made with polarized intestinal preparations. Thus, only a few works discriminate apical from basolateral transport activity. We briefly describe the main functions of each ABC subfamily reported for mammals and other fish organs to help understand their roles in the fish intestine. Our study considers immunohistochemical, histological, biochemical, molecular, physiological, and toxicological aspects of fish intestinal ABC proteins. We focus on the most extensively studied fish ABC proteins (subfamilies ABCB, ABCC, and ABCG), considering their apical or basolateral location and distribution along the intestine. We also discuss the implication of fish intestinal ABC proteins in the transport of physiological substrates and aquatic pollutants, such as pesticides, cyanotoxins, metals, hydrocarbons, and pharmaceutical products.
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Affiliation(s)
- Flavia Bieczynski
- Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue – Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Comahue, Neuquén, Argentina
| | - Julio C. Painefilú
- Instituto Patagónico de Tecnologías Biológicas y Geoambientales, Consejo Nacional de Investigaciones Científicas y Técnicas – Universidad Nacional del Comahue, Bariloche, Argentina
| | - Andrés Venturino
- Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue – Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Comahue, Neuquén, Argentina
| | - Carlos M. Luquet
- Laboratorio de Ecotoxicología Acuática, Subsede INIBIOMA-CEAN (CONICET – UNCo), Junín de los Andes, Argentina
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5
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Qiu Y, Li H, Xie J, Qiao X, Wu J. Identification of ABCC5 Among ATP-Binding Cassette Transporter Family as a New Biomarker for Hepatocellular Carcinoma Based on Bioinformatics Analysis. Int J Gen Med 2021; 14:7235-7246. [PMID: 34737618 PMCID: PMC8560065 DOI: 10.2147/ijgm.s333904] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/29/2021] [Indexed: 12/25/2022] Open
Abstract
Purpose Liver cancer is the fifth most common type of cancer worldwide, and the ATP-binding cassette (ABC) transporter family has been widely accepted as a cause of multidrug resistance. This study was conducted to explore the potential value and mechanisms of the ABC transporter gene family in the liver hepatocellular carcinoma (LIHC). Materials and Methods Data were collected from different public databases. UALCAN, ONCOMINE, and GEPIA were used to retrieve a selection of differently expressed and pathological stage-related genes among the ABC family. Principal component analysis (PCA) was utilized for grouping, and its prognostic value was evaluated by univariate and multivariate Cox analyses. The co-expression pattern was constructed with UALCAN, and the functional analyses were carried out with DAVID. The correlation between the biomarker and immune infiltration, genetic alteration frequency, and drug sensitivity were explored with TIMER, cBioPortal, GDSC and CTRP, respectively. Finally, tSNE algorithm was used to explore the distribution of ABCC5 expressed cells. Results Among the ABC transporter family members, ABCC5 was differently expressed and strongly related to the pathological stage of LIHC. PCA divided patients of LIHC into two groups, and Cox analyses demonstrated that ABCC5 was an independent risk factor of LIHC. Functional analyses indicated that the genes were enriched in the pathways of transmembrane transporter, ATPase activity, and bile secretion. ABCC5 is also associated with immune infiltration of cells like macrophages, neutrophils, and dendritic cells. The genetic alteration frequency of ABCC5 confirmed its potential value in LIHC. In addition, several drugs were explored and found to be relevant to LIHC. The t-SNE showed that expression of ABCC5 was most concentrated in macrophages, followed by hepatocytes. Conclusion ABCC5 may facilitate LIHC progression through different mechanisms and be a potential biomarker and target for diagnosis, prognosis, and therapy of LIHC.
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Affiliation(s)
- Yuting Qiu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Centre for Digestive Diseases, Beijing, 100050, People's Republic of China
| | - Haobo Li
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100029, People's Republic of China
| | - Jiaheng Xie
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, People's Republic of China
| | - Xinwei Qiao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Centre for Digestive Diseases, Beijing, 100050, People's Republic of China
| | - Jing Wu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Centre for Digestive Diseases, Beijing, 100050, People's Republic of China
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6
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Capurro V, Tomati V, Sondo E, Renda M, Borrelli A, Pastorino C, Guidone D, Venturini A, Giraudo A, Mandrup Bertozzi S, Musante I, Bertozzi F, Bandiera T, Zara F, Galietta LJV, Pedemonte N. Partial Rescue of F508del-CFTR Stability and Trafficking Defects by Double Corrector Treatment. Int J Mol Sci 2021; 22:ijms22105262. [PMID: 34067708 PMCID: PMC8156943 DOI: 10.3390/ijms22105262] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023] Open
Abstract
Deletion of phenylalanine at position 508 (F508del) in the CFTR chloride channel is the most frequent mutation in cystic fibrosis (CF) patients. F508del impairs the stability and folding of the CFTR protein, thus resulting in mistrafficking and premature degradation. F508del-CFTR defects can be overcome with small molecules termed correctors. We investigated the efficacy and properties of VX-445, a newly developed corrector, which is one of the three active principles present in a drug (Trikafta®/Kaftrio®) recently approved for the treatment of CF patients with F508del mutation. We found that VX-445, particularly in combination with type I (VX-809, VX-661) and type II (corr-4a) correctors, elicits a large rescue of F508del-CFTR function. In particular, in primary bronchial epithelial cells of CF patients, the maximal rescue obtained with corrector combinations including VX-445 was close to 60–70% of CFTR function in non-CF cells. Despite this high efficacy, analysis of ubiquitylation, resistance to thermoaggregation, protein half-life, and subcellular localization revealed that corrector combinations did not fully normalize F508del-CFTR behavior. Our study indicates that it is still possible to further improve mutant CFTR rescue with the development of corrector combinations having maximal effects on mutant CFTR structural and functional properties.
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Affiliation(s)
- Valeria Capurro
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (V.C.); (V.T.); (E.S.); (C.P.); (I.M.); (F.Z.)
| | - Valeria Tomati
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (V.C.); (V.T.); (E.S.); (C.P.); (I.M.); (F.Z.)
| | - Elvira Sondo
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (V.C.); (V.T.); (E.S.); (C.P.); (I.M.); (F.Z.)
| | - Mario Renda
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy; (M.R.); (A.B.); (D.G.); (A.V.)
| | - Anna Borrelli
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy; (M.R.); (A.B.); (D.G.); (A.V.)
| | - Cristina Pastorino
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (V.C.); (V.T.); (E.S.); (C.P.); (I.M.); (F.Z.)
| | - Daniela Guidone
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy; (M.R.); (A.B.); (D.G.); (A.V.)
| | - Arianna Venturini
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy; (M.R.); (A.B.); (D.G.); (A.V.)
| | - Alessandro Giraudo
- D3-PharmaChemistry, Fondazione Istituto Italiano di Tecnologia, 16163 Genova, Italy; (A.G.); (F.B.); (T.B.)
| | - Sine Mandrup Bertozzi
- Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
| | - Ilaria Musante
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (V.C.); (V.T.); (E.S.); (C.P.); (I.M.); (F.Z.)
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genova, Italy
| | - Fabio Bertozzi
- D3-PharmaChemistry, Fondazione Istituto Italiano di Tecnologia, 16163 Genova, Italy; (A.G.); (F.B.); (T.B.)
| | - Tiziano Bandiera
- D3-PharmaChemistry, Fondazione Istituto Italiano di Tecnologia, 16163 Genova, Italy; (A.G.); (F.B.); (T.B.)
| | - Federico Zara
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (V.C.); (V.T.); (E.S.); (C.P.); (I.M.); (F.Z.)
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genova, Italy
| | - Luis J. V. Galietta
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy; (M.R.); (A.B.); (D.G.); (A.V.)
- Department of Translational Medical Sciences (DISMET), University of Naples Federico II, 80131 Naples, Italy
- Correspondence: (L.J.V.G.); (N.P.)
| | - Nicoletta Pedemonte
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (V.C.); (V.T.); (E.S.); (C.P.); (I.M.); (F.Z.)
- Correspondence: (L.J.V.G.); (N.P.)
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7
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Ford RC, Hellmich UA. What monomeric nucleotide binding domains can teach us about dimeric ABC proteins. FEBS Lett 2020; 594:3857-3875. [PMID: 32880928 DOI: 10.1002/1873-3468.13921] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
The classic conceptualization of ATP binding cassette (ABC) transporter function is an ATP-dependent conformational change coupled to transport of a substrate across a biological membrane via the transmembrane domains (TMDs). The binding of two ATP molecules within the transporter's two nucleotide binding domains (NBDs) induces their dimerization. Despite retaining the ability to bind nucleotides, isolated NBDs frequently fail to dimerize. ABC proteins without a TMD, for example ABCE and ABCF, have NBDs tethered via elaborate linkers, further supporting that NBD dimerization does not readily occur for isolated NBDs. Intriguingly, even in full-length transporters, the NBD-dimerized, outward-facing state is not as frequently observed as might be expected. This leads to questions regarding what drives NBD interaction and the role of the TMDs or linkers. Understanding the NBD-nucleotide interaction and the subsequent NBD dimerization is thus pivotal for understanding ABC transporter activity in general. Here, we hope to provide new insights into ABC protein function by discussing the perplexing issue of (missing) NBD dimerization in isolation and in the context of full-length ABC proteins.
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Affiliation(s)
- Robert C Ford
- Faculty of Biology Medicine and Health, The University of Manchester, UK
| | - Ute A Hellmich
- Department of Chemistry, Johannes Gutenberg-University, Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Frankfurt, Germany
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8
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Meng X, Clews J, Ciuta AD, Martin ER, Ford RC. CFTR structure, stability, function and regulation. Biol Chem 2020; 400:1359-1370. [PMID: 30738013 DOI: 10.1515/hsz-2018-0470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/30/2019] [Indexed: 12/15/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a unique member of the ATP-binding cassette family of proteins because it has evolved into a channel. Mutations in CFTR cause cystic fibrosis, the most common genetic disease in people of European origin. The F508del mutation is found in about 90% of patients and here we present data that suggest its main effect is on CFTR stability rather than on the three-dimensional (3D) folded state. A survey of recent cryo-electron microscopy studies was carried out and this highlighted differences in terms of CFTR conformation despite similarities in experimental conditions. We further studied CFTR structure under various phosphorylation states and with the CFTR-interacting protein NHERF1. The coexistence of outward-facing and inward-facing conformations under a range of experimental conditions was suggested from these data. These results are discussed in terms of structural models for channel gating, and favour the model where the mostly disordered regulatory-region of the protein acts as a channel plug.
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Affiliation(s)
- Xin Meng
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Jack Clews
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Anca D Ciuta
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Eleanor R Martin
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Robert C Ford
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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9
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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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10
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Tosco A, Villella VR, Raia V, Kroemer G, Maiuri L. Cystic Fibrosis: New Insights into Therapeutic Approaches. CURRENT RESPIRATORY MEDICINE REVIEWS 2020. [DOI: 10.2174/1573398x15666190702151613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the identification of Cystic Fibrosis (CF) as a disease in 1938 until 2012, only
therapies to treat symptoms rather than etiological therapies have been used to treat the disease. Over
the last few years, new technologies have been developed, and gene editing strategies are now
moving toward a one-time cure. This review will summarize recent advances in etiological therapies
that target the basic defect in the CF Transmembrane Receptor (CFTR), the protein that is mutated in
CF. We will discuss how newly identified compounds can directly target mutated CFTR to improve
its function. Moreover, we will discuss how proteostasis regulators can modify the environment in
which the mutant CFTR protein is synthesized and decayed, thus restoring CFTR function. The
future of CF therapies lies in combinatory therapies that may be personalized for each CF patient.
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Affiliation(s)
- Antonella Tosco
- Department of Translational Medical Sciences, Pediatric Unit, Regional Cystic Fibrosis Center, Federico II University, Naples 80131, Italy
| | - Valeria R. Villella
- Division of Genetics and Cell Biology, European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Valeria Raia
- Department of Translational Medical Sciences, Pediatric Unit, Regional Cystic Fibrosis Center, Federico II University, Naples 80131, Italy
| | - Guido Kroemer
- Equipe11 labellisee Ligue Nationale Contrele Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Luigi Maiuri
- Division of Genetics and Cell Biology, European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan 20132, Italy
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11
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Kumar S, Ruiz N. Probing Conformational States of a Target Protein in Escherichia coli Cells by in vivo Cysteine Cross-linking Coupled with Proteolytic Gel Analysis. Bio Protoc 2019; 9:e3271. [PMID: 33654790 DOI: 10.21769/bioprotoc.3271] [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] [Received: 04/13/2019] [Revised: 05/23/2019] [Accepted: 05/27/2019] [Indexed: 11/02/2022] Open
Abstract
Transporters are dynamic membrane proteins that are essential to the physiology of cells. To function, transporters must cycle between various conformational states, so to understand their mechanistic details, it is critical to characterize how their structure changes during the transport cycle. One approach to studying the dynamics of transporters takes advantage of the chemistry of cysteine by using sulfhydryl-reactive, bi-functional cross-linkers to probe changes in the distance between two specific residues that have been substituted to cysteine. This approach is mostly used to study transporters in vitro, not in their natural cellular environment. Here we describe a protocol based on structure-guided cysteine cross-linking and proteolysis-coupled gel analysis to probe conformational changes of a target transporter in live Escherichia coli cells. Although cross-linking approaches have been used to probe the proximity between transmembrane segments in membrane proteins in vivo, to our knowledge this protocol is the first to be used to interrogate transporter dynamics in cells. The use of this protocol is optimal for proteins with known or modeled structures to guide the replacement of specific residues with cysteines and the selection of cross-linking agents with various spacer arm lengths. This protocol allows for discriminating easily cross-linked and uncross-linked species and does not require the often difficult or unavailable reconstitution of transport activity in an in vitro system. In addition, this protocol could be used to probe the conformation of transporters in cells treated with transport inhibitors in order to better understand their mechanism of action, and potentially dynamic interactions between domains in proteins that are not transporters.
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Affiliation(s)
- Sujeet Kumar
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
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Villella VR, Tosco A, Esposito S, Bona G, Raia V, Maiuri L. Mutation-specific therapies and drug repositioning in cystic fibrosis. Minerva Pediatr 2019; 71:287-296. [DOI: 10.23736/s0026-4946.19.05506-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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Learning the ABCs one at a time: structure and mechanism of ABC transporters. Biochem Soc Trans 2019; 47:23-36. [PMID: 30626703 DOI: 10.1042/bst20180147] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/16/2018] [Accepted: 11/29/2018] [Indexed: 12/21/2022]
Abstract
ATP-binding cassette (ABC) transporters are essential proteins that are found across all kingdoms of life. ABC transporters harness the energy of ATP hydrolysis to drive the import of nutrients inside bacterial cells or the export of toxic compounds or essential lipids across bacteria and eukaryotic membranes. Typically, ABC transporters consist of transmembrane domains (TMDs) and nucleotide-binding domains (NBDs) to bind their substrate and ATP, respectively. The TMDs dictate what ligands can be recognised, whereas the NBDs are the power engine of the ABC transporter, carrying out ATP binding and hydrolysis. It has been proposed that they utilise the alternating access mechanism, inward- to outward-facing conformation, to transport their substrates. Here, we will review the recent progress on the structure determination of eukaryotic and bacterial ABC transporters as well as the novel mechanisms that have also been proposed, that fall out of the alternating access mechanism model.
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Csizmadia G, Farkas B, Spagina Z, Tordai H, Hegedűs T. Quantitative comparison of ABC membrane protein type I exporter structures in a standardized way. Comput Struct Biotechnol J 2018; 16:396-403. [PMID: 30425800 PMCID: PMC6222291 DOI: 10.1016/j.csbj.2018.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/12/2018] [Accepted: 10/13/2018] [Indexed: 12/24/2022] Open
Abstract
An increasing number of ABC membrane protein structures are determined by cryo-electron microscopy and X-ray crystallography, consequently identifying differences between their conformations has become an arising issue. Therefore, we propose to define standardized measures for ABC Type I exporter structure characterization. We set conformational vectors, conftors, which describe the relative orientation of domains and can highlight structural differences. In addition, continuum electrostatics calculations were performed to characterize the energetics of membrane insertion illuminating functionally crucial regions. In summary, the proposed metrics contribute to deeper understanding of ABC membrane proteins' structural features, structure validation, and analysis of movements observed in a molecular dynamics trajectory. Moreover, the concept of standardized metrics can be applied not only to ABC membrane protein structures (http://conftors.hegelab.org).
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Key Words
- ABC proteins
- ABC, ATP binding cassette
- CFTR, cystic fibrosis transmembrane conductance regulator
- CG, coarse grained
- CH, coupling helix
- COG, center of geometry
- ICD, intracellular domain
- Membrane proteins
- NBD, nucleotide binding domain
- Quantitative structural properties
- Structure comparison
- Structure validation
- TH, transmembrane helix
- TM, transmembrane
- TMD, transmembrane domain
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Affiliation(s)
- Georgina Csizmadia
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Bianka Farkas
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.,Faculty of Information Technology, Pázmány Péter Catholic University, Budapest, Hungary
| | - Zoltán Spagina
- 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
| | - Tamás Hegedűs
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
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