1
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de Carvalho RSA, Rasel SI, Khandelwal NK, Tomasiak TM. Cryo-EM structure of the tetra-phosphorylated R-domain in Ycf1 reveals key interactions for transport regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583773. [PMID: 38496555 PMCID: PMC10942426 DOI: 10.1101/2024.03.06.583773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Many ATP-binding cassette (ABC) transporters are regulated by phosphorylation on long and disordered loops which present a challenge to visualize with structural methods. We have trapped an activated state of the regulatory domain (R-domain) of Yeast Cadmium Factor 1 (Ycf1) by enzymatically enriching the phosphorylated state. A 3.2 Å cryo-EM structure reveals an R-domain structure with four phosphorylated residues and a position for the entire R-domain. The structure reveals key R-domain interactions including a bridging interaction between NBD1 and NBD2 as well as an interaction with the R-insertion, another regulatory region. We systematically probe these interactions with a linker substitution strategy along the R-domain and find a close match with these interactions and survival under Ycf1-dependent growth conditions. We propose a model where four overlapping phosphorylation sites bridge several regions of Ycf1 to engage in a transport-competent state.
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Affiliation(s)
| | - Shamiul I Rasel
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Nitesh K Khandelwal
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
- Current Address: Department of Biochemistry and Biophysics, University of California - San Francisco, San Francisco, CA 94
| | - Thomas M Tomasiak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
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2
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Khandelwal NK, Tomasiak TM. Structural basis for autoinhibition by the dephosphorylated regulatory domain of Ycf1. Nat Commun 2024; 15:2389. [PMID: 38493146 PMCID: PMC10944535 DOI: 10.1038/s41467-024-46722-w] [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: 07/18/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
Yeast Cadmium Factor 1 (Ycf1) sequesters glutathione and glutathione-heavy metal conjugates into yeast vacuoles as a cellular detoxification mechanism. Ycf1 belongs to the C subfamily of ATP Binding Cassette (ABC) transporters characterized by long flexible linkers, notably the regulatory domain (R-domain). R-domain phosphorylation is necessary for activity, whereas dephosphorylation induces autoinhibition through an undefined mechanism. Because of its transient and dynamic nature, no structure of the dephosphorylated Ycf1 exists, limiting understanding of this R-domain regulation. Here, we capture the dephosphorylated Ycf1 using cryo-EM and show that the unphosphorylated R-domain indeed forms an ordered structure with an unexpected hairpin topology bound within the Ycf1 substrate cavity. This architecture and binding mode resemble that of a viral peptide inhibitor of an ABC transporter and the secreted bacterial WXG peptide toxins. We further reveal the subset of phosphorylation sites within the hairpin turn that drive the reorganization of the R-domain conformation, suggesting a mechanism for Ycf1 activation by phosphorylation-dependent release of R-domain mediated autoinhibition.
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Affiliation(s)
- Nitesh Kumar Khandelwal
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
- Department of Biochemistry and Biophysics, University of California - San Francisco, San Francisco, CA, 94158, USA
| | - Thomas M Tomasiak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.
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3
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Mazza T, Roumeliotis TI, Garitta E, Drew D, Rashid ST, Indiveri C, Choudhary JS, Linton KJ, Beis K. Structural basis for the modulation of MRP2 activity by phosphorylation and drugs. Nat Commun 2024; 15:1983. [PMID: 38438394 PMCID: PMC10912322 DOI: 10.1038/s41467-024-46392-8] [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: 10/05/2023] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
Multidrug resistance-associated protein 2 (MRP2/ABCC2) is a polyspecific efflux transporter of organic anions expressed in hepatocyte canalicular membranes. MRP2 dysfunction, in Dubin-Johnson syndrome or by off-target inhibition, for example by the uricosuric drug probenecid, elevates circulating bilirubin glucuronide and is a cause of jaundice. Here, we determine the cryo-EM structure of rat Mrp2 (rMrp2) in an autoinhibited state and in complex with probenecid. The autoinhibited state exhibits an unusual conformation for this class of transporter in which the regulatory domain is folded within the transmembrane domain cavity. In vitro phosphorylation, mass spectrometry and transport assays show that phosphorylation of the regulatory domain relieves this autoinhibition and enhances rMrp2 transport activity. The in vitro data is confirmed in human hepatocyte-like cells, in which inhibition of endogenous kinases also reduces human MRP2 transport activity. The drug-bound state reveals two probenecid binding sites that suggest a dynamic interplay with autoinhibition. Mapping of the Dubin-Johnson mutations onto the rodent structure indicates that many may interfere with the transition between conformational states.
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Affiliation(s)
- Tiziano Mazza
- Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, OX11 0FA, UK
- Department DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, 87036, Arcavacata di Rende, Italy
| | - Theodoros I Roumeliotis
- Functional Proteomics group, Chester Beatty Laboratories, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Elena Garitta
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, E1 2A, London, UK
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - S Tamir Rashid
- Department of Metabolism, Digestion & Reproduction, Imperial College London, W12 0NN, London, UK
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, 87036, Arcavacata di Rende, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnology (IBIOM), 70126, Bari, Italy
| | - Jyoti S Choudhary
- Functional Proteomics group, Chester Beatty Laboratories, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Kenneth J Linton
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, E1 2A, London, UK
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK.
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, OX11 0FA, UK.
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Hou T, Chen L. Sulfonylurea receptor 2 (SUR2), intricate sensors for intracellular Mg-nucleotides. Bioessays 2024; 46:e2300151. [PMID: 38227376 DOI: 10.1002/bies.202300151] [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: 08/16/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024]
Abstract
SUR2, similar to SUR1, is a regulatory subunit of the ATP-sensitive potassium channel (KATP), which plays a key role in numerous important physiological processes and is implicated in various diseases. Recent structural studies have revealed that, like SUR1, SUR2 can undergo ligand-dependent dynamic conformational changes, transitioning between an inhibitory inward-facing conformation and an activating occluded conformation. In addition, SUR2 possesses a unique inhibitory Regulatory helix (R helix) that is absent in SUR1. The binding of the activating Mg-ADP to NBD2 of SUR2 competes with the inhibitory Mg-ATP, thereby promoting the release of the R helix and initiating the activation process. Moreover, the signal generated by Mg-ADP binding to NBD2 might be directly transmitted to the TMD of SUR2, prior to NBD dimerization. Furthermore, the C-terminal 42 residues (C42) of SUR2 might allosterically regulate the kinetics of Mg-nucleotide binding on NBD2. These distinctive properties render SUR2 intricate sensors for intracellular Mg-nucleotides.
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Affiliation(s)
- Tianyi Hou
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, Beijing, China
| | - Lei Chen
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, Beijing, China
- National Biomedical Imaging Center, Peking University, Beijing, Beijing, China
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5
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Cui G, Strickland KM, Vazquez Cegla AJ, McCarty NA. Comparing ATPase activity of ATP-binding cassette subfamily C member 4, lamprey CFTR, and human CFTR using an antimony-phosphomolybdate assay. Front Pharmacol 2024; 15:1363456. [PMID: 38440176 PMCID: PMC10910009 DOI: 10.3389/fphar.2024.1363456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction: ATP-binding cassette (ABC) transporters use the hydrolysis of ATP to power the active transport of molecules, but paradoxically the cystic fibrosis transmembrane regulator (CFTR, ABCC7) forms an ion channel. We previously showed that ATP-binding cassette subfamily C member 4 (ABCC4) is the closest mammalian paralog to CFTR, compared to other ABC transporters. In addition, Lamprey CFTR (Lp-CFTR) is the oldest known CFTR ortholog and has unique structural and functional features compared to human CFTR (hCFTR). The availability of these evolutionarily distant orthologs gives us the opportunity to study the changes in ATPase activity that may be related to their disparate functions. Methods: We utilized the baculovirus expression system with Sf9 insect cells and made use of the highly sensitive antimony-phosphomolybdate assay for testing the ATPase activity of human ABCC4 (hABCC4), Lp-CFTR, and hCFTR under similar experimental conditions. This assay measures the production of inorganic phosphate (Pi) in the nanomolar range. Results: Crude plasma membranes were purified, and protein concentration, determined semi-quantitatively, of hABCC4, Lp-CFTR, and hCFTR ranged from 0.01 to 0.36 μg/μL. No significant difference in expression level was found although hABCC4 trended toward the highest level. hABCC4 was activated by ATP with the equilibrium constant (Kd) 0.55 ± 0.28 mM (n = 8). Estimated maximum ATPase rate (Vmax) for hABCC4 was about 0.2 nmol/μg/min when the protein was activated with 1 mM ATP at 37°C (n = 7). Estimated maximum ATPase rate for PKA-phosphorylated Lp-CFTR reached about half of hCFTR levels in the same conditions. Vmax for both Lp-CFTR and hCFTR were significantly increased in high PKA conditions compared to low PKA conditions. Maximum intrinsic ATPase rate of hABCC4 in the absence of substrate was twice that of hCFTR when activated in 1 mM ATP. Conclusion: The findings here suggest that while both ABCC4 and hCFTR bear one consensus and one degenerate ATPase site, the hCFTR exhibited a reduced intrinsic ATPase activity. In addition, ATPase activity in the CFTR lineage increased from Lp-CFTR to hCFTR. Finally, the studies pave the way to purify hABCC4, Lp-CFTR, and hCFTR from Sf9 cells for their structural investigation, including by cryo-EM, and for studies of evolution in the ABC transporter superfamily.
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Affiliation(s)
| | | | | | - Nael A. McCarty
- Division of Pulmonology, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory + Children’s Center for Cystic Fibrosis and Airways Disease Research, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, United States
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6
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Tóth Á, Crespi V, Janaszkiewicz A, Di Meo F. Computational and structural insights into the pre- and post-hydrolysis states of bovine multidrug resistance-associated protein 1. Basic Clin Pharmacol Toxicol 2023; 133:508-525. [PMID: 37038087 DOI: 10.1111/bcpt.13871] [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: 12/29/2022] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/12/2023]
Abstract
ATP-binding cassette C-family drug membrane transporters play an important role in local pharmacokinetics, that is, drug concentration in cellular compartments. From the structural point of view, only the bovine ortholog of the multidrug resistance-associated protein 1 (bMRP1) has been resolved. We here used μs-scaled molecular dynamics simulations to investigate the structure and dynamics of the bovine multidrug resistance-associated protein 1 in pre- and post-hydrolysis functional states. The present work aims to examine the slight but likely relevant structural differences between pre- and post-hydrolysis states of outward-facing conformations as well as the interactions between the multidrug resistance-associated protein 1 and the surrounding lipid bilayer. Global conformational dynamics show unfavourable extracellular opening associated with nucleotide-binding domain dimerization indicating that the post-hydrolysis state adopts a close-cleft conformation rather than an outward-open conformation. Our present simulations also highlight persistent interactions with annular cholesterol molecules and the expected active role of lipid bilayer in the allosteric communication between distant domains of the transporter.
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Affiliation(s)
- Ágota Tóth
- Inserm UMR 1248 Pharmacology & Transplantation, Univ. Limoges, Limoges, France
| | - Veronica Crespi
- Inserm UMR 1248 Pharmacology & Transplantation, Univ. Limoges, Limoges, France
| | | | - Florent Di Meo
- Inserm UMR 1248 Pharmacology & Transplantation, Univ. Limoges, Limoges, France
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7
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Wang J, Li X, Wang F, Cheng M, Mao Y, Fang S, Wang L, Zhou C, Hou W, Chen Y. Placing steroid hormones within the human ABCC3 transporter reveals a compatible amphiphilic substrate-binding pocket. EMBO J 2023; 42:e113415. [PMID: 37485728 PMCID: PMC10476276 DOI: 10.15252/embj.2022113415] [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: 12/31/2022] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
The human ABC transporter ABCC3 (also known as MRP3) transports a wide spectrum of substrates, including endogenous metabolites and exogenous drugs. Accordingly, it participates in multiple physiological processes and is involved in diverse human diseases such as intrahepatic cholestasis of pregnancy, which is caused by the intracellular accumulation of bile acids and estrogens. Here, we report three cryogenic electron microscopy structures of ABCC3: in the apo-form and in complexed forms bound to either the conjugated sex hormones β-estradiol 17-(β-D-glucuronide) and dehydroepiandrosterone sulfate. For both hormones, the steroid nuclei that superimpose against each other occupy the hydrophobic center of the transport cavity, whereas the two conjugation groups are separated and fixed by the hydrophilic patches in two transmembrane domains. Structural analysis combined with site-directed mutagenesis and ATPase activity assays revealed that ABCC3 possesses an amphiphilic substrate-binding pocket able to hold either conjugated hormone in an asymmetric pattern. These data build on consensus features of the substrate-binding pocket of MRPs and provide a structural platform for the rational design of inhibitors.
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Affiliation(s)
- Jie Wang
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Xu Li
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Fang‐Fang Wang
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Meng‐Ting Cheng
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Yao‐Xu Mao
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Shu‐Cheng Fang
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Liang Wang
- Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Cong‐Zhao Zhou
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Wen‐Tao Hou
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Yuxing Chen
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
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8
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Ding D, Hou T, Wei M, Wu JX, Chen L. The inhibition mechanism of the SUR2A-containing K ATP channel by a regulatory helix. Nat Commun 2023; 14:3608. [PMID: 37330603 PMCID: PMC10276813 DOI: 10.1038/s41467-023-39379-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 06/10/2023] [Indexed: 06/19/2023] Open
Abstract
KATP channels are metabolic sensors for intracellular ATP/ADP ratios, play essential roles in many physiological processes, and are implicated in a spectrum of pathological conditions. SUR2A-containing KATP channels differ from other subtypes in their sensitivity to Mg-ADP activation. However, the underlying structural mechanism remains poorly understood. Here we present a series of cryo-EM structures of SUR2A in the presence of different combinations of Mg-nucleotides and the allosteric inhibitor repaglinide. These structures uncover regulatory helix (R helix) on the NBD1-TMD2 linker, which wedges between NBD1 and NBD2. R helix stabilizes SUR2A in the NBD-separated conformation to inhibit channel activation. The competitive binding of Mg-ADP with Mg-ATP to NBD2 mobilizes the R helix to relieve such inhibition, allowing channel activation. The structures of SUR2B in similar conditions suggest that the C-terminal 42 residues of SUR2B enhance the structural dynamics of NBD2 and facilitate the dissociation of the R helix and the binding of Mg-ADP to NBD2, promoting NBD dimerization and subsequent channel activation.
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Affiliation(s)
- Dian Ding
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, 100871, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
- National Biomedical Imaging Center, Peking University, 100871, Beijing, China
| | - Tianyi Hou
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, 100871, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
- National Biomedical Imaging Center, Peking University, 100871, Beijing, China
| | - Miao Wei
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, 100871, Beijing, China
- National Biomedical Imaging Center, Peking University, 100871, Beijing, China
| | - Jing-Xiang Wu
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, 100871, Beijing, China
- National Biomedical Imaging Center, Peking University, 100871, Beijing, China
| | - Lei Chen
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, 100871, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
- National Biomedical Imaging Center, Peking University, 100871, Beijing, China.
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9
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Tóth Á, Janaszkiewicz A, Crespi V, Di Meo F. On the interplay between lipids and asymmetric dynamics of an NBS degenerate ABC transporter. Commun Biol 2023; 6:149. [PMID: 36737455 PMCID: PMC9898250 DOI: 10.1038/s42003-023-04537-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Multidrug resistance-associated proteins are ABC C-family exporters. They are crucial in pharmacology as they transport various substrates across membranes. However, the role of the degenerate nucleotide-binding site (NBS) remains unclear likewise the interplay with the surrounding lipid environment. Here, we propose a dynamic and structural overview of MRP1 from ca. 110 μs molecular dynamics simulations. ATP binding to NBS1 is likely maintained along several transport cycles. Asymmetric NBD behaviour is ensured by lower signal transduction from NBD1 to the rest of the protein owing to the absence of ball-and-socket conformation between NBD1 and coupling helices. Even though surrounding lipids play an active role in the allosteric communication between the substrate-binding pocket and NBDs, our results suggest that lipid composition has a limited impact, mostly by affecting transport kinetics. We believe that our work can be extended to other degenerate NBS ABC proteins and provide hints for deciphering mechanistic differences among ABC transporters.
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Affiliation(s)
- Ágota Tóth
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Angelika Janaszkiewicz
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Veronica Crespi
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Florent Di Meo
- Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute-Univ. Limoges, 2 rue du Prof. Descottes, 87000 F, Limoges, France.
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10
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A Structure-Based View on ABC-Transporter Linked to Multidrug Resistance. Molecules 2023; 28:molecules28020495. [PMID: 36677553 PMCID: PMC9862083 DOI: 10.3390/molecules28020495] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/29/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
The discovery of the first ATP-binding cassette (ABC) transporter, whose overexpression in cancer cells is responsible for exporting anticancer drugs out of tumor cells, initiated enormous efforts to overcome tumor cell multidrug resistance (MDR) by inhibition of ABC-transporter. Because of its many physiological functions, diverse studies have been conducted on the mechanism, function and regulation of this important group of transmembrane transport proteins. In this review, we will focus on the structural aspects of this transporter superfamily. Since the resolution revolution of electron microscope, experimentally solved structures increased rapidly. A summary of the structures available and an overview of recent structure-based studies are provided. More specifically, the artificial intelligence (AI)-based predictions from AlphaFold-2 will be discussed.
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11
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Driggers CM, Shyng SL. Mechanistic insights on KATP channel regulation from cryo-EM structures. J Gen Physiol 2022; 155:213723. [PMID: 36441147 PMCID: PMC9700523 DOI: 10.1085/jgp.202113046] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/19/2022] [Accepted: 11/08/2022] [Indexed: 11/29/2022] Open
Abstract
Gated by intracellular ATP and ADP, ATP-sensitive potassium (KATP) channels couple cell energetics with membrane excitability in many cell types, enabling them to control a wide range of physiological processes based on metabolic demands. The KATP channel is a complex of four potassium channel subunits from the Kir channel family, Kir6.1 or Kir6.2, and four sulfonylurea receptor subunits, SUR1, SUR2A, or SUR2B, from the ATP-binding cassette (ABC) transporter family. Dysfunction of KATP channels underlies several human diseases. The importance of these channels in human health and disease has made them attractive drug targets. How the channel subunits interact with one another and how the ligands interact with the channel to regulate channel activity have been long-standing questions in the field. In the past 5 yr, a steady stream of high-resolution KATP channel structures has been published using single-particle cryo-electron microscopy (cryo-EM). Here, we review the advances these structures bring to our understanding of channel regulation by physiological and pharmacological ligands.
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Affiliation(s)
- Camden M. Driggers
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health and Science University, Portland, OR
| | - Show-Ling Shyng
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health and Science University, Portland, OR,Correspondence to Show-Ling Shyng:
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12
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Law WWH, Kanelis V, Zamble DB. Biochemical studies highlight determinants for metal selectivity in the Escherichia coli periplasmic solute binding protein NikA. Metallomics 2022; 14:mfac084. [PMID: 36255398 PMCID: PMC9671101 DOI: 10.1093/mtomcs/mfac084] [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: 08/09/2022] [Accepted: 10/15/2022] [Indexed: 11/12/2022]
Abstract
Nickel is an essential micronutrient for the survival of many microbes. On account of the toxicity of nickel and its scarcity in the environment, microbes have evolved specific systems for uptaking and delivering nickel to enzymes. NikA, the solute binding protein for the ATP-binding cassette (ABC) importer NikABCDE, plays a vital role in the nickel homeostasis of Escherichia coli by selectively binding nickel over other metals in the metabolically complex periplasm. While the endogenous ligand for NikA is known to be the Ni(II)-(L-His)2 complex, the molecular basis by which NikA selectively binds Ni(II)-(L-His)2 is unclear, especially considering that NikA can bind multiple metal-based ligands with comparable affinity. Here we show that, regardless of its promiscuous binding activity, NikA preferentially interacts with Ni(II)-(L-His)2, even over other metal-amino acid ligands with an identical coordination geometry for the metal. Replacing both the Ni(II) and the L-His residues in Ni(II)-(L-His)2 compromises binding of the ligand to NikA, in part because these alterations affect the degree by which NikA closes around the ligand. Replacing H416, the only NikA residue that ligates the Ni(II), with other potential metal-coordinating amino acids decreases the binding affinity of NikA for Ni(II)-(L-His)2 and compromises uptake of Ni(II) into E. coli cells, likely due to altered metal selectivity of the NikA mutants. Together, the biochemical and in vivo studies presented here define key aspects of how NikA selects for Ni(II)-(L-His)2 over other metal complexes, and can be used as a reference for studies into the metal selectivity of other microbial solute binding proteins.
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Affiliation(s)
- Wayne W H Law
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Voula Kanelis
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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13
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Qiu J, Hou K, Li Q, Chen J, Li X, Hou H, Wang L, Liu J, Xue Q, Wang C. Boosting the Cannabidiol Production in Engineered Saccharomyces cerevisiae by Harnessing the Vacuolar Transporter BPT1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12055-12064. [PMID: 36122349 DOI: 10.1021/acs.jafc.2c05468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cannabidiol (CBD), the main nonpsychoactive cannabinoid in Cannabis sativa, has diverse applications in the pharmacological, food, and cosmetic industries. The long plantation period and the complex chemical structure of cannabidiol pose a great challenge on CBD supply. Here, we achieved de novo biosynthesis of cannabidiol in Saccharomyces cerevisiae. The CBD production was further enhanced by 2.53-fold through pushing the supply of precursors and fusion protein construction. Bile pigment transporter 1 (BPT1) was the most effective transporter for transferring cannabigerolic acid (CBGA) from the cytoplasm to the vacuole, which removed the physical barrier separating CBGA and its catalytic enzyme. The lowest binding energy of the CBGA-BPT1 complex confirmed a strong interaction between BPT1 and CBGA. A CBD yield of 6.92 mg/L was achieved, which was 100-fold higher than the yield generated by the starting strain. This study provides insights into high-level CBD-producing strain construction and lays the foundation for CBD supply.
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Affiliation(s)
- Jie Qiu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, P. R. China
- College of Medicine and Biomedicine, Huaqiao University, Quanzhou 362000, P. R. China
| | - Kangxin Hou
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, P. R. China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, P. R. China
| | - Qiang Li
- Exchange, Development and Service Center for Science and Technology Talents, The Ministry of Science and Technology (MoST), 54 Sanlihe Road, Xicheng, Beijing 100045, P. R. China
| | - Jialin Chen
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550014, P. R. China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, P. R. China
| | - Hongping Hou
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, P. R. China
| | - Liqiang Wang
- College of Medicine and Biomedicine, Huaqiao University, Quanzhou 362000, P. R. China
| | - Jia Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, P. R. China
| | - Qiang Xue
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, P. R. China
| | - Caixia Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, P. R. China
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14
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Liu Y, Wang X, Si B, Wang T, Wu Y, Liu Y, Zhou Y, Tong H, Zheng X, Xu A. Zinc oxide/graphene oxide nanocomposites efficiently inhibited cadmium-induced hepatotoxicity via releasing Zn ions and up-regulating MRP1 expression. ENVIRONMENT INTERNATIONAL 2022; 165:107327. [PMID: 35667343 DOI: 10.1016/j.envint.2022.107327] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/20/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Environmental cadmium (Cd) pollution has been verified to associated with various hepatic diseases, as Cd has been classified as one of the TOP 20 Hazardous Substances and liver is the main target of Cd poisoning. However, to design efficient hepatic antidotes with excellent detoxification capacity and reveal their underlying mechanism(s) are still challenges in Cd detoxification. Herein, ZnO/GO nanocomposites with favorable biocompatibility was uncovered their advanced function against Cd-elicited liver damage at the in situ level in vivo by 9.4 T magnetic resonance imaging (MRI). To explore the cellular detoxification mechanism, ZnO/GO nanocomposites was found to effectively inhibit the cyto- and geno-toxicity of Cd with the maximum antagonistic efficiency to be approximately 90%. Mechanistically, ZnO/GO nanocomposites competitively inhibited the cellular Cd uptake through releasing Zn ions, and significantly promoted Cd excretion via targeting the efflux pump of multidrug resistance associated protein1 (MRP1), which was confirmed by mass spectra and immunohistochemical analysis in kidney, a main excretion organ of Cd. Our data provided a novel approach against Cd-elicited hepatotoxic responses by constructed ZnO/GO nanocomposites both in vitro and in vivo, which may have promising application in prevention and detoxification for Cd poisoning.
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Affiliation(s)
- Yun Liu
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology; High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Science, Hefei 230031, PR China
| | - Xue Wang
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Bo Si
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology; High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Science, Hefei 230031, PR China
| | - Tong Wang
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology; High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Science, Hefei 230031, PR China
| | - Yun Wu
- Anhui Province Key Laboratory of High Field Magnetic Resonance Imaging; High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Science, Hefei 230031, PR China
| | - Ying Liu
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology; High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Science, Hefei 230031, PR China
| | - Yemian Zhou
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology; High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Science, Hefei 230031, PR China
| | - Haiyang Tong
- Anhui Province Key Laboratory of High Field Magnetic Resonance Imaging; High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Science, Hefei 230031, PR China
| | - Xinwei Zheng
- Anhui Province Key Laboratory of High Field Magnetic Resonance Imaging; High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Science, Hefei 230031, PR China.
| | - An Xu
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology; High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Science, Hefei 230031, PR China; Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, PR China.
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15
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Khandelwal NK, Millan CR, Zangari SI, Avila S, Williams D, Thaker TM, Tomasiak TM. The structural basis for regulation of the glutathione transporter Ycf1 by regulatory domain phosphorylation. Nat Commun 2022; 13:1278. [PMID: 35277487 PMCID: PMC8917219 DOI: 10.1038/s41467-022-28811-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 02/07/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractYeast Cadmium Factor 1 (Ycf1) sequesters heavy metals and glutathione into the vacuole to counter cell stress. Ycf1 belongs to the ATP binding cassette C-subfamily (ABCC) of transporters, many of which are regulated by phosphorylation on intrinsically-disordered domains. The regulatory mechanism of phosphorylation is still poorly understood. Here, we report two cryo-EM structures of Ycf1 at 3.4 Å and 4.0 Å resolution in inward-facing open conformations that capture previously unobserved ordered states of the intrinsically disordered regulatory domain (R-domain). R-domain phosphorylation is clearly evident and induces a topology promoting electrostatic and hydrophobic interactions with Nucleotide Binding Domain 1 (NBD1) and the Lasso motif. These interactions stay constant between the structures and are related by rigid body movements of the NBD1/R-domain complex. Biochemical data further show R-domain phosphorylation reorganizes the Ycf1 architecture and is required for maximal ATPase activity. Together, we provide insights into how R-domains control ABCC transporter activity.
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16
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Aller SG, Segrest JP. The regulatory domains of the lipid exporter ABCA1 form domain swapped latches. PLoS One 2022; 17:e0262746. [PMID: 35120130 PMCID: PMC8815970 DOI: 10.1371/journal.pone.0262746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/04/2022] [Indexed: 12/19/2022] Open
Abstract
ABCA1 and ABCA4 are enigmatic because they transport substrates in opposite directions yet share >50% amino acid identity. ABCA4 imports lipid conjugates but ABCA1 exports lipids. Both hydrolyze ATP to drive transport, and both contain cytoplasmic regulatory domains (RDs) following nucleotide-binding domains (NBDs) in the primary structure. The tertiary structures of several ABC importers, including ABCA4, show that each RD forms a domain-swapped latch that locks onto the opposing RD and holds the NBDs close together. Crucially, sequences encoding the RDs and their bridges are among the most conserved in the entire ABC-A subfamily. In the original cryo-EM structure of ABCA1, the RDs were modeled without crossover. After close inspection of that cryo-EM density map and the recent structure of ABCA4, we propose that the RDs of ABCA1 also form a domain-swapped latch. A refined ABCA1 model containing latches exhibited significantly improved overall protein geometry. Critically, the conserved crossover sequence leading to the RD-domain swap is directly supported by the original cryo-EM density map of ABCA1 and appears to have been overlooked. Our refined ABCA1 model suggests the possibility that ABCA1, despite being an exporter, has highly restrained NBDs that suggest a transport mechanism that is distinct from 'alternating access'.
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Affiliation(s)
- Stephen G. Aller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Jere P. Segrest
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
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17
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Vascular K ATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides. Proc Natl Acad Sci U S A 2021; 118:2109441118. [PMID: 34711681 PMCID: PMC8694068 DOI: 10.1073/pnas.2109441118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 11/24/2022] Open
Abstract
Vascular KATP channels formed by the potassium channel Kir6.1 and its regulatory protein SUR2B maintain blood pressure in the physiological range. Overactivity of the channel due to genetic mutations in either Kir6.1 or SUR2B causes severe cardiovascular pathologies known as Cantú syndrome. The cryogenic electron microscopy structures of the vascular KATP channel reported here show multiple, dynamically related conformations of the regulatory subunit SUR2B. Molecular dynamics simulations reveal the negatively charged ED-domain in SUR2B, a stretch of 15 glutamate (E) and aspartate (D) residues not previously resolved, play a key MgADP-dependent role in mediating interactions at the interface between the SUR2B and Kir6.1 subunits. Our findings provide a mechanistic understanding of how channel activity is regulated by intracellular MgADP. Vascular tone is dependent on smooth muscle KATP channels comprising pore-forming Kir6.1 and regulatory SUR2B subunits, in which mutations cause Cantú syndrome. Unique among KATP isoforms, they lack spontaneous activity and require Mg-nucleotides for activation. Structural mechanisms underlying these properties are unknown. Here, we determined cryogenic electron microscopy structures of vascular KATP channels bound to inhibitory ATP and glibenclamide, which differ informatively from similarly determined pancreatic KATP channel isoform (Kir6.2/SUR1). Unlike SUR1, SUR2B subunits adopt distinct rotational “propeller” and “quatrefoil” geometries surrounding their Kir6.1 core. The glutamate/aspartate-rich linker connecting the two halves of the SUR-ABC core is observed in a quatrefoil-like conformation. Molecular dynamics simulations reveal MgADP-dependent dynamic tripartite interactions between this linker, SUR2B, and Kir6.1. The structures captured implicate a progression of intermediate states between MgADP-free inactivated, and MgADP-bound activated conformations wherein the glutamate/aspartate-rich linker participates as mobile autoinhibitory domain, suggesting a conformational pathway toward KATP channel activation.
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18
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ATP-binding cassette transporters and neurodegenerative diseases. Essays Biochem 2021; 65:1013-1024. [PMID: 34415015 DOI: 10.1042/ebc20210012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022]
Abstract
ATP-binding cassette (ABC) transporters are one of the largest groups of transporter families in humans. ABC transporters mediate the translocation of a diverse range of substrates across cellular membranes, including amino acids, nucleosides, lipids, sugars and xenobiotics. Neurodegenerative diseases are a group of brain diseases that detrimentally affect neurons and other brain cells and are usually associated with deposits of pathogenic proteins in the brain. Major neurodegenerative diseases include Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. ABC transporters are highly expressed in the brain and have been implicated in a number of pathological processes underlying neurodegenerative diseases. This review outlines the current understanding of the role of ABC transporters in neurodegenerative diseases, focusing on some of the most important pathways, and also suggests future directions for research in this field.
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