1
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Bourgeois S, Houillier P. State of knowledge on ammonia handling by the kidney. Pflugers Arch 2024; 476:517-531. [PMID: 38448728 PMCID: PMC11006756 DOI: 10.1007/s00424-024-02940-1] [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: 12/21/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024]
Abstract
The disposal of ammonia, the main proton buffer in the urine, is important for acid-base homeostasis. Renal ammonia excretion is the predominant contributor to renal net acid excretion, both under basal condition and in response to acidosis. New insights into the mechanisms of renal ammonia production and transport have been gained in the past decades. Ammonia is the only urinary solute known to be produced in the kidney and selectively transported through the different parts of the nephron. Both molecular forms of total ammonia, NH3 and NH4+, are transported by specific proteins. Proximal tubular ammoniagenesis and the activity of these transport processes determine the eventual fate of total ammonia produced and excreted by the kidney. In this review, we summarized the state of the art of ammonia handling by the kidney and highlighted the newest processes described in the last decade.
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Affiliation(s)
- Soline Bourgeois
- Institut of Physiology, University of Zurich, Zurich, Switzerland.
| | - Pascal Houillier
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Centre National de La Recherche Scientifique (CNRS), EMR 8228, Paris, France
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2
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Holmberg SR, Sakamoto Y, Kato A, Romero MF. The role of Na +-coupled bicarbonate transporters (NCBT) in health and disease. Pflugers Arch 2024; 476:479-503. [PMID: 38536494 DOI: 10.1007/s00424-024-02937-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: 12/15/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 04/11/2024]
Abstract
Cellular and organism survival depends upon the regulation of pH, which is regulated by highly specialized cell membrane transporters, the solute carriers (SLC) (For a comprehensive list of the solute carrier family members, see: https://www.bioparadigms.org/slc/ ). The SLC4 family of bicarbonate (HCO3-) transporters consists of ten members, sorted by their coupling to either sodium (NBCe1, NBCe2, NBCn1, NBCn2, NDCBE), chloride (AE1, AE2, AE3), or borate (BTR1). The ionic coupling of SLC4A9 (AE4) remains controversial. These SLC4 bicarbonate transporters may be controlled by cellular ionic gradients, cellular membrane voltage, and signaling molecules to maintain critical cellular and systemic pH (acid-base) balance. There are profound consequences when blood pH deviates even a small amount outside the normal range (7.35-7.45). Chiefly, Na+-coupled bicarbonate transporters (NCBT) control intracellular pH in nearly every living cell, maintaining the biological pH required for life. Additionally, NCBTs have important roles to regulate cell volume and maintain salt balance as well as absorption and secretion of acid-base equivalents. Due to their varied tissue expression, NCBTs have roles in pathophysiology, which become apparent in physiologic responses when their expression is reduced or genetically deleted. Variations in physiological pH are seen in a wide variety of conditions, from canonically acid-base related conditions to pathologies not necessarily associated with acid-base dysfunction such as cancer, glaucoma, or various neurological diseases. The membranous location of the SLC4 transporters as well as recent advances in discovering their structural biology makes them accessible and attractive as a druggable target in a disease context. The role of sodium-coupled bicarbonate transporters in such a large array of conditions illustrates the potential of treating a wide range of disease states by modifying function of these transporters, whether that be through inhibition or enhancement.
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Affiliation(s)
- Shannon R Holmberg
- Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, 200 1st Street SW, Rochester, MN 55905, USA
- Biochemistry & Molecular Biology, Mayo Clinic College of Medicine & Science, 200 1st Street SW, Rochester, MN, USA
| | - Yohei Sakamoto
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-Ku, Yokohama, 226-8501, Japan
| | - Akira Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-Ku, Yokohama, 226-8501, Japan
| | - Michael F Romero
- Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, 200 1st Street SW, Rochester, MN 55905, USA.
- Nephrology & Hypertension, Mayo Clinic College of Medicine & Science, 200 1st Street SW, Rochester, MN, USA.
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3
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Zhang W, Ding D, Lu Y, Chen H, Jiang P, Zuo P, Wang G, Luo J, Yin Y, Luo J, Yin Y. Structural and functional insights into the lipid regulation of human anion exchanger 2. Nat Commun 2024; 15:759. [PMID: 38272905 PMCID: PMC10810954 DOI: 10.1038/s41467-024-44966-0] [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: 06/06/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Anion exchanger 2 (AE2) is an electroneutral Na+-independent Cl-/HCO3- exchanger belongs to the SLC4 transporter family. The widely expressed AE2 participates in a variety of physiological processes, including transepithelial acid-base secretion and osteoclastogenesis. Both the transmembrane domains (TMDs) and the N-terminal cytoplasmic domain (NTD) are involved in regulation of AE2 activity. However, the regulatory mechanism remains unclear. Here, we report a 3.2 Å cryo-EM structure of the AE2 TMDs in complex with PIP2 and a 3.3 Å full-length mutant AE2 structure in the resting state without PIP2. We demonstrate that PIP2 at the TMD dimer interface is involved in the substrate exchange process. Mutation in the PIP2 binding site leads to the displacement of TM7 and further stabilizes the interaction between the TMD and the NTD. Reduced substrate transport activity and conformation similar to AE2 in acidic pH indicating the central contribution of PIP2 to the function of AE2.
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Affiliation(s)
- Weiqi Zhang
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Dian Ding
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yishuo Lu
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Hongyi Chen
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Peijun Jiang
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Peng Zuo
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Guangxi Wang
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Juan Luo
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Yue Yin
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jianyuan Luo
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
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4
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Wang L, Hoang A, Gil-Iturbe E, Laganowsky A, Quick M, Zhou M. Mechanism of anion exchange and small-molecule inhibition of pendrin. Nat Commun 2024; 15:346. [PMID: 38184688 PMCID: PMC10771415 DOI: 10.1038/s41467-023-44612-1] [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: 06/24/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024] Open
Abstract
Pendrin (SLC26A4) is an anion exchanger that mediates bicarbonate (HCO3-) exchange for chloride (Cl-) and is crucial for maintaining pH and salt homeostasis in the kidney, lung, and cochlea. Pendrin also exports iodide (I-) in the thyroid gland. Pendrin mutations in humans lead to Pendred syndrome, causing hearing loss and goiter. Inhibition of pendrin is a validated approach for attenuating airway hyperresponsiveness in asthma and for treating hypertension. However, the mechanism of anion exchange and its inhibition by drugs remains poorly understood. We applied cryo-electron microscopy to determine structures of pendrin from Sus scrofa in the presence of either Cl-, I-, HCO3- or in the apo-state. The structures reveal two anion-binding sites in each protomer, and functional analyses show both sites are involved in anion exchange. The structures also show interactions between the Sulfate Transporter and Anti-Sigma factor antagonist (STAS) and transmembrane domains, and mutational studies suggest a regulatory role. We also determine the structure of pendrin in a complex with niflumic acid (NFA), which uncovers a mechanism of inhibition by competing with anion binding and impeding the structural changes necessary for anion exchange. These results reveal directions for understanding the mechanisms of anion selectivity and exchange and their regulations by the STAS domain. This work also establishes a foundation for analyzing the pathophysiology of mutations associated with Pendred syndrome.
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Affiliation(s)
- Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony Hoang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Eva Gil-Iturbe
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Matthias Quick
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
- Area Neuroscience - Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA.
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
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5
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Geertsma ER, Oliver D. SLC26 Anion Transporters. Handb Exp Pharmacol 2024; 283:319-360. [PMID: 37947907 DOI: 10.1007/164_2023_698] [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] [Indexed: 11/12/2023]
Abstract
Solute carrier family 26 (SLC26) is a family of functionally diverse anion transporters found in all kingdoms of life. Anions transported by SLC26 proteins include chloride, bicarbonate, and sulfate, but also small organic dicarboxylates such as fumarate and oxalate. The human genome encodes ten functional homologs, several of which are causally associated with severe human diseases, highlighting their physiological importance. Here, we review novel insights into the structure and function of SLC26 proteins and summarize the physiological relevance of human members.
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Affiliation(s)
- Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Dominik Oliver
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps University Marburg, Marburg, Germany.
- Center for Mind, Brain and Behavior (CMBB), Universities of Marburg and Giessen, Marburg, Giessen, Germany.
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6
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Zhong J, Dong J, Ruan W, Duan X. Potential Theranostic Roles of SLC4 Molecules in Human Diseases. Int J Mol Sci 2023; 24:15166. [PMID: 37894847 PMCID: PMC10606849 DOI: 10.3390/ijms242015166] [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: 08/29/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The solute carrier family 4 (SLC4) is an important protein responsible for the transport of various ions across the cell membrane and mediating diverse physiological functions, such as the ion transporting function, protein-to-protein interactions, and molecular transduction. The deficiencies in SLC4 molecules may cause multisystem disease involving, particularly, the respiratory system, digestive, urinary, endocrine, hematopoietic, and central nervous systems. Currently, there are no effective strategies to treat these diseases. SLC4 proteins are also found to contribute to tumorigenesis and development, and some of them are regarded as therapeutic targets in quite a few clinical trials. This indicates that SLC4 proteins have potential clinical prospects. In view of their functional characteristics, there is a critical need to review the specific functions of bicarbonate transporters, their related diseases, and the involved pathological mechanisms. We summarize the diseases caused by the mutations in SLC4 family genes and briefly introduce the clinical manifestations of these diseases as well as the current treatment strategies. Additionally, we illustrate their roles in terms of the physiology and pathogenesis that has been currently researched, which might be the future therapeutic and diagnostic targets of diseases and a new direction for drug research and development.
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Affiliation(s)
| | | | | | - Xiaohong Duan
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Disease, Shaanxi Key Laboratory of Stomatology, Department of Oral Biology & Clinic of Oral Rare Diseases and Genetic Diseases, School of Stomatology, The Fourth Military Medical University, Xi’an 710032, China; (J.Z.); (J.D.); (W.R.)
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7
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Lu Y, Zuo P, Chen H, Shan H, Wang W, Dai Z, Xu H, Chen Y, Liang L, Ding D, Jin Y, Yin Y. Structural insights into the conformational changes of BTR1/SLC4A11 in complex with PIP 2. Nat Commun 2023; 14:6157. [PMID: 37788993 PMCID: PMC10547724 DOI: 10.1038/s41467-023-41924-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023] Open
Abstract
BTR1 (SLC4A11) is a NH3 stimulated H+ (OH-) transporter belonging to the SLC4 family. Dysfunction of BTR1 leads to diseases such as congenital hereditary endothelial dystrophy (CHED) and Fuchs endothelial corneal dystrophy (FECD). However, the mechanistic basis of BTR1 activation by alkaline pH, transport activity regulation and pathogenic mutations remains elusive. Here, we present cryo-EM structures of human BTR1 in the outward-facing state in complex with its activating ligands PIP2 and the inward-facing state with the pathogenic R125H mutation. We reveal that PIP2 binds at the interface between the transmembrane domain and the N-terminal cytosolic domain of BTR1. Disruption of either the PIP2 binding site or protonation of PIP2 phosphate groups by acidic pH can transform BTR1 into an inward-facing conformation. Our results provide insights into the mechanisms of how the transport activity and conformation changes of BTR1 are regulated by PIP2 binding and interaction of TMD and NTD.
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Affiliation(s)
- Yishuo Lu
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Peng Zuo
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Hongyi Chen
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Hui Shan
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Weize Wang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Zonglin Dai
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | | | | | - Ling Liang
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Dian Ding
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yan Jin
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yuxin Yin
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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8
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Capper MJ, Yang S, Stone AC, Vatansever S, Zilberg G, Mathiharan YK, Habib R, Hutchinson K, Zhao Y, Schlessinger A, Mezei M, Osman R, Zhang B, Wacker D. Substrate binding and inhibition of the anion exchanger 1 transporter. Nat Struct Mol Biol 2023; 30:1495-1504. [PMID: 37679563 PMCID: PMC11008770 DOI: 10.1038/s41594-023-01085-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/28/2023] [Indexed: 09/09/2023]
Abstract
Anion exchanger 1 (AE1), a member of the solute carrier (SLC) family, is the primary bicarbonate transporter in erythrocytes, regulating pH levels and CO2 transport between lungs and tissues. Previous studies characterized its role in erythrocyte structure and provided insight into transport regulation. However, key questions remain regarding substrate binding and transport, mechanisms of drug inhibition and modulation by membrane components. Here we present seven cryo-EM structures in apo, bicarbonate-bound and inhibitor-bound states. These, combined with uptake and computational studies, reveal important molecular features of substrate recognition and transport, and illuminate sterol binding sites, to elucidate distinct inhibitory mechanisms of research chemicals and prescription drugs. We further probe the substrate binding site via structure-based ligand screening, identifying an AE1 inhibitor. Together, our findings provide insight into mechanisms of solute carrier transport and inhibition.
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Affiliation(s)
- Michael J Capper
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shifan Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander C Stone
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sezen Vatansever
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gregory Zilberg
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yamuna Kalyani Mathiharan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raul Habib
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yihan Zhao
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mihaly Mezei
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roman Osman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Zhang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Wacker
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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9
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Trejo F, Elizalde S, Mercado A, Gamba G, de losHeros P. SLC12A cryo-EM: analysis of relevant ion binding sites, structural domains, and amino acids. Am J Physiol Cell Physiol 2023; 325:C921-C939. [PMID: 37545407 DOI: 10.1152/ajpcell.00089.2023] [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: 03/13/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023]
Abstract
The solute carrier family 12A (SLC12A) superfamily of membrane transporters modulates the movement of cations coupled with chloride across the membrane. In doing so, these cotransporters are involved in numerous aspects of human physiology: cell volume regulation, ion homeostasis, blood pressure regulation, and neurological action potential via intracellular chloride concentration modulation. Their physiological characterization has been largely studied; however, understanding the mechanics of their function and the relevance of structural domains or specific amino acids has been a pending task. In recent years, single-particle cryogenic electron microscopy (cryo-EM) has been successfully applied to members of the SLC12A family including all K+:Cl- cotransporters (KCCs), Na+:K+:2Cl- cotransporter NKCC1, and recently Na+:Cl- cotransporter (NCC); revealing structural elements that play key roles in their function. The present review analyzes the data provided by these cryo-EM reports focusing on structural domains and specific amino acids involved in ion binding, domain interactions, and other important SCL12A structural elements. A comparison of cryo-EM data from NKCC1 and KCCs is presented in the light of the two recent NCC cryo-EM studies, to propose insight into structural elements that might also be found in NCC and are necessary for its proper function. In the final sections, the importance of key coordination residues for substrate specificity and their implication on various pathophysiological conditions and genetic disorders is reviewed, as this could provide the basis to correlate structural elements with the development of novel and selective treatments, as well as mechanistic insight into the function and regulation of cation-coupled chloride cotransporters (CCCs).
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Affiliation(s)
- Fátima Trejo
- Unidad de Investigación UNAM-INC, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stephanie Elizalde
- Departamento de Nefrología y Metabolismo Mineral, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Adriana Mercado
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Gerardo Gamba
- Departamento de Nefrología y Metabolismo Mineral, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Molecular Physiology Unit, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Paola de losHeros
- Unidad de Investigación UNAM-INC, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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10
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Zhekova HR, Ramirez-Echemendía DP, Sejdiu BI, Pushkin A, Tieleman DP, Kurtz I. Coarse-grained molecular dynamics simulations of lipid-protein interactions in SLC4 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546592. [PMID: 37425774 PMCID: PMC10327080 DOI: 10.1101/2023.06.26.546592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO 3 -, CO 3 2- , Cl - , Na + , K + , NH 3 and H + necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl - /HCO 3 - exchanger) and NBCe1 (Na + -CO 3 2- cotransporter). Previous computational studies of the outward facing (OF) state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed multiple 50 µs coarse-grained molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1 and NDCBE (a Na + -CO 3 2- /Cl - exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine (POPC), phosphatidylethanolamine (POPE), phosphatidylserine (POPS), and sphingomyelin (POSM). The recently resolved inward-facing (IF) state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, POPC, and POSM in the three studied proteins and their potential roles in the SLC4 transport function, conformational transition and protein dimerization were discussed. Statement of significance The SLC4 protein family is involved in critical physiological processes like pH and blood pressure regulation and maintenance of ion homeostasis. Its members can be found in various tissues. A number of studies suggest possible lipid regulation of the SLC4 function. However, the protein-lipid interactions in the SLC4 family are still poorly understood. Here we make use of long coarse-grained molecular dynamics simulations to assess the protein-lipid interactions in three SLC4 proteins with different transport modes, AE1, NBCe1, and NDCBE. We identify putative lipid binding sites for several lipid types of potential mechanistic importance, discuss them in the framework of the known experimental data and provide a necessary basis for further studies on lipid regulation of SLC4 function.
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11
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Lavoro A, Falzone L, Tomasello B, Conti GN, Libra M, Candido S. In silico analysis of the solute carrier (SLC) family in cancer indicates a link among DNA methylation, metabolic adaptation, drug response, and immune reactivity. Front Pharmacol 2023; 14:1191262. [PMID: 37397501 PMCID: PMC10308049 DOI: 10.3389/fphar.2023.1191262] [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: 03/21/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction: The oncogenic transformation is driven by genetic and epigenetic alterations influencing cancer cell fate. These alterations also result in metabolic reprogramming by modulating the expression of membrane Solute Carrier (SLC) transporters involved in biomolecules trafficking. SLCs act as tumor suppressors or promoters influencing cancer methylome, tumor growth, immune-escape, and chemoresistance. Methods: This in silico study aimed to identify the deregulated SLCs in various tumor types compared to normal tissues by analyzing the TCGA Target GTEx dataset. Furthermore, the relationship between SLCs expression and the most relevant tumor features was tackled along with their genetic regulation mediated by DNA methylation. Results: We identified 62 differentially expressed SLCs, including the downregulated SLC25A27 and SLC17A7, as well as the upregulated SLC27A2 and SLC12A8. Notably, SLC4A4 and SLC7A11 expression was associated with favorable and unfavorable outcome, respectively. Moreover, SLC6A14, SLC34A2, and SLC1A2 were linked to tumor immune responsiveness. Interestingly, SLC24A5 and SLC45A2 positively correlated with anti-MEK and anti-RAF sensitivity. The expression of relevant SLCs was correlated with hypo- and hyper-methylation of promoter and body region, showing an established DNA methylation pattern. Noteworthy, the positive association of cg06690548 (SLC7A11) methylation with cancer outcome suggests the independent predictive role of DNA methylation at a single nucleotide resolution. Discussion: Although our in silico overview revealed a wide heterogeneity depending on different SLCs functions and tumor types, we identified key SLCs and pointed out the role of DNA methylation as regulatory mechanism of their expression. Overall, these findings deserve further studies to identify novel cancer biomarkers and promising therapeutic targets.
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Affiliation(s)
- Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Luca Falzone
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori “Fondazione G. Pascale”, Naples, Italy
| | - Barbara Tomasello
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Giuseppe Nicolò Conti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, Italy
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12
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Zhang Q, Jian L, Yao D, Rao B, Xia Y, Hu K, Li S, Shen Y, Cao M, Qin A, Zhao J, Cao Y. The structural basis of the pH-homeostasis mediated by the Cl -/HCO 3- exchanger, AE2. Nat Commun 2023; 14:1812. [PMID: 37002221 PMCID: PMC10066210 DOI: 10.1038/s41467-023-37557-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
The cell maintains its intracellular pH in a narrow physiological range and disrupting the pH-homeostasis could cause dysfunctional metabolic states. Anion exchanger 2 (AE2) works at high cellular pH to catalyze the exchange between the intracellular HCO3- and extracellular Cl-, thereby maintaining the pH-homeostasis. Here, we determine the cryo-EM structures of human AE2 in five major operating states and one transitional hybrid state. Among those states, the AE2 shows the inward-facing, outward-facing, and intermediate conformations, as well as the substrate-binding pockets at two sides of the cell membrane. Furthermore, critical structural features were identified showing an interlock mechanism for interactions among the cytoplasmic N-terminal domain and the transmembrane domain and the self-inhibitory effect of the C-terminal loop. The structural and cell-based functional assay collectively demonstrate the dynamic process of the anion exchange across membranes and provide the structural basis for the pH-sensitive pH-rebalancing activity of AE2.
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Affiliation(s)
- Qing Zhang
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Liyan Jian
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Department of Orthopaedics, Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Deqiang Yao
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, 200127, Shanghai, China
| | - Bing Rao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Ying Xia
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Kexin Hu
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Shaobai Li
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Yafeng Shen
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Mi Cao
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - An Qin
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Department of Orthopaedics, Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Jie Zhao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Department of Orthopaedics, Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Yu Cao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China.
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China.
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13
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Beltran JL, McGrath LG, Caruso S, Bain RK, Hendrix CE, Kamran H, Johnston HG, Collings RM, Henry MCN, Abera TAL, Donoso VA, Carriker EC, Thurtle-Schmidt BH. Borate Transporters and SLC4 Bicarbonate Transporters Share Key Functional Properties. MEMBRANES 2023; 13:membranes13020235. [PMID: 36837738 PMCID: PMC9959716 DOI: 10.3390/membranes13020235] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/03/2023]
Abstract
Borate transporters are membrane transport proteins that regulate intracellular borate levels. In plants, borate is a micronutrient essential for growth but is toxic in excess, while in yeast, borate is unnecessary for growth and borate export confers tolerance. Borate transporters share structural homology with human bicarbonate transporters in the SLC4 family despite low sequence identity and differences in transported solutes. Here, we characterize the S. cerevisiae borate transporter Bor1p and examine whether key biochemical features of SLC4 transporters extend to borate transporters. We show that borate transporters and SLC4 transporters share multiple properties, including lipid-promoted dimerization, sensitivity to stilbene disulfonate-derived inhibitors, and a requirement for an acidic residue at the solute binding site. We also identify several amino acids critical for Bor1p function and show that disease-causing mutations in human SLC4A1 will eliminate in vivo function when their homologous mutations are introduced in Bor1p. Our data help elucidate mechanistic features of Bor1p and reveal significant functional properties shared between borate transporters and SLC4 transporters.
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14
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Lee SK, Occhipinti R, Moss FJ, Parker MD, Grichtchenko II, Boron WF. Distinguishing among HCO 3- , CO 3= , and H + as Substrates of Proteins That Appear To Be "Bicarbonate" Transporters. J Am Soc Nephrol 2023; 34:40-54. [PMID: 36288904 PMCID: PMC10103014 DOI: 10.1681/asn.2022030289] [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: 03/10/2022] [Accepted: 07/23/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Differentiating among HCO 3- , CO 3= , and H + movements across membranes has long seemed impossible. We now seek to discriminate unambiguously among three alternate mechanisms: the inward flux of 2 HCO 3- (mechanism 1), the inward flux of 1 CO 3= (mechanism 2), and the CO 2 /HCO 3- -stimulated outward flux of 2 H + (mechanism 3). METHODS As a test case, we use electrophysiology and heterologous expression in Xenopus oocytes to examine SLC4 family members that appear to transport "bicarbonate" ("HCO 3- "). RESULTS First, we note that cell-surface carbonic anhydrase should catalyze the forward reaction CO 2 +OH - →HCO 3- if HCO 3- is the substrate; if it is not, the reverse reaction should occur. Monitoring changes in cell-surface pH ( Δ pH S ) with or without cell-surface carbonic anhydrase, we find that the presumed Cl-"HCO 3 " exchanger AE1 (SLC4A1) does indeed transport HCO 3- (mechanism 1) as long supposed, whereas the electrogenic Na/"HCO 3 " cotransporter NBCe1 (SLC4A4) and the electroneutral Na + -driven Cl-"HCO 3 " exchanger NDCBE (SLC4A8) do not. Second, we use mathematical simulations to show that each of the three mechanisms generates unique quantities of H + at the cell surface (measured as Δ pH S ) per charge transported (measured as change in membrane current, ΔIm ). Calibrating ΔpH S /Δ Im in oocytes expressing the H + channel H V 1, we find that our NBCe1 data align closely with predictions of CO 3= transport (mechanism 2), while ruling out HCO 3- (mechanism 1) and CO 2 /HCO 3- -stimulated H + transport (mechanism 3). CONCLUSIONS Our surface chemistry approach makes it possible for the first time to distinguish among HCO 3- , CO 3= , and H + fluxes, thereby providing insight into molecular actions of clinically relevant acid-base transporters and carbonic-anhydrase inhibitors.
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Affiliation(s)
- Seong-Ki Lee
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Rossana Occhipinti
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Fraser J. Moss
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Mark D. Parker
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio
- Department of Physiology and Biophysics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York
| | | | - Walter F. Boron
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio
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15
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Kurtz I, Schwartz GJ. Base (HCO3-/CO32-) Transport Properties of SLC4 Proteins: New Insights in Acid-Base Kidney Physiology. J Am Soc Nephrol 2023; 34:8-13. [PMID: 36719145 PMCID: PMC10101619 DOI: 10.1681/asn.0000000000000008] [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: 09/15/2022] [Accepted: 09/30/2022] [Indexed: 01/22/2023] Open
Abstract
H+ or base transporters and channels in the mammalian genome play important roles in the maintenance of numerous cellular biochemical and physiologic processes throughout the body. Among the known base transporters, those within the SLC4 and SLC26 gene families are involved in cell, transepithelial, and whole organ function. Whether the functional properties of these transporters involve HCO3-, CO32-, or HCO3-/CO32- stimulated H+ (or OH-) transport has not received widespread attention in the literature. Accordingly, "bicarbonate" is the term typically used in most textbooks without greater specificity. Moreover, clinicians and physiologists have historically focused on the blood HCO3- concentration as the base term in the Henderson-Hasselbalch equation in the analysis of clinical acid-base abnormalities, thus, bicarbonate has been assumed to be the species reabsorbed along the nephron as required to maintain the blood [HCO3-] at approximately 25 mM. However, accumulating data in the literature suggest that carbonate, rather than bicarbonate, is the species absorbed across the proximal tubule basolateral membrane, whereas in the collecting duct, bicarbonate is indeed transported. Various experimental approaches leading to this new concept are herein reviewed.
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Affiliation(s)
- Ira Kurtz
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
- Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, California
| | - George J. Schwartz
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
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16
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Yang W, Lu S, Peng L, Zhang Z, Zhang Y, Guo D, Ma F, Hua Y, Chen X. Integrated analysis of necroptosis-related genes for evaluating immune infiltration and colon cancer prognosis. Front Immunol 2022; 13:1085038. [PMID: 36618366 PMCID: PMC9814966 DOI: 10.3389/fimmu.2022.1085038] [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: 10/31/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Background Colon cancer (CC) is the second most common gastrointestinal malignancy. About one in five patients have already developed distant metastases at the time of initial diagnosis, and up to half of patients develop distant metastases from initial local disease, which leads to a poor prognosis for CC patients. Necroptosis plays a key role in promoting tumor growth in different tumors. The purpose of this study was to construct a prognostic model composed of necroptosis-related genes (NRGs) in CC. Methods The Cancer Genome Atlas was used to obtain information on clinical features and gene expression. Gene expression differential analysis, weighted gene co-expression network analysis, univariate Cox regression analysis and the least absolute shrinkage and selection operator regression algorithm were utilized to identify prognostic NRGs. Thereafter, a risk scoring model was established based on the NRGs. Biological processes and pathways were identified by gene ontology and gene set enrichment analysis (GSEA). Further, protein-protein interaction and ceRNA networks were constructed based on mRNA-miRNA-lncRNA. Finally, the effect of necroptosis related risk score on different degrees of immune cell infiltration was evaluated. Results CALB1, CHST13, and SLC4A4 were identified as NRGs of prognostic significance and were used to establish a risk scoring model. The time-dependent receiver operating characteristic curve analysis revealed that the model could well predict the 1-, 3-, and 5-year overall survival (OS). Further, GSEA suggested that the NRGs may participate in biological processes, such as the WNT pathway and JAK-Stat pathway. Eight key hub genes were identified, and a ceRNA regulatory network, which comprised 1 lncRNA, 5 miRNAs and 3 mRNAs, was constructed. Immune infiltration analysis revealed that the low-risk group had significantly higher immune-related scores than the high-risk group. A nomogram of the model was constructed based on the risk score, necroptosis, and the clinicopathological features (age and TNM stage). The calibration curves implied that the model was effective at predicting the 1-, 3-, and 5-year OS of CC. Conclusion Our NRG-based prognostic model can assist in the evaluation of CC prognosis and the identification of therapeutic targets for CC.
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Affiliation(s)
- Wei Yang
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Shuaibing Lu
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Liangqun Peng
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Zhandong Zhang
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yonglei Zhang
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Dandan Guo
- Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fei Ma
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yawei Hua
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Xiaobing Chen
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China,Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China,*Correspondence: Xiaobing Chen,
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17
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CryoEM structures of anion exchanger 1 capture multiple states of inward- and outward-facing conformations. Commun Biol 2022; 5:1372. [PMID: 36517642 PMCID: PMC9751308 DOI: 10.1038/s42003-022-04306-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Anion exchanger 1 (AE1, band 3) is a major membrane protein of red blood cells and plays a key role in acid-base homeostasis, urine acidification, red blood cell shape regulation, and removal of carbon dioxide during respiration. Though structures of the transmembrane domain (TMD) of three SLC4 transporters, including AE1, have been resolved previously in their outward-facing (OF) state, no mammalian SLC4 structure has been reported in the inward-facing (IF) conformation. Here we present the cryoEM structures of full-length bovine AE1 with its TMD captured in both IF and OF conformations. Remarkably, both IF-IF homodimers and IF-OF heterodimers were detected. The IF structures feature downward movement in the core domain with significant unexpected elongation of TM11. Molecular modeling and structure guided mutagenesis confirmed the functional significance of residues involved in TM11 elongation. Our data provide direct evidence for an elevator-like mechanism of ion transport by an SLC4 family member.
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18
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Smorodina E, Diankin I, Tao F, Qing R, Yang S, Zhang S. Structural informatic study of determined and AlphaFold2 predicted molecular structures of 13 human solute carrier transporters and their water-soluble QTY variants. Sci Rep 2022; 12:20103. [PMID: 36418372 PMCID: PMC9684436 DOI: 10.1038/s41598-022-23764-y] [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: 07/29/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
Solute carrier transporters are integral membrane proteins, and are important for diverse cellular nutrient transports, metabolism, energy demand, and other vital biological activities. They have recently been implicated in pancreatic cancer and other cancer metastasis, angiogenesis, programmed cell death and proliferation, cell metabolism and chemo-sensitivity. Here we report the study of 13 human solute carrier membrane transporters using the highly accurate AlphaFold2 predictions of 3D protein structures. In the native structures, there are hydrophobic amino acids leucine (L), isoleucine (I), valine (V) and phenylalanine (F) in the transmembrane alpha-helices. These hydrophobic amino acids L, I, V, F are systematically replaced by hydrophilic amino acids glutamine (Q), threonine (T) and tyrosine (Y), thus the QTY code. Therefore, these QTY variant transporters become water-soluble without requiring detergents. We present the superposed structures of these native solute carrier transporters and their water-soluble QTY variants. The superposed structures show remarkable similarity with RMSD ~ 1 Å-< 3 Å despite > 46% protein sequence substitutions in transmembrane alpha-helices. We also show the differences of surface hydrophobicity between the native solute carrier transporters and their QTY variants. Our study may further stimulate designs of water-soluble transmembrane proteins and other aggregated proteins for drug discovery and biotechnological applications.
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Affiliation(s)
- Eva Smorodina
- grid.55325.340000 0004 0389 8485Laboratory for Computational and Systems Immunology, Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Igor Diankin
- grid.78780.300000 0004 0613 1044Department of Computer Science, American University of Armenia, Yerevan, Armenia
| | - Fei Tao
- grid.16821.3c0000 0004 0368 8293Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Rui Qing
- grid.16821.3c0000 0004 0368 8293Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Steve Yang
- PT Metiska Farma, Daerah Khusus Ibukota, Jakarta, 12220 Indonesia
| | - Shuguang Zhang
- grid.116068.80000 0001 2341 2786Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
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19
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Romero MF. Who's on first …Na + , HCO 3 - or CO 3 2- ? J Physiol 2022; 600:3005-3006. [PMID: 35593728 DOI: 10.1113/jp282945] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/17/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Michael F Romero
- Physiology & Biomedical Engineering, Nephrology & Hypertension, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA
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20
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Sauer DB, Marden JJ, Sudar JC, Song J, Mulligan C, Wang DN. Structural basis of ion - substrate coupling in the Na +-dependent dicarboxylate transporter VcINDY. Nat Commun 2022; 13:2644. [PMID: 35551191 PMCID: PMC9098524 DOI: 10.1038/s41467-022-30406-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022] Open
Abstract
The Na+-dependent dicarboxylate transporter from Vibrio cholerae (VcINDY) is a prototype for the divalent anion sodium symporter (DASS) family. While the utilization of an electrochemical Na+ gradient to power substrate transport is well established for VcINDY, the structural basis of this coupling between sodium and substrate binding is not currently understood. Here, using a combination of cryo-EM structure determination, succinate binding and site-directed cysteine alkylation assays, we demonstrate that the VcINDY protein couples sodium- and substrate-binding via a previously unseen cooperative mechanism by conformational selection. In the absence of sodium, substrate binding is abolished, with the succinate binding regions exhibiting increased flexibility, including HPinb, TM10b and the substrate clamshell motifs. Upon sodium binding, these regions become structurally ordered and create a proper binding site for the substrate. Taken together, these results provide strong evidence that VcINDY's conformational selection mechanism is a result of the sodium-dependent formation of the substrate binding site.
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Affiliation(s)
- David B Sauer
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer J Marden
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | - Joseph C Sudar
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | - Jinmei Song
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | | | - Da-Neng Wang
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA.
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA.
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Liu Z, Wang Q, Zhai G, Ke S, Yu X, Guo J. SLC4A4 promotes prostate cancer progression in vivo and in vitro via AKT-mediated signalling pathway. Cancer Cell Int 2022; 22:127. [PMID: 35305629 PMCID: PMC8933877 DOI: 10.1186/s12935-022-02546-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/10/2022] [Indexed: 01/23/2023] Open
Abstract
Abstract
Background
Prostate cancer (PCa) is the second leading cause of cancer-related male deaths worldwide. The purpose of this study was to investigate the effects of homo sapiens solute carrier family 4 member 4 (SLC4A4), which encodes the electrogenic Na+/HCO3− cotransporter isoform 1 (NBCe1), in the development and progression of PCa.
Methods
The expression levels of SLC4A4 in PCa and normal prostate tissues were evaluated by immunohistochemistry. The SLC4A4 knockdown cell model was structured by lentiviral infection, and the knockdown efficiency was validated by RT-qPCR and Western blotting. The effects of SLC4A4 knockdown on cell proliferation, apoptosis and cycle, migration, and invasion were detected by Celigo cell counting assay and CCK-8 assay, flow cytometry analysis, wound-healing, and Transwell assay, respectively. Tumor growth in nude mice was surveyed by in vivo imaging and Ki-67 staining. Furthermore, underlying mechanism of SLC4A4 silence induced inhibition of PCa progression was explored by human phospho-kinase array.
Results
Our results revealed that SLC4A4 expression was up-regulated in PCa tissues and human PCa cell lines. High expression of SLC4A4 in tumor specimens was significantly correlated with disease progression. SLC4A4 knockdown inhibited cell proliferation, migration and invasion, while facilitated apoptosis, which was also confirmed in vivo. Moreover, SLC4A4 promoted PCa progression through the AKT-mediated signalling pathway.
Conclusion
The results of this study indicated that SLC4A4 overexpression was closely associated with the progression of PCa; SLC4A4 knockdown suppressed PCa development in vitro and in vivo. SLC4A4 acts as a tumor promotor in PCa by regulating key components of the AKT pathway and may therefore act as a potential therapeutic target for PCa treatment.
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22
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Doyen D, Poët M, Jarretou G, Pisani DF, Tauc M, Cougnon M, Argentina M, Bouret Y, Counillon L. Intracellular pH Control by Membrane Transport in Mammalian Cells. Insights Into the Selective Advantages of Functional Redundancy. Front Mol Biosci 2022; 9:825028. [PMID: 35252350 PMCID: PMC8896879 DOI: 10.3389/fmolb.2022.825028] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/06/2022] [Indexed: 12/16/2022] Open
Abstract
Intracellular pH is a vital parameter that is maintained close to neutrality in all mammalian cells and tissues and acidic in most intracellular compartments. After presenting the main techniques used for intracellular an vesicular pH measurements we will briefly recall the main molecular mechanisms that affect and regulate intracellular pH. Following this we will discuss the large functional redundancy found in the transporters of H+ or acid-base equivalents. For this purpose, we will use mathematical modeling to simulate cellular response to persistent and/or transient acidification, in the presence of different transporters, single or in combination. We will also test the presence or absence of intracellular buffering. This latter section will highlight how modeling can yield fundamental insight into deep biological questions such as the utility of functional redundancy in natural selection.
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Affiliation(s)
- Denis Doyen
- Université Côte d’Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
- Centre Hospitalier Universitaire de Nice, Service de Médecine Intensive Réanimation, Hôpital Archet 1, Nice, France
| | - Mallorie Poët
- Université Côte d’Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - Gisèle Jarretou
- Université Côte d’Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - Didier F. Pisani
- Université Côte d’Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - Michel Tauc
- Université Côte d’Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - Marc Cougnon
- Université Côte d’Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - Mederic Argentina
- Université Côte d’Azur, CNRS, Institut de Physique de Nice, INPHYNI, Nice, France
| | - Yann Bouret
- Centre Hospitalier Universitaire de Nice, Service de Médecine Intensive Réanimation, Hôpital Archet 1, Nice, France
| | - Laurent Counillon
- Université Côte d’Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
- *Correspondence: Laurent Counillon,
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23
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Collin GB, Shi L, Yu M, Akturk N, Charette JR, Hyde LF, Weatherly SM, Pera MF, Naggert JK, Peachey NS, Nishina PM, Krebs MP. A Splicing Mutation in Slc4a5 Results in Retinal Detachment and Retinal Pigment Epithelium Dysfunction. Int J Mol Sci 2022; 23:2220. [PMID: 35216333 PMCID: PMC8875008 DOI: 10.3390/ijms23042220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 12/29/2022] Open
Abstract
Fluid and solute transporters of the retinal pigment epithelium (RPE) are core components of the outer blood-retinal barrier. Characterizing these transporters and their role in retinal homeostasis may provide insights into ocular function and disease. Here, we describe RPE defects in tvrm77 mice, which exhibit hypopigmented patches in the central retina. Mapping and nucleotide sequencing of tvrm77 mice revealed a disrupted 5' splice donor sequence in Slc4a5, a sodium bicarbonate cotransporter gene. Slc4a5 expression was reduced 19.7-fold in tvrm77 RPE relative to controls, and alternative splice variants were detected. SLC4A5 was localized to the Golgi apparatus of cultured human RPE cells and in apical and basal membranes. Fundus imaging, optical coherence tomography, microscopy, and electroretinography (ERG) of tvrm77 mice revealed retinal detachment, hypopigmented patches corresponding to neovascular lesions, and retinal folds. Detachment worsened and outer nuclear layer thickness decreased with age. ERG a- and b-wave response amplitudes were initially normal but declined in older mice. The direct current ERG fast oscillation and light peak were reduced in amplitude at all ages, whereas other RPE-associated responses were unaffected. These results link a new Slc4a5 mutation to subretinal fluid accumulation and altered light-evoked RPE electrophysiological responses, suggesting that SLC4A5 functions at the outer blood-retinal barrier.
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Affiliation(s)
- Gayle B. Collin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; (G.B.C.); (L.S.); (N.A.); (J.R.C.); (L.F.H.); (S.M.W.); (M.F.P.); (J.K.N.)
| | - Lanying Shi
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; (G.B.C.); (L.S.); (N.A.); (J.R.C.); (L.F.H.); (S.M.W.); (M.F.P.); (J.K.N.)
| | - Minzhong Yu
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA; (M.Y.); (N.S.P.)
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Nurten Akturk
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; (G.B.C.); (L.S.); (N.A.); (J.R.C.); (L.F.H.); (S.M.W.); (M.F.P.); (J.K.N.)
| | - Jeremy R. Charette
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; (G.B.C.); (L.S.); (N.A.); (J.R.C.); (L.F.H.); (S.M.W.); (M.F.P.); (J.K.N.)
| | - Lillian F. Hyde
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; (G.B.C.); (L.S.); (N.A.); (J.R.C.); (L.F.H.); (S.M.W.); (M.F.P.); (J.K.N.)
| | - Sonia M. Weatherly
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; (G.B.C.); (L.S.); (N.A.); (J.R.C.); (L.F.H.); (S.M.W.); (M.F.P.); (J.K.N.)
| | - Martin F. Pera
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; (G.B.C.); (L.S.); (N.A.); (J.R.C.); (L.F.H.); (S.M.W.); (M.F.P.); (J.K.N.)
| | - Jürgen K. Naggert
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; (G.B.C.); (L.S.); (N.A.); (J.R.C.); (L.F.H.); (S.M.W.); (M.F.P.); (J.K.N.)
| | - Neal S. Peachey
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA; (M.Y.); (N.S.P.)
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, 9500 Euclid Avenue, Cleveland, OH 44195, USA
- Research Service, Louis Stokes Cleveland VA Medical Center, 10701 East Boulevard, Cleveland, OH 44106, USA
| | - Patsy M. Nishina
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; (G.B.C.); (L.S.); (N.A.); (J.R.C.); (L.F.H.); (S.M.W.); (M.F.P.); (J.K.N.)
| | - Mark P. Krebs
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; (G.B.C.); (L.S.); (N.A.); (J.R.C.); (L.F.H.); (S.M.W.); (M.F.P.); (J.K.N.)
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24
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Wu H, Liu S, Su P, Xie Z, Gui T, Zhao L, Liu Y, Chen L. Molecular insight into coordination sites for substrates and their coupling kinetics in Na
+
/HCO
3
−
cotransporter NBCe1. J Physiol 2022; 600:3083-3111. [DOI: 10.1113/jp282034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/03/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Han Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
| | - Shiyong Liu
- School of Physics Huazhong University of Science and Technology Wuhan 430074 China
| | - Pan Su
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
| | - Zhang‐Dong Xie
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
| | - Tian‐Xiang Gui
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
| | - Lei Zhao
- Department of Obstetrics Maternal and Child Health Hospital of Hubei Province Wuhan 430070 China
| | - Ying Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
| | - Li‐Ming Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
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25
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Lack of Charge Interaction in the Ion Binding Site Determines Anion Selectivity in the Sodium Bicarbonate Cotransporter NBCe1. Int J Mol Sci 2022; 23:ijms23010532. [PMID: 35008963 PMCID: PMC8745181 DOI: 10.3390/ijms23010532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 02/01/2023] Open
Abstract
The Na/HCO3 cotransporter NBCe1 is a member of SLC4A transporters that move HCO3− across cell membranes and regulate intracellular pH or transepithelial HCO3 transport. NBCe1 is highly selective to HCO3− and does not transport other anions; the molecular mechanism of anion selectivity is presently unclear. We previously reported that replacing Asp555 with a Glu (D555E) in NBCe1 induces increased selectivity to other anions, including Cl−. This finding is unexpected because all SLC4A transporters contain either Asp or Glu at the corresponding position and maintain a high selectivity to HCO3−. In this study, we tested whether the Cl− transport in D555E is mediated by an interaction between residues in the ion binding site. Human NBCe1 and mutant transporters were expressed in Xenopus oocytes, and their ability to transport Cl− was assessed by two-electrode voltage clamp. The results show that the Cl− transport is induced by a charge interaction between Glu555 and Lys558. The bond length between the two residues is within the distance for a salt bridge, and the ionic strength experiments confirm an interaction. This finding indicates that the HCO3− selectivity in NBCe1 is established by avoiding a specific charge interaction in the ion binding site, rather than maintaining such an interaction.
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26
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Jaramillo-Martinez V, Ganapathy V, Urbatsch IL. Peptide Tags and Domains for Expression and Detection of Mammalian Membrane Proteins at the Cell Surface. Methods Mol Biol 2022; 2507:337-358. [PMID: 35773591 DOI: 10.1007/978-1-0716-2368-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Normal functions of cell-surface proteins are dependent on their proper trafficking from the site of synthesis to the cell surface. Transport proteins mediating solute transfer across the plasma membrane constitute an important group of cell-surface proteins. There are several diseases resulting from mutations in these proteins that interfere with their transport function or trafficking, depending on the impact of the mutations on protein folding and structure. Recent advances in successful treatment of some of these diseases with small molecules which correct the mutations-induced folding and structural changes underline the need for detailed structural and biophysical characterization of membrane proteins. This requires methods to express and purify these proteins using heterologous expression systems. Here, using the solute carrier (SLC) transporter NaCT (Na+-coupled citrate transporter) as an example, we describe experimental strategies for this approach. We chose this example because several mutations in NaCT, distributed throughout the protein, cause a severe neurologic disease known as early infantile epileptic encephalopathy-25 (EIEE-25). NaCT was modified with various peptide tags, including a RGS-His10, a Twin-Strep, the SUMOstar domain, and an enhanced green fluorescent protein (EGFP), each alone or in various combinations. When transiently expressed in HEK293 cells, recombinant NaCT proteins underwent complex glycosylation, compartmentalized with the plasma membrane, and exhibited citrate transport activity similar to the nontagged protein. Surface NaCT expression was enhanced by the presence of SUMOstar on the N-terminus. The dual-purpose peptide epitopes RGS-His10 and Twin-Strep facilitated detection of NaCT by immunohistochemistry and western blot and may serve useful tags for affinity purification. This approach sets the stage for future analyses of mutant NaCT proteins that may alter protein folding and trafficking. It also demonstrates the capability of a transient mammalian cell expression system to produce human NaCT of sufficient quality and quantity to augment future biophysical and structural studies and drug discovery efforts.
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Affiliation(s)
- Valeria Jaramillo-Martinez
- Departments of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Vadivel Ganapathy
- Cell Biology and Biochemistry, and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Ina L Urbatsch
- Cell Biology and Biochemistry, and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
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27
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Holzhüter K, Geertsma ER. Uniport, Not Proton-Symport, in a Non-Mammalian SLC23 Transporter. J Mol Biol 2021; 434:167393. [PMID: 34896363 DOI: 10.1016/j.jmb.2021.167393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/17/2021] [Accepted: 12/01/2021] [Indexed: 10/25/2022]
Abstract
SLC23 family members are transporters of either nucleobases or ascorbate. While the mammalian SLC23 ascorbate transporters are sodium-coupled, the non-mammalian nucleobase transporters have been proposed, but not formally shown, to be proton-coupled symporters. This assignment is exclusively based on in vivo transport assays using protonophores. Here, by establishing the first in vitro transport assay for this protein family, we demonstrate that a representative member of the SLC23 nucleobase transporters operates as a uniporter instead. We explain these conflicting assignments by identifying a critical role of uracil phosphoribosyltransferase, the enzyme converting uracil to UMP, in driving uracil uptake in vivo. Detailed characterization of uracil phosphoribosyltransferase reveals that the sharp reduction of uracil uptake in whole cells in presence of protonophores is caused by acidification-induced enzyme inactivation. The SLC23 family therefore consists of both uniporters and symporters in line with the structurally related SLC4 and SLC26 families that have previously been demonstrated to accommodate both transport modes as well.
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Affiliation(s)
- Katharina Holzhüter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt am Main, Germany
| | - Eric R Geertsma
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt am Main, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany.
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28
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Yamazaki O, Yamashita M, Li J, Ochiai-Homma F, Yoshida T, Hirahashi J, Furukawa T, Kozuma K, Fujigaki Y, Seki G, Hayashi M, Shibata S. A novel I551F variant of the Na +/HCO 3- cotransporter NBCe1-A shows reduced cell surface expression, resulting in diminished transport activity. Am J Physiol Renal Physiol 2021; 321:F771-F784. [PMID: 34719949 DOI: 10.1152/ajprenal.00584.2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Homozygous mutations in SLC4A4, which encodes the electrogenic Na+/[Formula: see text] cotransporter (NBCe1), cause proximal renal tubular acidosis associated with extrarenal symptoms. Although 17` mutated sites in SLC4A4 have thus far been identified among patients with proximal renal tubular acidosis, the physiological significance of other nonsynonymous single-nucleotide variants (SNVs) remains largely undetermined. Here, we investigated the functional properties of SNVs in NBCe1. From the National Center for Biotechnology Information dbSNP database, we identified 13 SNVs that have not previously been characterized in the highly conserved, transmembrane domains of NBCe1-A. Immunocytochemical analysis revealed that the I551F variant was present predominantly in the cytoplasm in human embryonic kidney (HEK)-293 cells, whereas all other SNVs did not show as dramatic a change in subcellular distribution. Western blot analysis in HEK-293 cells demonstrated that the I551F variant showed impaired glycosylation and a 69% reduction in cell surface levels. To determine the role of I551 in more detail, we examined the significance of various artificial mutants in both nonpolarized HEK-293 cells and polarized Madin-Darby canine kidney cells, which indicated that only I551F substitution resulted in cytoplasmic retention. Moreover, functional analysis using Xenopus oocytes demonstrated that the I551F variant had a significantly reduced activity corresponding to 39% of that of the wild-type, whereas any other SNVs and artificial I551 mutants did not show significant changes in activity. Finally, immunofluorescence experiments in HEK-293 cells indicated that the I551F variant retained wild-type NBCe1-A in the cytoplasm. These data demonstrate that the I551F variant of NBCe1-A shows impaired transport activity predominantly through cytoplasmic retention and suggest that the variant can have a dominant negative effect by forming complexes with wild-type NBCe1-A.NEW & NOTEWORTHY Electrogenic Na+/[Formula: see text] cotransporter 1-A (NBCe1-A) in the proximal tubule regulates the acid/base balance and fluid volume homeostasis. From the National Center for Biotechnology Information dbSNP database, we identified the I551F variant of NBCe1-A, which showed reduced glycosylation, cell surface expression, and transport activity. We also found that the I551F variant can exert a dominant negative effect on wild-type NBCe1-A, suggesting its physiological significance.
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Affiliation(s)
- Osamu Yamazaki
- Division of Nephrology, Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan.,Department of General Medicine, Keio University School of Medicine, Tokyo, Japan.,Apheresis and Dialysis Center, Keio University School of Medicine, Tokyo, Japan
| | - Maho Yamashita
- Apheresis and Dialysis Center, Keio University School of Medicine, Tokyo, Japan
| | - Jinping Li
- Division of Nephrology, Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Fumika Ochiai-Homma
- Division of Nephrology, Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Tadashi Yoshida
- Department of General Medicine, Keio University School of Medicine, Tokyo, Japan.,Apheresis and Dialysis Center, Keio University School of Medicine, Tokyo, Japan
| | - Junichi Hirahashi
- Department of General Medicine, Keio University School of Medicine, Tokyo, Japan.,Apheresis and Dialysis Center, Keio University School of Medicine, Tokyo, Japan
| | - Taiji Furukawa
- Department of Laboratory Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Ken Kozuma
- Division of Cardiology, Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Yoshihide Fujigaki
- Division of Nephrology, Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | | | - Matsuhiko Hayashi
- Department of General Medicine, Keio University School of Medicine, Tokyo, Japan.,Apheresis and Dialysis Center, Keio University School of Medicine, Tokyo, Japan.,Kawakita General Hospital, Center for Clinical Education, Tokyo, Japan
| | - Shigeru Shibata
- Division of Nephrology, Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan
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29
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Bajrovic I, Le MD, Davis MM, Croyle MA. Evaluation of intermolecular interactions required for thermostability of a recombinant adenovirus within a film matrix. J Control Release 2021; 341:118-131. [PMID: 34780881 DOI: 10.1016/j.jconrel.2021.11.012] [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: 07/09/2021] [Revised: 11/02/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022]
Abstract
Thermostability of vaccines and biologic drugs are key to increasing global access to a variety of life-saving agents. In this report, we characterize interactions between a novel zwitterionic surfactant and adenovirus serotype 5 which allow the virus to remain stable at room temperature in a thin film matrix. Complexity of the adenovirus capsid and the polydispersity of the surfactant required use of a variety of techniques to achieve this goal. The CMC of the surfactant in Tris buffer (pH 6.5) was estimated to be 0.7-1.17 × 10-4 M by the pyrene 1:3 ratio method. TEM images depict micelle formation around virus capsids. An estimated Kd of the virus-surfactant interaction of 2.25 × 10-9 M was determined by isothermal titration calorimetry. Associated data suggest that this interaction may be thermodynamically favorable and entropically driven. A competitive saturation study and TEM images indicate that the surfactant also binds to hexon proteins on the virus capsid. Taken together, these data support the working hypothesis that the surfactant is capable of forming micelles in the solid and liquid state and that it forms a protective coating around the virus by binding to hexon proteins on the virus capsid during the film forming process.
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Affiliation(s)
- Irnela Bajrovic
- Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, 2409 University Ave., Austin, TX, USA
| | - Matthew D Le
- Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, 2409 University Ave., Austin, TX, USA
| | - Madison M Davis
- Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, 2409 University Ave., Austin, TX, USA
| | - Maria A Croyle
- Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, 2409 University Ave., Austin, TX, USA; LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX, USA.
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30
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Wang W, Tsirulnikov K, Zhekova HR, Kayık G, Khan HM, Azimov R, Abuladze N, Kao L, Newman D, Noskov SY, Zhou ZH, Pushkin A, Kurtz I. Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE. Nat Commun 2021; 12:5690. [PMID: 34584093 PMCID: PMC8478935 DOI: 10.1038/s41467-021-25998-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023] Open
Abstract
SLC4 transporters play significant roles in pH regulation and cellular sodium transport. The previously solved structures of the outward facing (OF) conformation for AE1 (SLC4A1) and NBCe1 (SLC4A4) transporters revealed an identical overall fold despite their different transport modes (chloride/bicarbonate exchange versus sodium-carbonate cotransport). However, the exact mechanism determining the different transport modes in the SLC4 family remains unknown. In this work, we report the cryo-EM 3.4 Å structure of the OF conformation of NDCBE (SLC4A8), which shares transport properties with both AE1 and NBCe1 by mediating the electroneutral exchange of sodium-carbonate with chloride. This structure features a fully resolved extracellular loop 3 and well-defined densities corresponding to sodium and carbonate ions in the tentative substrate binding pocket. Further, we combine computational modeling with functional studies to unravel the molecular determinants involved in NDCBE and SLC4 transport.
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Affiliation(s)
- Weiguang Wang
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA ,grid.509979.b0000 0004 7666 6191Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles, CA USA
| | - Kirill Tsirulnikov
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Hristina R. Zhekova
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Gülru Kayık
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Hanif Muhammad Khan
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Rustam Azimov
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Natalia Abuladze
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Liyo Kao
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Debbie Newman
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Sergei Yu. Noskov
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Z. Hong Zhou
- grid.509979.b0000 0004 7666 6191Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA USA
| | - Alexander Pushkin
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Ira Kurtz
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Brain Research Institute, University of California, Los Angeles, CA USA
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31
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Du L, Zahra A, Jia M, Wang Q, Wu J. Understanding the Functional Expression of Na+-Coupled SLC4 Transporters in the Renal and Nervous Systems: A Review. Brain Sci 2021; 11:1276. [PMID: 34679341 PMCID: PMC8534249 DOI: 10.3390/brainsci11101276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 11/25/2022] Open
Abstract
Acid-base homeostasis is crucial for numerous physiological processes. Na+/HCO3- cotransporters (NBCs) belong to the solute carrier 4 (SLC4) family, which regulates intracellular pH as well as HCO3- absorption and secretion. However, knowledge of the structural functions of these proteins remains limited. Electrogenic NBC (NBCe-1) is thought to be the primary factor promoting the precise acid-base equilibrium in distinct cell types for filtration and reabsorption, as well as the function of neurons and glia. NBC dysregulation is strongly linked to several diseases. As such, the need for special drugs that interfere with the transmission function of NBC is becoming increasingly urgent. In this review, we focus on the structural and functional characteristics of NBCe1, and discuss the roles of NBCe1 in the kidney, central nervous system (CNS), and related disorders, we also summarize the research on NBC inhibitors. NBCe1 and the related pathways should be further investigated, so that new medications may be developed to address the related conditions.
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Affiliation(s)
- Le Du
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China; (L.D.); (A.Z.)
| | - Aqeela Zahra
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China; (L.D.); (A.Z.)
| | - Meng Jia
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; (M.J.); (Q.W.)
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Disease, Beijing 100070, China
| | - Qun Wang
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; (M.J.); (Q.W.)
- National Clinical Research Center for Neurological Disease, Beijing 100070, China
| | - Jianping Wu
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China; (L.D.); (A.Z.)
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; (M.J.); (Q.W.)
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Disease, Beijing 100070, China
- Health Science Center, Yangtze University, Jingzhou 434023, China
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Dvorak V, Wiedmer T, Ingles-Prieto A, Altermatt P, Batoulis H, Bärenz F, Bender E, Digles D, Dürrenberger F, Heitman LH, IJzerman AP, Kell DB, Kickinger S, Körzö D, Leippe P, Licher T, Manolova V, Rizzetto R, Sassone F, Scarabottolo L, Schlessinger A, Schneider V, Sijben HJ, Steck AL, Sundström H, Tremolada S, Wilhelm M, Wright Muelas M, Zindel D, Steppan CM, Superti-Furga G. An Overview of Cell-Based Assay Platforms for the Solute Carrier Family of Transporters. Front Pharmacol 2021; 12:722889. [PMID: 34447313 PMCID: PMC8383457 DOI: 10.3389/fphar.2021.722889] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
The solute carrier (SLC) superfamily represents the biggest family of transporters with important roles in health and disease. Despite being attractive and druggable targets, the majority of SLCs remains understudied. One major hurdle in research on SLCs is the lack of tools, such as cell-based assays to investigate their biological role and for drug discovery. Another challenge is the disperse and anecdotal information on assay strategies that are suitable for SLCs. This review provides a comprehensive overview of state-of-the-art cellular assay technologies for SLC research and discusses relevant SLC characteristics enabling the choice of an optimal assay technology. The Innovative Medicines Initiative consortium RESOLUTE intends to accelerate research on SLCs by providing the scientific community with high-quality reagents, assay technologies and data sets, and to ultimately unlock SLCs for drug discovery.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Helena Batoulis
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Felix Bärenz
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Eckhard Bender
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Daniela Digles
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | - Laura H. Heitman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefanie Kickinger
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Daniel Körzö
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Philipp Leippe
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas Licher
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | | | | | | | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vanessa Schneider
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Hubert J. Sijben
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | | | | | | | | | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Diana Zindel
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Claire M. Steppan
- Pfizer Worldwide Research, Development and Medical, Groton, MA, United States
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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Structure and function of an Arabidopsis thaliana sulfate transporter. Nat Commun 2021; 12:4455. [PMID: 34294705 PMCID: PMC8298490 DOI: 10.1038/s41467-021-24778-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Plant sulfate transporters (SULTR) mediate absorption and distribution of sulfate (SO42-) and are essential for plant growth; however, our understanding of their structures and functions remains inadequate. Here we present the structure of a SULTR from Arabidopsis thaliana, AtSULTR4;1, in complex with SO42- at an overall resolution of 2.8 Å. AtSULTR4;1 forms a homodimer and has a structural fold typical of the SLC26 family of anion transporters. The bound SO42- is coordinated by side-chain hydroxyls and backbone amides, and further stabilized electrostatically by the conserved Arg393 and two helix dipoles. Proton and SO42- are co-transported by AtSULTR4;1 and a proton gradient significantly enhances SO42- transport. Glu347, which is ~7 Å from the bound SO42-, is required for H+-driven transport. The cytosolic STAS domain interacts with transmembrane domains, and deletion of the STAS domain or mutations to the interface compromises dimer formation and reduces SO42- transport, suggesting a regulatory function of the STAS domain.
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Structural and functional insights into the mechanism of action of plant borate transporters. Sci Rep 2021; 11:12328. [PMID: 34112901 PMCID: PMC8192573 DOI: 10.1038/s41598-021-91763-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/28/2021] [Indexed: 02/05/2023] Open
Abstract
Boron has essential roles in plant growth and development. BOR proteins are key in the active uptake and distribution of boron, and regulation of intracellular boron concentrations. However, their mechanism of action remains poorly studied. BOR proteins are homologues of the human SLC4 family of transporters, which includes well studied mammalian transporters such as the human Anion Exchanger 1 (hAE1). Here we generated Arabidopsis thaliana BOR1 (AtBOR1) variants based (i) on known disease causing mutations of hAE1 (S466R, A500R) and (ii) a loss of function mutation (D311A) identified in the yeast BOR protein, ScBOR1p. The AtBOR1 variants express in yeast and localise to the plasma membrane, although both S466R and A500R exhibit lower expression than the WT AtBOR1 and D311A. The D311A, S466R and A500R mutations result in a loss of borate efflux activity in a yeast bor1p knockout strain. A. thaliana plants containing these three individual mutations exhibit substantially decreased growth phenotypes in soil under conditions of low boron. These data confirm an important role for D311 in the function of the protein and show that mutations equivalent to disease-causing mutations in hAE1 have major effects in AtBOR1. We also obtained a low resolution cryo-EM structure of a BOR protein from Oryza sativa, OsBOR3, lacking the 30 C-terminal amino acid residues. This structure confirms the gate and core domain organisation previously observed for related proteins, and is strongly suggestive of an inward facing conformation.
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Plant transporters involved in combating boron toxicity: beyond 3D structures. Biochem Soc Trans 2021; 48:1683-1696. [PMID: 32779723 PMCID: PMC7458394 DOI: 10.1042/bst20200164] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Membrane transporters control the movement and distribution of solutes, including the disposal or compartmentation of toxic substances that accumulate in plants under adverse environmental conditions. In this minireview, in the light of the approaching 100th anniversary of unveiling the significance of boron to plants (K. Warington, 1923; Ann. Bot.37, 629) we discuss the current state of the knowledge on boron transport systems that plants utilise to combat boron toxicity. These transport proteins include: (i) nodulin-26-like intrinsic protein-types of aquaporins, and (ii) anionic efflux (borate) solute carriers. We describe the recent progress made on the structure–function relationships of these transport proteins and point out that this progress is integral to quantitative considerations of the transporter's roles in tissue boron homeostasis. Newly acquired knowledge at the molecular level has informed on the transport mechanics and conformational states of boron transport systems that can explain their impact on cell biology and whole plant physiology. We expect that this information will form the basis for engineering transporters with optimised features to alleviate boron toxicity tolerance in plants exposed to suboptimal soil conditions for sustained food production.
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36
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Cecchetti C, Scull NJ, Mohan TC, Alguel Y, Jones AMC, Cameron AD, Byrne B. Transfer of stabilising mutations between different secondary active transporter families. FEBS Open Bio 2021; 11:1685-1694. [PMID: 33932145 PMCID: PMC8167854 DOI: 10.1002/2211-5463.13168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/25/2021] [Accepted: 04/15/2021] [Indexed: 11/24/2022] Open
Abstract
Integral membrane transporters play essential roles in the movement of substrates across biological membranes. One approach to produce transporters suitable for structural studies is to introduce mutations that reduce conformational flexibility and increase stability. However, it can be difficult to predict which mutations will result in a more stable protein. Previously, we stabilised the uric acid‐xanthine transporter, UapA, a member of the SLC23 family, through introduction of a single‐point mutation, G411V, trapping the protein in the inward‐facing conformation. Here, we attempted to stabilise the structurally related BOR1 transporter from Arabidopsis thaliana, a member of the SLC4 family, by introducing the equivalent substitution. We identified possible residues, P362 and M363, in AtBOR1, likely to be equivalent to the G411 of UapA, and generated four mutants, P362V or L and M363F or Y. Stability analysis using heated Fluorescent Size Exclusion Chromatography indicated that the M363F/Y mutants were more stable than the WT AtBOR1 and P362V/L mutants. Furthermore, functional complementation analysis revealed that the M363F/Y mutants exhibited reduced transport activity compared to the P362V/L and WT proteins. Purification and crystallisation of the M363F/Y proteins yielded crystals that diffracted better than WT (5.5 vs 7 Å). We hypothesise that the increased bulk of the F and Y substitutions limits the ability of the protein to undergo the conformational rearrangements associated with transport. These proteins represent a basis for future studies on AtBOR1.
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Affiliation(s)
| | - Nicola J Scull
- Department of Life Sciences, Imperial College London, UK
| | | | - Yilmaz Alguel
- Department of Life Sciences, Imperial College London, UK
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Identification of multiple substrate binding sites in SLC4 transporters in the outward-facing conformation: Insights into the transport mechanism. J Biol Chem 2021; 296:100724. [PMID: 33932403 PMCID: PMC8191340 DOI: 10.1016/j.jbc.2021.100724] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 01/17/2023] Open
Abstract
Solute carrier family 4 (SLC4) transporters mediate the transmembrane transport of HCO3-, CO32-, and Cl- necessary for pH regulation, transepithelial H+/base transport, and ion homeostasis. Substrate transport with varying stoichiometry and specificity is achieved through an exchange mechanism and/or through coupling of the uptake of anionic substrates to typically co-transported Na+. Recently solved outward-facing structures of two SLC4 members (human anion exchanger 1 [hAE1] and human electrogenic sodium bicarbonate cotransporter 1 [hNBCe1]) with different transport modes (Cl-/HCO3- exchange versus Na+-CO32- symport) revealed highly conserved three-dimensional organization of their transmembrane domains. However, the exact location of the ion binding sites and their protein-ion coordination motifs are still unclear. In the present work, we combined site identification by ligand competitive saturation mapping and extensive molecular dynamics sampling with functional mutagenesis studies which led to the identification of two substrate binding sites (entry and central) in the outward-facing states of hAE1 and hNBCe1. Mutation of residues in the identified binding sites led to impaired transport in both proteins. We also showed that R730 in hAE1 is crucial for anion binding in both entry and central sites, whereas in hNBCe1, a Na+ acts as an anchor for CO32- binding to the central site. Additionally, protonation of the central acidic residues (E681 in hAE1 and D754 in hNBCe1) alters the ion dynamics in the permeation cavity and may contribute to the transport mode differences in SLC4 proteins. These results provide a basis for understanding the functional differences between hAE1 and hNBCe1 and may facilitate potential drug development for diseases such as proximal and distal renal tubular acidosis.
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38
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Pizzagalli MD, Bensimon A, Superti‐Furga G. A guide to plasma membrane solute carrier proteins. FEBS J 2021; 288:2784-2835. [PMID: 32810346 PMCID: PMC8246967 DOI: 10.1111/febs.15531] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022]
Abstract
This review aims to serve as an introduction to the solute carrier proteins (SLC) superfamily of transporter proteins and their roles in human cells. The SLC superfamily currently includes 458 transport proteins in 65 families that carry a wide variety of substances across cellular membranes. While members of this superfamily are found throughout cellular organelles, this review focuses on transporters expressed at the plasma membrane. At the cell surface, SLC proteins may be viewed as gatekeepers of the cellular milieu, dynamically responding to different metabolic states. With altered metabolism being one of the hallmarks of cancer, we also briefly review the roles that surface SLC proteins play in the development and progression of cancer through their influence on regulating metabolism and environmental conditions.
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Affiliation(s)
- Mattia D. Pizzagalli
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Ariel Bensimon
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Giulio Superti‐Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Center for Physiology and PharmacologyMedical University of ViennaAustria
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39
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Fairweather SJ, Shah N, Brӧer S. Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 21:13-127. [PMID: 33052588 DOI: 10.1007/5584_2020_584] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carriers form one of three major superfamilies of membrane transporters in humans, and include uniporters, exchangers and symporters. Following several decades of molecular characterisation, multiple solute carriers that form obligatory heteromers with unrelated subunits are emerging as a distinctive principle of membrane transporter assembly. Here we comprehensively review experimentally established heteromeric solute carriers: SLC3-SLC7 amino acid exchangers, SLC16 monocarboxylate/H+ symporters and basigin/embigin, SLC4A1 (AE1) and glycophorin A exchanger, SLC51 heteromer Ost α-Ost β uniporter, and SLC6 heteromeric symporters. The review covers the history of the heteromer discovery, transporter physiology, structure, disease associations and pharmacology - all with a focus on the heteromeric assembly. The cellular locations, requirements for complex formation, and the functional role of dimerization are extensively detailed, including analysis of the first complete heteromer structures, the SLC7-SLC3 family transporters LAT1-4F2hc, b0,+AT-rBAT and the SLC6 family heteromer B0AT1-ACE2. We present a systematic analysis of the structural and functional aspects of heteromeric solute carriers and conclude with common principles of their functional roles and structural architecture.
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Affiliation(s)
- Stephen J Fairweather
- Research School of Biology, Australian National University, Canberra, ACT, Australia. .,Resarch School of Chemistry, Australian National University, Canberra, ACT, Australia.
| | - Nishank Shah
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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40
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Sauer DB, Song J, Wang B, Hilton JK, Karpowich NK, Mindell JA, Rice WJ, Wang DN. Structure and inhibition mechanism of the human citrate transporter NaCT. Nature 2021; 591:157-161. [PMID: 33597751 PMCID: PMC7933130 DOI: 10.1038/s41586-021-03230-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022]
Abstract
Citrate is most well-known as an intermediate in the TCA cycle of the cell. In addition to this essential role in energy metabolism, the tricarboxylate anion also acts as both a precursor and a regulator of fatty acid synthesis 1–3. Thus, the rate of fatty acid synthesis correlates directly with the cytosolic citrate concentration 4,5. Liver cells import citrate via the sodium-dependent citrate transporter NaCT (SLC13A5), and as a consequence this protein is a potential target for anti-obesity drugs. To understand the structural basis of its inhibition mechanism, we have determined cryo-electron microscopy structures of human NaCT in complex with citrate and with a small molecule inhibitor. These structures reveal how the inhibitor, bound at the same site as citrate, arrests the protein’s transport cycle. The NaCT-inhibitor structure also explains why the compound selectively inhibits NaCT over two homologous human dicarboxylate transporters, and suggests ways to further improve the affinity and selectivity. Finally, the NaCT structures provide a framework for understanding how various mutations abolish NaCT’s transport activity in the brain and thereby cause SLC13A5-Epilepsy in newborns 6–8.
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Affiliation(s)
- David B Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA
| | - Jacob K Hilton
- Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nathan K Karpowich
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA.,Janssen Pharmaceuticals, Spring House, PA, USA
| | - Joseph A Mindell
- Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - William J Rice
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA. .,Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA.
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA. .,Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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The electrogenic sodium bicarbonate cotransporter and its roles in the myocardial ischemia-reperfusion induced cardiac diseases. Life Sci 2021; 270:119153. [PMID: 33539911 DOI: 10.1016/j.lfs.2021.119153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/06/2021] [Accepted: 01/22/2021] [Indexed: 12/19/2022]
Abstract
Cardiac tissue ischemia/hypoxia increases glycolysis and lactic acid accumulation in cardiomyocytes, leading to intracellular metabolic acidosis. Sodium bicarbonate cotransporters (NBCs) play a vital role in modulating intracellular pH and maintaining sodium ion concentrations in cardiomyocytes. Cardiomyocytes mainly express electrogenic sodium bicarbonate cotransporter (NBCe1), which has been demonstrated to participate in myocardial ischemia/reperfusion (I/R) injury. This review outlines the structural and functional properties of NBCe1, summarizes the signaling pathways and factors that may regulate the activity of NBCe1, and reviews the roles of NBCe1 in the pathogenesis of I/R-induced cardiac diseases. Further studies revealing the regulatory mechanisms of NBCe1 activity should provide novel therapeutic targets for preventing I/R-induced cardiac diseases.
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42
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Su P, Wu H, Wang M, Cai L, Liu Y, Chen LM. IRBIT activates NBCe1-B by releasing the auto-inhibition module from the transmembrane domain. J Physiol 2020; 599:1151-1172. [PMID: 33237573 PMCID: PMC7898672 DOI: 10.1113/jp280578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
Key points The electrogenic Na+/HCO3−cotransporter NBCe1‐B is widely expressed in many tissues, including pancreas, submandibular gland, brain, heart, etc. NBCe1‐B has very low activity under basal condition due to auto‐inhibition, but can be fully activated by protein interaction with the IP3R‐binding protein released with inositol 1,4,5‐trisphosphate (IRBIT). The structural components of the auto‐inhibition domain and the IRBIT‐binding domain of NBCe1‐B are finely characterized based on systematic mutations in the present study and data from previous studies. Reducing negative charges on the cytosol side of the transmembrane domain greatly decreases the magnitude of the auto‐inhibition of NBCe1‐B. We propose that the auto‐inhibition domain functions as a brake module that inactivates NBCe1‐B by binding to, via electrostatic attraction, the transmembrane domain; IRBIT activates NBCe1‐B by releasing the brake from the transmembrane domain via competitive binding to the auto‐inhibition domain.
Abstract The electrogenic Na+/HCO3− cotransporter NBCe1‐B is widely expressed in many tissues in the body. NBCe1‐B exhibits only basal activity due to the action of the auto‐inhibition domain (AID) in its unique amino‐terminus. However, NBCe1‐B can be activated by interaction with the IP3R‐binding protein released with inositol 1,4,5‐trisphosphate (IRBIT). Here, we investigate the molecular mechanism underlying the auto‐inhibition of NBCe1‐B and its activation by IRBIT. The IRBIT‐binding domain (IBD) of NBCe1‐B spans residues 1−52, essentially consisting of two arms, one negatively charged (residues 1−24) and the other positively charged (residues 40−52). The AID mainly spans residues 40−85, overlapping with the IBD in the positively charged arm. The magnitude of auto‐inhibition of NBCe1‐B is greatly decreased by manipulating the positively charged residues in the AID or by replacing a set of negatively charged residues with neutral ones in the transmembrane domain. The interaction between IRBIT and NBCe1‐B is abolished by mutating a set of negatively charged Asp/Glu residues (to Asn/Gln) plus a set of Ser/Thr residues (to Ala) in the PEST domain of IRBIT. However, this interaction is not affected by replacing the same set of Ser/Thr residues in the PEST domain with Asp. We propose that: (1) the AID, acting as a brake, binds to the transmembrane domain via electrostatic interaction to slow down NBCe1‐B; (2) IRBIT activates NBCe1‐B by releasing the brake from the transmembrane domain. The electrogenic Na+/HCO3−cotransporter NBCe1‐B is widely expressed in many tissues, including pancreas, submandibular gland, brain, heart, etc. NBCe1‐B has very low activity under basal condition due to auto‐inhibition, but can be fully activated by protein interaction with the IP3R‐binding protein released with inositol 1,4,5‐trisphosphate (IRBIT). The structural components of the auto‐inhibition domain and the IRBIT‐binding domain of NBCe1‐B are finely characterized based on systematic mutations in the present study and data from previous studies. Reducing negative charges on the cytosol side of the transmembrane domain greatly decreases the magnitude of the auto‐inhibition of NBCe1‐B. We propose that the auto‐inhibition domain functions as a brake module that inactivates NBCe1‐B by binding to, via electrostatic attraction, the transmembrane domain; IRBIT activates NBCe1‐B by releasing the brake from the transmembrane domain via competitive binding to the auto‐inhibition domain.
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Affiliation(s)
- Pan Su
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
| | - Han Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
| | - Meng Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
| | - Lu Cai
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
| | - Ying Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
| | - Li-Ming Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
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Birch J, Cheruvara H, Gamage N, Harrison PJ, Lithgo R, Quigley A. Changes in Membrane Protein Structural Biology. BIOLOGY 2020; 9:E401. [PMID: 33207666 PMCID: PMC7696871 DOI: 10.3390/biology9110401] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022]
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Harish Cheruvara
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Peter J. Harrison
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ryan Lithgo
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, Leicestershire, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
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Jaramillo-Martinez V, Urbatsch IL, Ganapathy V. Functional Distinction between Human and Mouse Sodium-Coupled Citrate Transporters and Its Biologic Significance: An Attempt for Structural Basis Using a Homology Modeling Approach. Chem Rev 2020; 121:5359-5377. [PMID: 33040525 DOI: 10.1021/acs.chemrev.0c00529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
NaCT (SLC13A5; mINDY), a sodium-coupled citrate transporter, is the mammalian ortholog of Drosophila INDY. Loss-of-function mutations in human NaCT cause severe complications with neonatal epilepsy and encephalopathy (EIEE25). Surprisingly, mice lacking this transporter do not have this detrimental brain phenotype. The marked differences in transport kinetics between mouse and human NaCTs provide at least a partial explanation for this conundrum, but a structural basis for the differences is lacking. Neither human nor mouse NaCT has been crystallized, and any information known on their structures is based entirely on what was inferred from the structure of VcINDY, a related transporter in bacteria. Here, we highlight the functional features of human and mouse NaCTs and provide a plausible molecular basis for the differences based on a full-length homology modeling approach. The transport characteristics of human NaCT markedly differ from those of VcINDY. Therefore, the modeling with VcINDY as the template is flawed, but this is the best available option at this time. With the newly deduced model, we determined the likely locations of the disease-causing mutations and propose a new classification for the mutations based on their location and potential impact on transport function. This new information should pave the way for future design and development of novel therapeutics to restore the lost function of the mutant transporters as a treatment strategy for patients with EIEE25.
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Affiliation(s)
- Valeria Jaramillo-Martinez
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Membrane Protein Research and Center of Excellence for Translational Neuroscience and Therapeutics, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Vadivel Ganapathy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Membrane Protein Research and Center of Excellence for Translational Neuroscience and Therapeutics, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
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Sauer DB, Trebesch N, Marden JJ, Cocco N, Song J, Koide A, Koide S, Tajkhorshid E, Wang DN. Structural basis for the reaction cycle of DASS dicarboxylate transporters. eLife 2020; 9:e61350. [PMID: 32869741 PMCID: PMC7553777 DOI: 10.7554/elife.61350] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/31/2020] [Indexed: 01/09/2023] Open
Abstract
Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the cell by the divalent anion sodium symporter (DASS) family of plasma membrane transporters, which contains both cotransporters and exchangers. While DASS proteins transport substrates via an elevator mechanism, to date structures are only available for a single DASS cotransporter protein in a substrate-bound, inward-facing state. We report multiple cryo-EM and X-ray structures in four different states, including three hitherto unseen states, along with molecular dynamics simulations, of both a cotransporter and an exchanger. Comparison of these outward- and inward-facing structures reveal how the transport domain translates and rotates within the framework of the scaffold domain through the transport cycle. Additionally, we propose that DASS transporters ensure substrate coupling by a charge-compensation mechanism, and by structural changes upon substrate release.
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Affiliation(s)
- David B Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Noah Trebesch
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Jennifer J Marden
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Nicolette Cocco
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Akiko Koide
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Department of Medicine, New York University School of MedicineNew YorkUnited States
| | - Shohei Koide
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Department of Medicine, New York University School of MedicineNew YorkUnited States
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
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46
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Functional (un)cooperativity in elevator transport proteins. Biochem Soc Trans 2020; 48:1047-1055. [PMID: 32573703 DOI: 10.1042/bst20190970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 11/17/2022]
Abstract
The activity of enzymes is subject to regulation at multiple levels. Cooperativity, the interconnected behavior of active sites within a protein complex, directly affects protein activity. Cooperativity is a mode of regulation that requires neither extrinsic factors nor protein modifications. Instead, it allows enzymes themselves to modulate reaction rates. Cooperativity is an important regulatory mechanism in soluble proteins, but also examples of cooperative membrane proteins have been described. In this review, we summarize the current knowledge on interprotomer cooperativity in elevator-type proteins, a class of membrane transporters characterized by large rigid-body movements perpendicular to the membrane, and highlight well-studied examples and experimental approaches.
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Tu J, Zhang B, Fang G, Chang W, Zhao Y. Neddylation-mediated Nedd4-2 activation regulates ubiquitination modification of renal NBCe1. Exp Cell Res 2020; 390:111958. [DOI: 10.1016/j.yexcr.2020.111958] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/11/2022]
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Yang H, Lu Y, Lan W, Huang B, Lin J. Down-regulated Solute Carrier Family 4 Member 4 Predicts Poor Progression in Colorectal Cancer. J Cancer 2020; 11:3675-3684. [PMID: 32284764 PMCID: PMC7150457 DOI: 10.7150/jca.36696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 01/18/2020] [Indexed: 12/18/2022] Open
Abstract
Aim: To identify potential key candidate genes, whose expression and clinical significance was further assessed in colorectal cancer (CRC). Methods: Three original microarray datasets (GSE41328, GSE22598, and GSE23878) from NCBI-GEO were used to analyze differentially expressed genes (DEGs) in CRC. Online database analyses through Oncomine and GEIPA were performed to evaluate SLC4A4 expression and explore the prognostic merit of SLC4A4 expression, which was further confirmed by analyses from QPCR based cDNA array and IHC based tissue microarray (TMA). STRING website was used to explore the interaction between SLC4A4 with other DEGs based on the protein-protein interaction (PPI) networks. Results: Analysis of three original microarray datasets from GEO identified 82 shared, differentially expressed genes (28 upregulated and 54 down-regulated) in CRC tissues. Online analyses from Oncomine and GEIPA revealed lower SLC4A4 mRNA expression in CRC tissues compared to adjacent normal tissues, which were further confirmed by QPCR based cDNA array and IHC based TMA analyses on both mRNA and protein levels. Survival analyses through GEIPA and from TMA demonstrated that low SLC4A4 expression is correlated with worse overall survival among patients with CRC. Survival analysis from Kaplan-meier plotter demonstrated that low SLC4A4 expression is significantly associated with poor progression (including relapse-free survival, overall survival, distant metastasis-free survival, post-progression survival) of patients with breast cancer, lung cancer, gastric cancer, and ovarian cancer. PPI analysis found that SLC4A4 is highly correlated with various genes, including SLC9A3, SLC26A6, ENSG00000214921, SLC26A4, SLC9A3R1, and SLC9A1. Conclusion: The mRNA and protein levels of SLC4A4 were decreased in CRC tissues, and low expression of SLC4A4 significantly correlated with shorter survival of CRC patients and poorer progression of patients with breast cancer, lung cancer, gastric cancer and ovarian cancer, suggesting potential role of SLC4A4 on tumor suppression and prognostic prediction in multiple malignancies including CRC.
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Affiliation(s)
- Hong Yang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Yao Lu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Weilan Lan
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Bin Huang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Jiumao Lin
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
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Zhekova HR, Sakuma T, Johnson R, Concilio SC, Lech PJ, Zdravkovic I, Damergi M, Suksanpaisan L, Peng KW, Russell SJ, Noskov S. Mapping of Ion and Substrate Binding Sites in Human Sodium Iodide Symporter (hNIS). J Chem Inf Model 2020; 60:1652-1665. [PMID: 32134653 DOI: 10.1021/acs.jcim.9b01114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human sodium iodide symporter (hNIS) is a theranostic reporter gene which concentrates several clinically approved SPECT and PET radiotracers and plays an essential role for the synthesis of thyroid hormones as an iodide transporter in the thyroid gland. Development of hNIS mutants which could enhance translocation of the desired imaging ions is currently underway. Unfortunately, it is hindered by lack of understanding of the 3D organization of hNIS and its relation to anion transport. There are no known crystal structures of hNIS in any of its conformational states. Homology modeling can be very effective in such situations; however, the low sequence identity between hNIS and relevant secondary transporters with available experimental structures makes the choice of a template and the generation of 3D models nontrivial. Here, we report a combined application of homology modeling and molecular dynamics refining of the hNIS structure in its semioccluded state. The modeling was based on templates from the LeuT-fold protein family and was done with emphasis on the refinement of the substrate-ion binding pocket. The consensus model developed in this work is compared to available biophysical and biochemical experimental data for a number of different LeuT-fold proteins. Some functionally important residues contributing to the formation of putative binding sites and permeation pathways for the cotransported Na+ ions and I- substrate were identified. The model predictions were experimentally tested by generation of mutant versions of hNIS and measurement of relative (to WT hNIS) 125I- uptake of 35 hNIS variants.
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Affiliation(s)
- Hristina R Zhekova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Toshie Sakuma
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Ryan Johnson
- Imanis Life Sciences, Rochester, Minnesota 55901, United States
| | - Susanna C Concilio
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States.,Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Patrycja J Lech
- Imanis Life Sciences, Rochester, Minnesota 55901, United States
| | - Igor Zdravkovic
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Mirna Damergi
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Kah-Whye Peng
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Stephen J Russell
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Sergei Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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50
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Abstract
The transport of materials across membranes is a vital process for all aspects of cellular function, including growth, metabolism, and communication. Protein transporters are the molecular gates that control this movement and serve as key points of regulation for these processes, thus representing an attractive class of therapeutic targets. With more than 400 members, the solute carrier (SLC) membrane transport proteins are the largest family of transporters, yet, they are pharmacologically underexploited relative to other protein families and many of the available chemical tools possess suboptimal selectivity and efficacy. Fortuitously, there is increased interest in elucidating the physiological roles of SLCs as well as growing recognition of their therapeutic potential. This Perspective provides an overview of the SLC superfamily, including their biochemical and functional features, as well as their roles in various human diseases. In particular, we explore efforts and associated challenges toward drugging SLCs, as well as highlight opportunities for future drug discovery.
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Affiliation(s)
- Wesley Wei Wang
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Leandro Gallo
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Appaso Jadhav
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Richard Hawkins
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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