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Debbiche R, Elbahnsi A, Uguen K, Ka C, Callebaut I, Le Gac G. Insights into the role of glycerophospholipids on the iron export function of SLC40A1 and the molecular mechanisms of ferroportin disease. FASEB J 2024; 38:e23725. [PMID: 38959016 DOI: 10.1096/fj.202400337r] [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: 02/12/2024] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 07/04/2024]
Abstract
SLC40A1 is the sole iron export protein reported in mammals. In humans, its dysfunction is responsible for ferroportin disease, an inborn error of iron metabolism transmitted as an autosomal dominant trait and observed in different ethnic groups. As a member of the major facilitator superfamily, SLC40A1 requires a series of conformational changes to enable iron translocation across the plasma membrane. The influence of lipids on protein stability and its conformational changes has been little investigated to date. Here, we combine molecular dynamics simulations of SLC40A1 embedded in membrane bilayers with experimental alanine scanning mutagenesis to analyze the specific role of glycerophospholipids. We identify four basic residues (Lys90, Arg365, Lys366, and Arg371) that are located at the membrane-cytosol interface and consistently interact with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) molecules. These residues surround a network of salt bridges and hydrogens bonds that play a critical role in stabilizing SLC40A1 in its basal outward-facing conformation. More deeply embedded in the plasma membrane, we identify Arg179 as a charged amino acid residue also tightly interacting with lipid polar heads. This results in a local deformation of the lipid bilayer. Interestingly, Arg179 is adjacent to Arg178, which forms a functionally important salt-bridge with Asp473 and is a recurrently associated with ferroportin disease when mutated to glutamine. We demonstrate that the two p.Arg178Gln and p.Arg179Thr missense variants have similar functional behaviors. These observations provide insights into the role of phospholipids in the formation/disruption of the SLC40A1 inner gate, and give a better understanding of the diversity of molecular mechanisms of ferroportin disease.
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Affiliation(s)
- Rim Debbiche
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Ahmad Elbahnsi
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Paris, France
| | - Kévin Uguen
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- CHU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Brest, France
| | - Chandran Ka
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- CHU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Brest, France
| | - Isabelle Callebaut
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Paris, France
| | - Gérald Le Gac
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- CHU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Brest, France
- Laboratory of Excellence GR-Ex, Paris, France
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Parker JL, Kato T, Kuteyi G, Sitsel O, Newstead S. Molecular basis for selective uptake and elimination of organic anions in the kidney by OAT1. Nat Struct Mol Biol 2023; 30:1786-1793. [PMID: 37482561 PMCID: PMC10643130 DOI: 10.1038/s41594-023-01039-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023]
Abstract
In mammals, the kidney plays an essential role in maintaining blood homeostasis through the selective uptake, retention or elimination of toxins, drugs and metabolites. Organic anion transporters (OATs) are responsible for the recognition of metabolites and toxins in the nephron and their eventual urinary excretion. Inhibition of OATs is used therapeutically to improve drug efficacy and reduce nephrotoxicity. The founding member of the renal organic anion transporter family, OAT1 (also known as SLC22A6), uses the export of α-ketoglutarate (α-KG), a key intermediate in the Krebs cycle, to drive selective transport and is allosterically regulated by intracellular chloride. However, the mechanisms linking metabolite cycling, drug transport and intracellular chloride remain obscure. Here, we present cryogenic-electron microscopy structures of OAT1 bound to α-KG, the antiviral tenofovir and clinical inhibitor probenecid, used in the treatment of Gout. Complementary in vivo cellular assays explain the molecular basis for α-KG driven drug elimination and the allosteric regulation of organic anion transport in the kidney by chloride.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Takafumi Kato
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Gabriel Kuteyi
- Department of Biochemistry, University of Oxford, Oxford, UK
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Oleg Sitsel
- Department of Biochemistry, University of Oxford, Oxford, UK
- Max Planck Institute of Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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3
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Dou T, Lian T, Shu S, He Y, Jiang J. The substrate and inhibitor binding mechanism of polyspecific transporter OAT1 revealed by high-resolution cryo-EM. Nat Struct Mol Biol 2023; 30:1794-1805. [PMID: 37845412 DOI: 10.1038/s41594-023-01123-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Organic anion transporters (OATs) of the SLC22 family have crucial roles in the transport of organic anions, including metabolites and therapeutic drugs, and in transporter-mediated drug-drug interactions. In the kidneys, OATs facilitate the elimination of metabolic waste products and xenobiotics. However, their transport activities can lead to the accumulation of certain toxic compounds within cells, causing kidney damage. Moreover, OATs are important drug targets, because their inhibition modulates the elimination or retention of substrates linked to diseases. Despite extensive research on OATs, the molecular basis of their substrate and inhibitor binding remains poorly understood. Here we report the cryo-EM structures of rat OAT1 (also known as SLC22A6) and its complexes with para-aminohippuric acid and probenecid at 2.1, 2.8 and 2.9 Å resolution, respectively. Our findings reveal a highly conserved substrate binding mechanism for SLC22 transporters, wherein four aromatic residues form a cage to accommodate the polyspecific binding of diverse compounds.
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Affiliation(s)
- Tongyi Dou
- Laboratory of Membrane Proteins and Structural Biology, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Tengfei Lian
- Laboratory of Membrane Proteins and Structural Biology, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Shi Shu
- Laboratory of Membrane Proteins and Structural Biology, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Yi He
- Fermentation Facility, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Jiansen Jiang
- Laboratory of Membrane Proteins and Structural Biology, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA.
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Janaszkiewicz A, Tóth Á, Faucher Q, Arnion H, Védrenne N, Barin-Le Guellec C, Marquet P, Di Meo F. Substrate binding and lipid-mediated allostery in the human organic anion transporter 1 at the atomic-scale. Biomed Pharmacother 2023; 160:114342. [PMID: 36739760 DOI: 10.1016/j.biopha.2023.114342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
The Organic Anion Transporter 1 is a membrane transporter known for its central role in drug elimination by the kidney. hOAT1 is an antiporter translocating substrate in exchange for a-ketoglutarate. The understanding of hOAT1 structure and function remains limited due to the absence of resolved structure of hOAT1. Benefiting from conserved structural and functional patterns shared with other Major Facilitator Superfamily transporters, the present study intended to investigate fragments of hOAT1 transport function and modulation of its activity in order to make a step forward the understanding of its transport cycle. μs-long molecular dynamics simulation of hOAT1 were carried out suggesting two plausible binding sites for a typical substrate, adefovir, in line with experimental observations. The well-known B-like motif binding site was observed in line with previous studies. However, we here propose a new inner binding cavity which is expected to be involved in substrate translocation event. Binding modes of hOAT1 co-substrate α-ketoglutarate were also investigated suggesting that it may bind to highly conserved intracellular motifs. We here hypothesise that α-ketoglutarate may disrupt the pseudo-symmetrical intracellular charge-relay system which in turn may participate to the destabilisation of OF conformation. Investigations regarding allosteric communications along hOAT1 also suggest that substrate binding event might modulate the dynamics of intracellular charge relay system, assisted by surrounding lipids as active partners. We here proposed a structural rationalisation of transport impairments observed for two single nucleotide polymorphisms, p.Arg50His and p.Arg454Gln suggesting that the present model may be used to transport dysfunctions arising from hOAT1 mutations.
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Affiliation(s)
| | - Ágota Tóth
- Inserm U1248 Pharmacology & Transplantation, Univ. Limoges, 87000 Limoges, France
| | - Quentin Faucher
- Inserm U1248 Pharmacology & Transplantation, Univ. Limoges, 87000 Limoges, France; Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utre-cht University, 3584 CG Utrecht, The Netherlands
| | - Hélène Arnion
- Inserm U1248 Pharmacology & Transplantation, Univ. Limoges, 87000 Limoges, France
| | - Nicolas Védrenne
- Inserm U1248 Pharmacology & Transplantation, Univ. Limoges, 87000 Limoges, France
| | - Chantal Barin-Le Guellec
- Inserm U1248 Pharmacology & Transplantation, Univ. Limoges, 87000 Limoges, France; CHU de Tours, 2 Boulevard Tonnellé, 37044 Tours, France
| | - Pierre Marquet
- Inserm U1248 Pharmacology & Transplantation, Univ. Limoges, 87000 Limoges, France; Department of Pharmacology and Toxicology, CHU Limoges, F-87000 Limoges, France
| | - Florent Di Meo
- Inserm U1248 Pharmacology & Transplantation, Univ. Limoges, 87000 Limoges, France.
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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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