1
|
Chowdhury S, Pal K. Architecture and rearrangements of a sperm-specific Na +/H + exchanger. RESEARCH SQUARE 2023:rs.3.rs-3396005. [PMID: 37886505 PMCID: PMC10602139 DOI: 10.21203/rs.3.rs-3396005/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The sperm-specific sodium hydrogen exchanger, SLC9C1, underlies hyperpolarization and cyclic nucleotide stimulated proton fluxes across sperm membranes and regulates their hyperactivated motility. SLC9C1 is the first known instance of an ion transporter that uses a canonical voltage-sensing domain (VSD) and an evolutionarily conserved cyclic nucleotide binding domain (CNBD) to influence the dynamics of its ion-exchange domain (ED). The structural organization of this 'tripartite transporter' and the mechanisms whereby it integrates physical (membrane voltage) and chemical (cyclic nucleotide) cues are unknown. In this study, we use single particle cryo-electron microscopy to determine structures of a metazoan SLC9C1 in different conformational states. We find that the three structural domains are uniquely organized around a distinct ring-shaped scaffold that we call the 'allosteric ring domain' or ARD. The ARD undergoes coupled proton-dependent rearrangements with the ED and acts as a 'signaling hub' enabling allosteric communication between the key functional modules of sp9C1. We demonstrate that binding of cAMP causes large conformational changes in the cytoplasmic domains and disrupts key ARD-linked interfaces. We propose that these structural changes rescue the transmembrane domains from an auto-inhibited state and facilitate their functional dynamics. Our study provides a structural framework to understand and further probe electrochemical linkage in SLC9C1.
Collapse
|
2
|
Winkelmann I, Uzdavinys P, Kenney IM, Brock J, Meier PF, Wagner LM, Gabriel F, Jung S, Matsuoka R, von Ballmoos C, Beckstein O, Drew D. Crystal structure of the Na +/H + antiporter NhaA at active pH reveals the mechanistic basis for pH sensing. Nat Commun 2022; 13:6383. [PMID: 36289233 PMCID: PMC9606361 DOI: 10.1038/s41467-022-34120-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
The strict exchange of protons for sodium ions across cell membranes by Na+/H+ exchangers is a fundamental mechanism for cell homeostasis. At active pH, Na+/H+ exchange can be modelled as competition between H+ and Na+ to an ion-binding site, harbouring either one or two aspartic-acid residues. Nevertheless, extensive analysis on the model Na+/H+ antiporter NhaA from Escherichia coli, has shown that residues on the cytoplasmic surface, termed the pH sensor, shifts the pH at which NhaA becomes active. It was unclear how to incorporate the pH senor model into an alternating-access mechanism based on the NhaA structure at inactive pH 4. Here, we report the crystal structure of NhaA at active pH 6.5, and to an improved resolution of 2.2 Å. We show that at pH 6.5, residues in the pH sensor rearrange to form new salt-bridge interactions involving key histidine residues that widen the inward-facing cavity. What we now refer to as a pH gate, triggers a conformational change that enables water and Na+ to access the ion-binding site, as supported by molecular dynamics (MD) simulations. Our work highlights a unique, channel-like switch prior to substrate translocation in a secondary-active transporter.
Collapse
Affiliation(s)
- Iven Winkelmann
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Povilas Uzdavinys
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ian M. Kenney
- grid.215654.10000 0001 2151 2636Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ 85287 USA
| | - Joseph Brock
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pascal F. Meier
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lina-Marie Wagner
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Florian Gabriel
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Sukkyeong Jung
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Rei Matsuoka
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Christoph von Ballmoos
- grid.5734.50000 0001 0726 5157Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Oliver Beckstein
- grid.215654.10000 0001 2151 2636Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ 85287 USA
| | - David Drew
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| |
Collapse
|
3
|
Karmazyn M, Pierce GN, Fliegel L. The Remaining Conundrum of the Role of the Na +/H + Exchanger Isoform 1 (NHE1) in Cardiac Physiology and Pathology: Can It Be Rectified? Rev Cardiovasc Med 2022; 23:284. [PMID: 39076631 PMCID: PMC11266974 DOI: 10.31083/j.rcm2308284] [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: 06/08/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 07/31/2024] Open
Abstract
The mammalian Na + /H + exchanger (NHE) is a family of ubiquitous membrane proteins present in humans. Isoform one (NHE1) is present on the plasma membrane and regulates intracellular pH by removal of one intracellular proton in exchange for one extracellular sodium thus functioning as an electroneutral process. Human NHE1 has a 500 amino acid membrane domain plus a C-terminal 315 amino acid, regulatory cytosolic tail. It is regulated through a cytosolic regulatory C-terminal tail which is subject to phosphorylation and is modulated by proteins and lipids. Substantial evidence has implicated NHE1 activity in both myocardial ischemia and reperfusion damage and myocardial remodeling resulting in heart failure. Experimental data show excellent cardioprotection with NHE1 inhibitors although results from clinical results have been mixed. In cardiac surgery patients receiving the NHE1 inhibitor cariporide, subgroups showed beneficial effects of treatment. However, in one trial this was associated with a significantly increased incidence of ischemic strokes. This likely reflected both inappropriate dosing regimens as well as overly high drug doses. We suggest that further progress towards NHE1 inhibition as a treatment for cardiovascular disease is warranted through the development of novel compounds to inhibit NHE1 that are structurally different than those previously used in compromised clinical trials. Some novel pyrazinoyl guanidine inhibitors of NHE1 are already in development and the recent elucidation of the three-dimensional structure of the NHE1 protein and identity of the inhibitor binding site may facilitate development. An alternative approach may also be to control the endogenous regulation of activity of NHE1, which is activated in disease.
Collapse
Affiliation(s)
- Morris Karmazyn
- Department of Physiology and Pharmacology, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Grant N. Pierce
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St. Boniface Hospital, and Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
| | - Larry Fliegel
- Department of Biochemistry, University Alberta, Edmonton, AB T6G 2H7, Canada
| |
Collapse
|
4
|
Kühlbrandt W. Forty years in cryoEM of membrane proteins. Microscopy (Oxf) 2022; 71:i30-i50. [PMID: 35275191 PMCID: PMC8855526 DOI: 10.1093/jmicro/dfab041] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/05/2021] [Accepted: 11/10/2021] [Indexed: 12/13/2022] Open
Abstract
In a surprisingly short time, electron cryo-microscopy (cryoEM) has developed from a niche technique in structural biology to a mainstream method practiced in a rapidly growing number of laboratories around the world. From its beginnings about 40 years ago, cryoEM has had a major impact on the study of membrane proteins, in particular the energy-converting systems from bacterial, mitochondrial and chloroplast membranes. Early work on two-dimensional crystals attained resolutions ∼3.5 Å, but at present, single-particle cryoEM delivers much more detailed structures without crystals. Electron cryo-tomography of membranes and membrane-associated proteins adds valuable context, usually at lower resolution. The review ends with a brief outlook on future prospects.
Collapse
Affiliation(s)
- Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, Frankfurt am Main 60438, Germany
| |
Collapse
|
5
|
Hu Y, Li YV. The change of intracellular zinc distribution after strong acid challenge. INTERNATIONAL JOURNAL OF PHYSIOLOGY, PATHOPHYSIOLOGY AND PHARMACOLOGY 2021; 13:94-101. [PMID: 34336133 PMCID: PMC8310881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/18/2020] [Indexed: 06/13/2023]
Abstract
Zinc (Zn2+) is stored in the nucleus, endoplasmic reticulum (ER), Golgi apparatus, mitochondria, lysosomes, and zinc-binding proteins. The acidity of the microenvironment affects the binding between zinc and proteins in which zinc become free or loosely bound. In this study, when cells were treated with an acidic medium, we started seeing free zinc 'hot spots' or zincosomes where we found bright zinc fluorescence. The rising free zinc quickly across whole cells with both intensity and distribution were pH-dependent. Interestingly, the nucleus was more sensitive to acidic treatment as the increase of nuclear zinc was faster and higher than the increase of cytosolic zinc. In addition, we re-cultured strong acid-challenged cells in a normal medium. Comparing to the control, these cells exhibited multiple zinc 'hot spots' beside the nucleus, suggesting that free zinc became more extensively distributed. To investigate further the function of zinc in cell shaping and morphological changes, we categorized strong acid-challenged cells into different shapes and found that the proportion of each cell shape had changed after the acid challenge. These acid-induced changes of the cell shape percentage were partially reversed by the reduction of zinc, suggesting that zinc participated in directing the cell shapes and morphologies during cell growth. Our findings reveal that acidic pH affects the dynamics of cellular zinc by making zinc more accessible to cellular compartments and zinc-binding proteins, which provided new insights into understanding the cellular behavior and the function of zinc in it.
Collapse
Affiliation(s)
- Yuli Hu
- Molecular & Cellular Biology Graduate Program, Departments of Biological Sciences and Biomedical Sciences, Ohio University Athens, OH 45701, USA
| | - Yang V Li
- Molecular & Cellular Biology Graduate Program, Departments of Biological Sciences and Biomedical Sciences, Ohio University Athens, OH 45701, USA
| |
Collapse
|
6
|
Hu Y, Li YV. Expression of SSEA-4 and Oct-4 from somatic cells in primary mouse gastric cell culture induced by brief strong acid. Mol Cell Biochem 2021; 476:2813-2821. [PMID: 33733429 DOI: 10.1007/s11010-021-04124-2] [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: 10/09/2020] [Accepted: 02/26/2021] [Indexed: 11/29/2022]
Abstract
Environmental changes can stress and alter biology at the molecular and cellular level. For example, metal-protein interaction is a classic physic and biological property of nature, which is fundamentally influenced by acidity. Here, we report a unique cellular reprogramming phenomenon in that a brief strong acid treatment induced the expression of pluripotent stem cell (PSC) markers. We used strong acid to briefly challenge mix-cultured gastric cells, and then subcultured survived cells in a normal cell culture medium. We found that survival acid-treated cells expressed PSC markers detected by commonly used pluripotent antibodies such as SSEA-4 and Oct4. In addition, we observed that the survived cells from the acid challenge grew faster during the second and third weeks of subculture and had a relative short doubling time (DT) than the controls. PSC marker-labeled 'older' cells also presented immature cell-like morphology with some having marker Oct4 in the nucleus. Finally, the expression of the markers appeared to be sensitive to metal ion chelation. Removal of the metals during a brief acid treatment reduced pluripotent marker-positive cells, suggesting the dissociation of metals from metal-binding proteins may be a factor involved in the induction of stem cell markers. Our findings reveal that somatic cells appear to possess a plasticity feature to express pluripotent marker proteins or to select cell subpopulations that express pluripotent marker proteins when cells are transiently exposed to strong acid. It opens new directions for understanding conserved regulatory mechanisms involved in cellular survival under stressful stimulation.
Collapse
Affiliation(s)
- Yuli Hu
- Molecular & Cellular Biology Graduate Program, Departments of Biological Sciences and Biomedical Sciences, Ohio University, Athens, OH, 45701, USA
| | - Yang V Li
- Molecular & Cellular Biology Graduate Program, Departments of Biological Sciences and Biomedical Sciences, Ohio University, Athens, OH, 45701, USA. .,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, 346 Irvine Hall, Athens, OH, 45701, USA.
| |
Collapse
|
7
|
Structural and Functional Changes in the Na +/H + Exchanger Isoform 1, Induced by Erk1/2 Phosphorylation. Int J Mol Sci 2019; 20:ijms20102378. [PMID: 31091671 PMCID: PMC6566726 DOI: 10.3390/ijms20102378] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/15/2022] Open
Abstract
The human Na+/H+ exchanger isoform 1 (NHE1) is a plasma membrane transport protein that plays an important role in pH regulation in mammalian cells. Because of the generation of protons by intermediary metabolism as well as the negative membrane potential, protons accumulate within the cytosol. Extracellular signal-regulated kinase (ERK)-mediated regulation of NHE1 is important in several human pathologies including in the myocardium in heart disease, as well as in breast cancer as a trigger for growth and metastasis. NHE1 has a N-terminal, a 500 amino acid membrane domain, and a C-terminal 315 amino acid cytosolic domain. The C-terminal domain regulates the membrane domain and its effects on transport are modified by protein binding and phosphorylation. Here, we discuss the physiological regulation of NHE1 by ERK, with an emphasis on the critical effects on structure and function. ERK binds directly to the cytosolic domain at specific binding domains. ERK also phosphorylates NHE1 directly at multiple sites, which enhance NHE1 activity with subsequent downstream physiological effects. The NHE1 cytosolic regulatory tail possesses both ordered and disordered regions, and the disordered regions are stabilized by ERK-mediated phosphorylation at a phosphorylation motif. Overall, ERK pathway mediated phosphorylation modulates the NHE1 tail, and affects the activity, structure, and function of this membrane protein.
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Masrati G, Dwivedi M, Rimon A, Gluck-Margolin Y, Kessel A, Ashkenazy H, Mayrose I, Padan E, Ben-Tal N. Broad phylogenetic analysis of cation/proton antiporters reveals transport determinants. Nat Commun 2018; 9:4205. [PMID: 30310075 PMCID: PMC6181914 DOI: 10.1038/s41467-018-06770-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 09/24/2018] [Indexed: 11/08/2022] Open
Abstract
Cation/proton antiporters (CPAs) play a major role in maintaining living cells' homeostasis. CPAs are commonly divided into two main groups, CPA1 and CPA2, and are further characterized by two main phenotypes: ion selectivity and electrogenicity. However, tracing the evolutionary relationships of these transporters is challenging because of the high diversity within CPAs. Here, we conduct comprehensive evolutionary analysis of 6537 representative CPAs, describing the full complexity of their phylogeny, and revealing a sequence motif that appears to determine central phenotypic characteristics. In contrast to previous suggestions, we show that the CPA1/CPA2 division only partially correlates with electrogenicity. Our analysis further indicates two acidic residues in the binding site that carry the protons in electrogenic CPAs, and a polar residue in the unwound transmembrane helix 4 that determines ion selectivity. A rationally designed triple mutant successfully converted the electrogenic CPA, EcNhaA, to be electroneutral.
Collapse
Affiliation(s)
- Gal Masrati
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat-Aviv, 69978, Tel-Aviv, Israel
| | - Manish Dwivedi
- Department of Biological Chemistry, The Alexander Silberman Inst. of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Abraham Rimon
- Department of Biological Chemistry, The Alexander Silberman Inst. of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yael Gluck-Margolin
- Department of Biological Chemistry, The Alexander Silberman Inst. of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Amit Kessel
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat-Aviv, 69978, Tel-Aviv, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat-Aviv, 69978, Tel-Aviv, Israel
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plant, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat-Aviv, 69978, Tel-Aviv, Israel
| | - Etana Padan
- Department of Biological Chemistry, The Alexander Silberman Inst. of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat-Aviv, 69978, Tel-Aviv, Israel.
| |
Collapse
|
10
|
Dutta D, Fliegel L. Molecular modeling and inhibitor docking analysis of the Na +/H + exchanger isoform one 1. Biochem Cell Biol 2018; 97:333-343. [PMID: 30058365 DOI: 10.1139/bcb-2018-0158] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Na+/H+ exchanger isoform one (NHE1) is a mammalian plasma membrane protein that removes intracellular protons, thereby elevating intracellular pH (pHi). NHE1 uses the energy of allowing an extracellular sodium down its gradient into cells to remove one intracellular proton. The ubiquitous protein has several important physiological and pathological influences on mammalian cells as a result of its activity. The three-dimensional structure of human NHE1 (hNHE1) is not known. Here, we modeled NHE1 based on the structure of MjNhaP1 of Methanocaldoccocus jannaschii in combination with biochemical surface accessibility data. hNHE1 contained 12 transmembrane segments including a characteristic Na+/H+ antiporter fold of two transmembrane segments with a helix - extended region - helix conformation crossing each other within the membrane. Amino acids 363-410 mapped principally to the extracellular surface as an extracellular loop (EL5). A large preponderance of amino acids shown to be surface accessible by biochemical experiments mapped near to, or on, the extracellular surface. Docking of Na+/H+ exchanger inhibitors to the extracellular surface suggested that inhibitor binding on an extracellular site is made up from several amino acids of different regions of the protein. The results present a novel testable, three-dimensional model illustrating NHE1 structure and accounting for experimental biochemical data.
Collapse
Affiliation(s)
- Debajyoti Dutta
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.,Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Larry Fliegel
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.,Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| |
Collapse
|
11
|
Yang Z, Meng Y, Zhao Q, Cheng B, Xu P, Yang C. Critical Functions of Region 1-67 and Helix XIII in Retaining the Active Structure of NhaD Antiporter in Halomonas sp. Y2. Front Microbiol 2018; 9:831. [PMID: 29770128 PMCID: PMC5942162 DOI: 10.3389/fmicb.2018.00831] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/11/2018] [Indexed: 11/13/2022] Open
Abstract
NhaD-type antiporters are mainly distributed in various Proteobacteria, especially in marine microorganisms and human pathogens. This distribution as well as the pathogenic properties of these strains suggest that these antiporters contribute to the regulation of high osmoregulation and are potential drug targets. Two NhaD homologs, NhaD1 and NhaD2, from the halotolerant and alkaliphilic Halomonas sp. Y2 exhibits similar, high in vitro activity, but remarkably different in vivo functions. To search for critical domains or residues involved in these differences of physiological functions, various chimeras composed of NhaD1 and NhaD2 segments were generated. Two regions at residues 1–67 and 464–492 were found to be responsible for the robust in vivo function of NhaD2, and region 464–492 is also crucial to the pH response of the antiporter. In particular, the completely abolished activity of KNabc/N463r, highly recovered activity while very weakly recovered ion resistance of the KNabc/N463r-C7 chimera, suggested that transmembrane helix (TM) XIII is crucial for the robust ion resistance of NhaD2. Using site-directed mutagenesis, seven hydrophobic residues in TM XIII were identified as key residues for the ion translocation of NhaD2. Compared with the fluorescence resonance energy transfer (FRET) profile in the wild-type NhaD2, the reduced FRET efficiency of N463r chimeras provided solid evidence for conformational changes in the N463r fusion protein and consequently verified the structural functions of TM XIII in the pH activation and physiological functions of NhaD2.
Collapse
Affiliation(s)
- Zhou Yang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Jinan, China
| | - Yiwei Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Jinan, China
| | - Qi Zhao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Jinan, China
| | - Bin Cheng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Jinan, China
| | - Ping Xu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Jinan, China
| | - Chunyu Yang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Jinan, China
| |
Collapse
|
12
|
Asp133 Residue in NhaA Na+/H+ Antiporter Is Required for Stability Cation Binding and Transport. J Mol Biol 2018; 430:867-880. [DOI: 10.1016/j.jmb.2018.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 11/18/2022]
|
13
|
Dutta D, Fliegel L. Structure and function of yeast and fungal Na + /H + antiporters. IUBMB Life 2017; 70:23-31. [PMID: 29219228 DOI: 10.1002/iub.1701] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/21/2017] [Indexed: 12/22/2022]
Abstract
Sodium proton antiporters (or sodium proton exchangers [NHEs]) are a critical family of membrane proteins that exchange sodium for protons across cell membranes. In yeast and plants, their primary function is to keep the sodium concentration low inside the cytoplasm. One class of NHE constitutively expressed in yeast is the plasma membrane Na+ /H+ antiporter, and another class is expressed on the endosomal/vacuolar membrane. At present, four bacterial plasma membrane antiporter structures are known and nuclear magnetic resonance structures are available for the membrane spanning transmembrane helices of mammalian and yeast NHEs. Additionally, a vast amount of mutational data are available on the role of individual amino acids and critical motifs involved in transport. We combine this information to obtain a more detailed picture of the yeast NHE plasma membrane protein and review mechanisms of transport, conserved motifs, unique residues important in function, and regulation of these proteins. The Na+ /H+ antiporter of Schizosaccharomyces pombe, SpNHE1, is an interesting model protein in an easy to study system and is representative of fungal Na+ /H+ antiporters. © IUBMB Life, 70(1):23-31, 2018.
Collapse
Affiliation(s)
- Debajyoti Dutta
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Larry Fliegel
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
14
|
Dissecting the proton transport pathway in electrogenic Na +/H + antiporters. Proc Natl Acad Sci U S A 2017; 114:E1101-E1110. [PMID: 28154142 DOI: 10.1073/pnas.1614521114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sodium/proton exchangers of the SLC9 family mediate the transport of protons in exchange for sodium to help regulate intracellular pH, sodium levels, and cell volume. In electrogenic Na+/H+ antiporters, it has been assumed that two ion-binding aspartate residues transport the two protons that are later exchanged for one sodium ion. However, here we show that we can switch the antiport activity of the bacterial Na+/H+ antiporter NapA from being electrogenic to electroneutral by the mutation of a single lysine residue (K305). Electroneutral lysine mutants show similar ion affinities when driven by [Formula: see text]pH, but no longer respond to either an electrochemical potential ([Formula: see text]) or could generate one when driven by ion gradients. We further show that the exchange activity of the human Na+/H+ exchanger NHA2 (SLC9B2) is electroneutral, despite harboring the two conserved aspartic acid residues found in NapA and other bacterial homologues. Consistently, the equivalent residue to K305 in human NHA2 has been replaced with arginine, which is a mutation that makes NapA electroneutral. We conclude that a transmembrane embedded lysine residue is essential for electrogenic transport in Na+/H+ antiporters.
Collapse
|
15
|
Abstract
The structures of transport proteins have been steadily revealed in the last few decades, and yet the conversion of this information into molecular-level understanding of their function is still lagging behind. In this study, we try to elucidate how the action of the archaeal sodium/proton antiporter MjNhaP1 depends on its structure-energy relationship. To this end, we calculate the binding energies of its substrates and evaluate the conformational change barrier, focusing on the rotation of the catalytic residue D161. We find that sodium ions and protons compete against a common binding site and that the accessibility of this binding site is restricted to either the inside or outside of the cell. We suggest that the rotation of D161 χ1 angle correlates with the conformational change and is energetically unfavorable when D161 does not bind any substrate. This restriction ensures coupling between the sodium ions and the protons, allowing MjNhaP1 and probably other similar transporters to exchange substrates with minimal leak. Using Monte Carlo simulations we demonstrate the feasibility of our model. Overall we present a complete picture that reproduces the electroneutral (at 1:1 substrate ratio) and coupled transport activity of MjNhaP1 including the energetic basis for the criteria provided by Jardetzky half a century ago.
Collapse
Affiliation(s)
- Raphael Alhadeff
- Department of Chemistry, University of Southern California , SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California , SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States
| |
Collapse
|
16
|
Affiliation(s)
- David Drew
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065;
| |
Collapse
|
17
|
Expression and characterization of the SOS1 Arabidopsis salt tolerance protein. Mol Cell Biochem 2016; 415:133-43. [DOI: 10.1007/s11010-016-2685-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/12/2016] [Indexed: 10/22/2022]
|
18
|
Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters. Nat Struct Mol Biol 2016; 23:248-55. [PMID: 26828964 DOI: 10.1038/nsmb.3164] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/30/2015] [Indexed: 11/09/2022]
Abstract
To fully understand the transport mechanism of Na(+)/H(+) exchangers, it is necessary to clearly establish the global rearrangements required to facilitate ion translocation. Currently, two different transport models have been proposed. Some reports have suggested that structural isomerization is achieved through large elevator-like rearrangements similar to those seen in the structurally unrelated sodium-coupled glutamate-transporter homolog GltPh. Others have proposed that only small domain movements are required for ion exchange, and a conventional rocking-bundle model has been proposed instead. Here, to resolve these differences, we report atomic-resolution structures of the same Na(+)/H(+) antiporter (NapA from Thermus thermophilus) in both outward- and inward-facing conformations. These data combined with cross-linking, molecular dynamics simulations and isothermal calorimetry suggest that Na(+)/H(+) antiporters provide alternating access to the ion-binding site by using elevator-like structural transitions.
Collapse
|
19
|
Sodium-Proton (Na+/H+) Antiporters: Properties and Roles in Health and Disease. Met Ions Life Sci 2016; 16:391-458. [DOI: 10.1007/978-3-319-21756-7_12] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
20
|
Liu Y, Basu A, Li X, Fliegel L. Topological analysis of the Na+/H+ exchanger. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015. [DOI: 10.1016/j.bbamem.2015.07.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
21
|
Brath U, Swamy SI, Veiga AX, Tung CC, Van Petegem F, Erdélyi M. Paramagnetic Ligand Tagging To Identify Protein Binding Sites. J Am Chem Soc 2015; 137:11391-8. [PMID: 26289584 PMCID: PMC4583072 DOI: 10.1021/jacs.5b06220] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Transient
biomolecular interactions are the cornerstones of the
cellular machinery. The identification of the binding sites for low
affinity molecular encounters is essential for the development of
high affinity pharmaceuticals from weakly binding leads but is hindered
by the lack of robust methodologies for characterization of weakly
binding complexes. We introduce a paramagnetic ligand tagging approach
that enables localization of low affinity protein–ligand binding
clefts by detection and analysis of intermolecular protein NMR pseudocontact
shifts, which are invoked by the covalent attachment of a paramagnetic
lanthanoid chelating tag to the ligand of interest. The methodology
is corroborated by identification of the low millimolar volatile anesthetic
interaction site of the calcium sensor protein calmodulin. It presents
an efficient route to binding site localization for low affinity complexes
and is applicable to rapid screening of protein–ligand systems
with varying binding affinity.
Collapse
Affiliation(s)
- Ulrika Brath
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Shashikala I Swamy
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Alberte X Veiga
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Ching-Chieh Tung
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, BC V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, BC V6T 1Z3, Canada
| | - Máté Erdélyi
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| |
Collapse
|
22
|
|
23
|
Paulino C, Wöhlert D, Kapotova E, Yildiz Ö, Kühlbrandt W. Structure and transport mechanism of the sodium/proton antiporter MjNhaP1. eLife 2014; 3:e03583. [PMID: 25426803 PMCID: PMC4381896 DOI: 10.7554/elife.03583] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 11/14/2014] [Indexed: 11/13/2022] Open
Abstract
Sodium/proton antiporters are essential for sodium and pH homeostasis and play a major role in human health and disease. We determined the structures of the archaeal sodium/proton antiporter MjNhaP1 in two complementary states. The inward-open state was obtained by x-ray crystallography in the presence of sodium at pH 8, where the transporter is highly active. The outward-open state was obtained by electron crystallography without sodium at pH 4, where MjNhaP1 is inactive. Comparison of both structures reveals a 7° tilt of the 6 helix bundle. (22)Na(+) uptake measurements indicate non-cooperative transport with an activity maximum at pH 7.5. We conclude that binding of a Na(+) ion from the outside induces helix movements that close the extracellular cavity, open the cytoplasmic funnel, and result in a ∼5 Å vertical relocation of the ion binding site to release the substrate ion into the cytoplasm.
Collapse
Affiliation(s)
- Cristina Paulino
- Department of Structural
Biology, Max Planck Institute of
Biophysics, Frankfurt
am Main, Germany
| | - David Wöhlert
- Department of Structural
Biology, Max Planck Institute of
Biophysics, Frankfurt
am Main, Germany
| | - Ekaterina Kapotova
- Department of Structural
Biology, Max Planck Institute of
Biophysics, Frankfurt
am Main, Germany
| | - Özkan Yildiz
- Department of Structural
Biology, Max Planck Institute of
Biophysics, Frankfurt
am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural
Biology, Max Planck Institute of
Biophysics, Frankfurt
am Main, Germany
| |
Collapse
|
24
|
Wöhlert D, Kühlbrandt W, Yildiz O. Structure and substrate ion binding in the sodium/proton antiporter PaNhaP. eLife 2014; 3:e03579. [PMID: 25426802 PMCID: PMC4381880 DOI: 10.7554/elife.03579] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 11/25/2014] [Indexed: 11/29/2022] Open
Abstract
Sodium/proton antiporters maintain intracellular pH and sodium levels. Detailed
structures of antiporters with bound substrate ions are essential for understanding
how they work. We have resolved the substrate ion in the dimeric, electroneutral
sodium/proton antiporter PaNhaP from Pyrococcus abyssi at 3.2
Å, and have determined its structure in two different conformations at pH 8 and
pH 4. The ion is coordinated by three acidic sidechains, a water molecule, a serine
and a main-chain carbonyl in the unwound stretch of trans-membrane helix 5 at the
deepest point of a negatively charged cytoplasmic funnel. A second narrow polar
channel may facilitate proton uptake from the cytoplasm. Transport activity of PaNhaP
is cooperative at pH 6 but not at pH 5. Cooperativity is due to pH-dependent
allosteric coupling of protomers through two histidines at the dimer interface.
Combined with comprehensive transport studies, the structures of PaNhaP offer unique
new insights into the transport mechanism of sodium/proton antiporters. DOI:http://dx.doi.org/10.7554/eLife.03579.001 Although the membrane that surrounds a cell is effective at separating the inside of
a cell from the outside environment, certain molecules must enter or leave the cell
for it to work correctly. One way this transport can occur is via proteins embedded
in the cell membrane, called transporters. Transporters that are found in all organisms include the sodium/proton antiporters,
which exchange protons from inside the cell with sodium ions from outside. However,
exactly how the antiporter works was unknown. Previous work suggested that the structure and activity of the sodium/proton
antiporter changes as the acidity of its environment changes, but the precise details
of how this occurs were unclear. Wöhlert et al. have now crystallised a
sodium/proton antiporter from a single-celled organism called Pyrococcus
abyssi, a species of archaea that has been found living in hydrothermal
vents deep in the Pacific Ocean. The structures the protein takes on in different
functional states were then deduced from these crystals using a technique called
X-ray crystallography. Using heavy thallium ions instead of sodium ions, which are
less visible to X-rays, Wöhlert et al. found the site in the antiporter where
the transported ion binds as it moves through the membrane. The antiporter has a funnel-shaped cavity that faces inwards (into the cell) in both
acidic and alkaline conditions, although a second narrow channel that is open in
alkaline conditions is blocked in acidic conditions by small protein rearrangements.
Wöhlert et al. suggest that the differences between both structures explain how
the antiporter tunes its ability to bind to the ions it transports. Wöhlert et al. further measured the activity of the antiporter and observed that
the transport of ions was most rapid under slightly acidic conditions. In more acidic
conditions, the sodium ion cannot bind to the antiporter, and in an alkaline
environment, the sodium ions bind too strongly to the antiporter; in both cases, the
ions cannot be transported. Comparing the findings presented here with separate work that uncovers the structure
of the sodium/proton antiporter in a different species of archaea revealed very
similar structures. Related transporters are also found in mammals, and defects in
these transporters can lead to problems with the heart and kidneys. A better
understanding of the sodium/proton antiporter structure could therefore help to
develop new treatments for these conditions. DOI:http://dx.doi.org/10.7554/eLife.03579.002
Collapse
Affiliation(s)
- David Wöhlert
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ozkan Yildiz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| |
Collapse
|
25
|
Hrgovic I, Glavic Z, Kovacic Z, Mulic S, Zunic L, Hrgovic Z. Repeated administration of inhibitors for ion pumps reduce markedly tumor growth in vivo. Med Arch 2014; 68:76-8. [PMID: 24937925 PMCID: PMC4291850 DOI: 10.5455/medarh.2014.68.76-78] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Introduction: Measurements of extracellular pH show that the micro environment of malignant tumors is more acidic than that of normal cells, whereas pH does not differ appreciable in normal and malignant cells. The acid micro environment of tumors is created by the secretion of tumor factors and ATP hydrolysis in hypoxic tumor tissue. In order to survive in a low pH-environment tumor cells develop regulatory mechanisms which keep their intracellular pH stable. Two of the most important systems are the Na+/H+ ion pump and the Na-dependent HCO3-/Cl- pump of stilbenian derivatives. Material and methods: Experiments were carried out on DBA mice of both sexes at the age of 4 month. Laboratory animals were grown in our institute and supplied with food and aqua ad libitum. Results: After termination of the experiments the mean tumor diameter in the control group was 12.4±0.8mm, in group A it was 6.9±0.6mm, and in group B we measured 6.6±3.1mm. At the final day the tumor size in treated animals was twice as small as in the control group. In addition we observed the rate of survival. In the control group only 18% of the animals were still alive at day 18. Considering the rate of survival a statistically significant difference between treated and untreated animals was observed. The survival of tumor cells is dependent on the function of these ion pumps which keep their intracellular pH values constant in the setting of an acid extracellular environment. Conclusion: The activity of the ion pump is especially important at the beginning of cell division and in cell proliferation. Our in vivo experiments demonstrate that prolonged administration of intratumoral ion pump inhibitors suppresses tumor growth as well as enhances survival of tumor-bearing animals. Research of inhibitors of ion pumps and their action in tumor growth opens new perspectives into pathophysiology of malignant tumors and may create new therapeutic options.
Collapse
Affiliation(s)
- Igor Hrgovic
- Department of Dermatology, University hospital J.E. Goethe, Frankfurt, Germany
| | - Zeljko Glavic
- Department of Surgery, Hospital J.J. Strossmayera, Osijek, Croatia
| | - Zeljko Kovacic
- Department of Ophtalmology, University hospital, Split, Croatia
| | - Smaila Mulic
- Faculty of medicine, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Lejla Zunic
- Faculty of Health Sciences, University of Zenica, Zenica, Bosnia and Herzegovina
| | - Zlatko Hrgovic
- Department of Gynecology, University hospital J.J. Strossmayera, Osijek, Croatia
- Corresponding author: prof Zlatko Htgovic, MD, PhD. Department of Gynecology, University hospital J.J. Strossmayera, Osijek, Croatia. E-mail:
| |
Collapse
|