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El Salamouni NS, Buckley BJ, Lee R, Ranson M, Kelso MJ, Yu H. Ion Transport and Inhibitor Binding by Human NHE1: Insights from Molecular Dynamics Simulations and Free Energy Calculations. J Phys Chem B 2024; 128:440-450. [PMID: 38185879 DOI: 10.1021/acs.jpcb.3c05863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The human Na+/H+ exchanger (NHE1) plays a crucial role in maintaining intracellular pH by regulating the electroneutral exchange of a single intracellular H+ for one extracellular Na+ across the plasma membrane. Understanding the molecular mechanisms governing ion transport and the binding of inhibitors is of importance in the development of anticancer therapeutics targeting NHE1. In this context, we performed molecular dynamics (MD) simulations based on the recent cryo-electron microscopy (cryo-EM) structures of outward- and inward-facing conformations of NHE1. These simulations allowed us to explore the dynamics of the protein, examine the ion-translocation pore, and confirm that Asp267 is the ion-binding residue. Our free energy calculations did not show a significant difference between Na+ and K+ binding at the ion-binding site. Consequently, Na+ over K+ selectivity cannot be solely explained by differences in ion binding. Our MD simulations involving NHE1 inhibitors (cariporide and amiloride analogues) maintained stable interactions with Asp267 and Glu346. Our study highlights the importance of the salt bridge between the positively charged acylguanidine moiety and Asp267, which appears to play a role in the competitive inhibitory mechanism for this class of inhibitors. Our computational study provides a detailed mechanistic interpretation of experimental data and serves the basis of future structure-based inhibitor design.
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Affiliation(s)
- Nehad S El Salamouni
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Benjamin J Buckley
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Richmond Lee
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Marie Ranson
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Michael J Kelso
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
- ARC Centre of Excellence in Quantum Biotechnology, University of Wollongong, Wollongong, NSW 2522, Australia
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Poet M, Doyen D, Van Obberghen E, Jarretou G, Bouret Y, Counillon L. How Does Our Knowledge on the Na+/H+ Exchanger NHE1 Obtained by Biochemical and Molecular Analyses Keep up With Its Recent Structure Determination? Front Physiol 2022; 13:907587. [PMID: 35910559 PMCID: PMC9334524 DOI: 10.3389/fphys.2022.907587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/06/2022] [Indexed: 11/23/2022] Open
Abstract
Na+/H+ exchangers are membrane transporters conserved in all living systems and therefore are assumed to be amongst the most ancestral molecular devices that equipped the first protocells. Following the cloning and sequencing of its gene, the mammalian NHE1, that regulates pH and volume in all cells, has been thoroughly scrutinized by molecular and biochemical analyses. Those gave a series of crucial clues concerning its topology, dimeric organization, pharmacological profile, regulation, and the role of key amino acids. Recently thanks to cryogenic Electron Microscopy (Cryo-EM) the long-awaited molecular structures have been revealed. With this information in mind we will challenge the robustness of the earlier conclusions and highlight how the new information enriches our understanding of this key cellular player. At the mechanistic level, we will pinpoint how the NHE1 3D structures reveal that the previously identified amino acids and regions are organized to coordinate transported cations, and shape the allosteric transition that makes NHE1 able to sense intracellular pH and be regulated by signaling pathways.
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Affiliation(s)
- Mallorie Poet
- Université Côte d’Azur, CNRS, Laboratoire de PhysioMédecine Moléculaire (LP2M), Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - Denis Doyen
- Université Côte d’Azur, CNRS, Laboratoire de PhysioMédecine Moléculaire (LP2M), Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
- Centre Hospitalier Universitaire de Nice, Nice, France
| | - Emmanuel Van Obberghen
- Université Côte d’Azur, CNRS, Laboratoire de PhysioMédecine Moléculaire (LP2M), Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
- Centre Hospitalier Universitaire de Nice, Nice, France
| | - Gisèle Jarretou
- Université Côte d’Azur, CNRS, Laboratoire de PhysioMédecine Moléculaire (LP2M), Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - Yann Bouret
- Université Côte d’Azur, CNRS, Institut de Physique de Nice (INPHYNI), Valbonne, France
| | - Laurent Counillon
- Université Côte d’Azur, CNRS, Laboratoire de PhysioMédecine Moléculaire (LP2M), Nice, France
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
- *Correspondence: Laurent Counillon,
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Dong Y, Li H, Ilie A, Gao Y, Boucher A, Zhang XC, Orlowski J, Zhao Y. Structural basis of autoinhibition of the human NHE3-CHP1 complex. SCIENCE ADVANCES 2022; 8:eabn3925. [PMID: 35613257 PMCID: PMC9132474 DOI: 10.1126/sciadv.abn3925] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Sodium-proton exchanger 3 (NHE3/SLC9A3) located in the apical membrane of renal and gastrointestinal epithelia mediates salt and fluid absorption and regulates pH homeostasis. As an auxiliary regulatory factor of NHE proteins, calcineurin B homologous protein 1 (CHP1) facilitates NHE3 maturation, plasmalemmal expression, and pH sensitivity. Dysfunctions of NHE3 are associated with renal and digestive system disorders. Here, we report the cryo-electron microscopy structure of the human NHE3-CHP1 complex in its inward-facing conformation. We found that a cytosolic helix-loop-helix motif in NHE3 blocks the intracellular cavity formed between the core and dimerization domains, functioning as an autoinhibitory element and hindering substrate transport. Furthermore, two phosphatidylinositol molecules are found to bind to the peripheric juxtamembrane sides of the complex, function as anchors to stabilize the complex, and may thus enhance its transport activity.
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Affiliation(s)
- Yanli Dong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alina Ilie
- Department of Physiology, McGill University, Montreal, Canada
| | - Yiwei Gao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Annie Boucher
- Department of Physiology, McGill University, Montreal, Canada
| | - Xuejun Cai Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - John Orlowski
- Department of Physiology, McGill University, Montreal, Canada
| | - Yan Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Amino Acids 785, 787 of the Na +/H + Exchanger Cytoplasmic Tail Modulate Protein Activity and Tail Conformation. Int J Mol Sci 2021; 22:ijms222111349. [PMID: 34768780 PMCID: PMC8583816 DOI: 10.3390/ijms222111349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022] Open
Abstract
The mammalian Na+/H+ exchanger isoform 1 (NHE1) is a plasma membrane protein ubiquitously present in humans. It regulates intracellular pH by removing an intracellular proton in exchange for an extracellular sodium. It consists of a 500 amino acid membrane domain plus a 315 amino acid, regulatory cytosolic tail. Here, we investigated the effect of mutation of two amino acids of the regulatory tail, Ser785 and Ser787, that were similar in location and context to two amino acids of the Arabidopsis Na+/H+ exchanger SOS1. Mutation of these two amino acids to either Ala or phosphomimetic Glu did not affect surface targeting but led to a slight reduction in the level of protein expressed. The activity of the NHE1 protein was reduced in the phosphomimetic mutations and the effect was due to a decrease in Vmax activity. The Ser to Glu mutations also caused a change in the apparent molecular weight of both the full-length protein and of the cytosolic tail of NHE1. A conformational change in this region was indicated by differential trypsin sensitivity. We also found that a peptide containing amino acids 783–790 bound to several more proximal regions of the NHE1 tail in in vitro protein interaction experiments. The results are the first characterization of these two amino acids and show that they have significant effects on enzyme kinetics and the structure of the NHE1 protein.
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Characterization of modeled inhibitory binding sites on isoform one of the Na +/H + exchanger. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183648. [PMID: 33992631 DOI: 10.1016/j.bbamem.2021.183648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 12/31/2022]
Abstract
Mammalian Na+/H+ exchanger isoform one (NHE1) is a plasma membrane protein responsible for pH regulation in mammalian cells. Excess activity of the protein promotes heart disease and is a trigger of metastasis in cancer. Inhibitors of the protein exist but problems in specificity have delayed their clinical application. Here we examined amino acids involved in two modeled inhibitor binding sites (A, B) in human NHE1. Twelve mutations (Asp159, Phe348, Ser351, Tyr381, Phe413, Leu465, Gly466, Tyr467, Leu468, His473, Met476, Leu481) were made and characterized. Mutants S351A, F413A, Y467A, L468A, M476A and L481A had 40-70% of wild type expression levels, while G466A and H473A expressed 22% ~ 30% of the wild type levels. Most mutants, were targeted to the cell surface at levels similar to wild type NHE1, approximately 50-70%, except for F413A and G466A, which had very low surface targeting. Most of the mutants had measurable activity except for D159A, F413A and G466A. Resistance to inhibition by EMD87580 was elevated in mutants F438A, L465A and L468A and reduced in mutants S351A, Y381A, H473A, M476A and L481A. All mutants with large alterations in inhibitory properties showed reduced Na+ affinity. The greatest changes in activity and inhibitor sensitivity were in mutants present in binding site B which is more closely associated with TM4 and C terminal of extracellular loop 5, and is situated between the putative scaffolding domain and transport domain. The results help define the inhibitor binding domain of the NHE1 protein and identify new amino acids involved in inhibitor binding.
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Blair S, Li X, Dutta D, Chamot D, Fliegel L, Goss G. Rainbow Trout ( Oncorhynchus mykiss) Na +/H + Exchangers tNhe3a and tNhe3b Display Unique Inhibitory Profiles Dissimilar from Mammalian NHE Isoforms. Int J Mol Sci 2021; 22:ijms22042205. [PMID: 33672216 PMCID: PMC7926675 DOI: 10.3390/ijms22042205] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 01/05/2023] Open
Abstract
Freshwater fishes maintain an internal osmolality of ~300 mOsm, while living in dilute environments ranging from 0 to 50 mOsm. This osmotic challenge is met at least partially, by Na+/H+ exchangers (NHE) of fish gill and kidney. In this study, we cloned, expressed, and pharmacologically characterized fish-specific Nhes of the commercially important species Oncorhynchus mykiss. Trout (t) Nhe3a and Nhe3b isoforms from gill and kidney were expressed and characterized in an NHE-deficient cell line. Western blotting and immunocytochemistry confirmed stable expression of the tagged trout tNhe proteins. To measure NHE activity, a transient acid load was induced in trout tNhe expressing cells and intracellular pH was measured. Both isoforms demonstrated significant activity and recovered from an acute acid load. The effect of the NHE transport inhibitors amiloride, EIPA (5-(N-ethyl-N-isopropyl)-amiloride), phenamil, and DAPI was examined. tNhe3a was inhibited in a dose-dependent manner by amiloride and EIPA and tNhe3a was more sensitive to amiloride than EIPA, unlike mammalian NHE1. tNhe3b was inhibited by high concentrations of amiloride, while even in the presence of high concentrations of EIPA (500 µM), some activity of tNhe3b remained. Phenamil and DAPI were ineffective at inhibiting tNhe activity of either isoform. The current study aids in understanding the pharmacology of fish ion transporters. Both isoforms display inhibitory profiles uniquely different from mammalian NHEs and show resistance to inhibition. Our study allows for more direct interpretation of past, present, and future fish-specific sodium transport studies, with less reliance on mammalian NHE data for interpretation.
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Affiliation(s)
- Salvatore Blair
- Department of Biology, Winthrop University, Rock Hill, SC 29733, USA;
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada;
| | - Xiuju Li
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (X.L.); (D.D.); (L.F.)
| | - Debajyoti Dutta
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (X.L.); (D.D.); (L.F.)
| | - Danuta Chamot
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada;
| | - Larry Fliegel
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (X.L.); (D.D.); (L.F.)
| | - Greg Goss
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada;
- Correspondence: ; Tel.: +1-780-492-1276; Fax: +1-780-492-9234
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Acidic residues of extracellular loop 3 of the Na +/H + exchanger type 1 are important in cation transport. Mol Cell Biochem 2020; 468:13-20. [PMID: 32130622 DOI: 10.1007/s11010-020-03707-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/21/2020] [Indexed: 12/11/2022]
Abstract
Mammalian Na+/H+ exchanger type I isoform (NHE1) is a ubiquitously expressed membrane protein that regulates intracellular pH (pHi) by removing one intracellular proton in exchange for one extracellular sodium ion. Abnormal activity of the protein occurs in cardiovascular disease and breast cancer. The purpose of this study is to examine the role of negatively charged amino acids of extracellular loop 3 (EL3) in the activity of the NHE protein. We mutated glutamic acid 217 and aspartic acid 226 to alanine, and to glutamine and asparagine, respectively. We examined effects on expression levels, cell surface targeting and activity of NHE1, and also characterized affinity for extracellular sodium and lithium ions. Individual mutation of these amino acids had little effect on protein function. However, mutation of both these amino acids together impaired transport, decreasing the Vmax for both Na+ and Li+ ions. We suggested that amino acids E217 and D226 form part of a negatively charged coordination sphere, which facilitates cation transport in the NHE1 protein.
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Yeves AM, Ennis IL. Na +/H + exchanger and cardiac hypertrophy. HIPERTENSION Y RIESGO VASCULAR 2019; 37:22-32. [PMID: 31601481 DOI: 10.1016/j.hipert.2019.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/16/2019] [Accepted: 09/03/2019] [Indexed: 12/31/2022]
Abstract
Reactive cardiac hypertrophy (CH) is an increase in heart mass in response to hemodynamic overload. Exercise-induced CH emerges as an adaptive response with improved cardiac function, in contrast to pathological CH that represents a risk factor for cardiovascular health. The Na+/H+ exchanger (NHE-1) is a membrane transporter that not only regulates intracellular pH but also intracellular Na+ concentration. In the scenario of cardiovascular diseases, myocardial NHE-1 is activated by a variety of stimuli, such as neurohumoral factors and mechanical stress, leading to intracellular Na+ overload and activation of prohypertrophic cascades. NHE-1 hyperactivity is intimately linked to heart diseases, including ischemia-reperfusion injury, maladaptive CH and heart failure. In this review, we will present evidence to support that the NHE-1 hyperactivity constitutes a "switch on/off" for the pathological phenotype during CH development. We will also discuss some classical and novel strategies to avoid NHE-1 hyperactivity, and that are therefore worthwhile to improve cardiovascular health.
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Affiliation(s)
- A M Yeves
- Centro de Investigaciones Cardiovasculares "Horacio E. Cingolani", Facultad de Ciencias Médicas, Universidad Nacional de La Plata - CONICET, Calle 60 y 120, 1900 La Plata, Argentina
| | - I L Ennis
- Centro de Investigaciones Cardiovasculares "Horacio E. Cingolani", Facultad de Ciencias Médicas, Universidad Nacional de La Plata - CONICET, Calle 60 y 120, 1900 La Plata, Argentina.
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Dutta D, Ullah A, Bibi S, Fliegel L. Functional Analysis of Conserved Transmembrane Charged Residues and a Yeast Specific Extracellular Loop of the Plasma Membrane Na +/H + Antiporter of Schizosaccharomyces pombe. Sci Rep 2019; 9:6191. [PMID: 30996236 PMCID: PMC6470128 DOI: 10.1038/s41598-019-42658-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/01/2019] [Indexed: 01/20/2023] Open
Abstract
The Na+/H+ exchanger of the plasma membrane of S. pombe (SpNHE1) removes excess intracellular sodium in exchange for an extracellular proton. We examined the functional role of acidic amino acids of a yeast specific periplasmic extracellular loop 6 (EL6) and of Glu74 and Arg77 of transmembrane segment 3. Glu74 and Arg77 are conserved in yeast species while Glu74 is conserved throughout various phyla. The mutation E74A caused a minor effect, while mutation R77A had a larger effect on the ability of SpNHE1 to confer salt tolerance. Mutation of both residues to Ala or Glu also eliminated the ability to confer salt tolerance. Arg341 and Arg342 were also necessary for SpNHE1 transport in S. pombe. Deletion of 3 out of 4 acidic residues (Asp389, Glu390, Glu392, Glu397) of EL6 did not greatly affect SpNHE1 function while deletion of all did. Replacement of EL6 with a segment from the plant Na+/H+ exchanger SOS1 also did not affect function. We suggest that EL6 forms part of a cation coordination sphere, attracting cations for transport but that the region is not highly specific for the location of acidic charges. Overall, we identified a number of polar amino acids important in SpNHE1 function.
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Affiliation(s)
- Debajyoti Dutta
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Asad Ullah
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Sana Bibi
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Larry Fliegel
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.
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