1
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Dong F, Lojko P, Bazzone A, Bernhard F, Borodina I. Transporter function characterization via continuous-exchange cell-free synthesis and solid supported membrane-based electrophysiology. Bioelectrochemistry 2024; 159:108732. [PMID: 38810322 DOI: 10.1016/j.bioelechem.2024.108732] [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: 02/28/2024] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Functional characterization of transporters is impeded by the high cost and technical challenges of current transporter assays. Thus, in this work, we developed a new characterization workflow that combines cell-free protein synthesis (CFPS) and solid supported membrane-based electrophysiology (SSME). For this, membrane protein synthesis was accomplished in a continuous exchange cell-free system (CECF) in the presence of nanodiscs. The resulting transporters expressed in nanodiscs were incorporated into proteoliposomes and assayed in the presence of different substrates using the surface electrogenic event reader. As a proof of concept, we validated this workflow to express and characterize five diverse transporters: the drug/H+-coupled antiporters EmrE and SugE, the lactose permease LacY, the Na+/H+ antiporter NhaA from Escherichia coli, and the mitochondrial carrier AAC2 from Saccharomyces cerevisiae. For all transporters kinetic parameters, such as KM, IMAX, and pH dependency, were evaluated. This robust and expedite workflow (e.g., can be executed within only five workdays) offers a convenient direct functional assessment of transporter protein activity and has the ability to facilitate applications of transporters in medical and biotechnological research.
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Affiliation(s)
- Fang Dong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Pawel Lojko
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | | | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
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2
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Zou J, Mitra K, Anees P, Oettinger D, Ramirez JR, Veetil AT, Gupta PD, Rao R, Smith JJ, Kratsios P, Krishnan Y. A DNA nanodevice for mapping sodium at single-organelle resolution. Nat Biotechnol 2024; 42:1075-1083. [PMID: 37735265 PMCID: PMC11004682 DOI: 10.1038/s41587-023-01950-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 08/15/2023] [Indexed: 09/23/2023]
Abstract
Cellular sodium ion (Na+) homeostasis is integral to organism physiology. Our current understanding of Na+ homeostasis is largely limited to Na+ transport at the plasma membrane. Organelles may also contribute to Na+ homeostasis; however, the direction of Na+ flow across organelle membranes is unknown because organellar Na+ cannot be imaged. Here we report a pH-independent, organelle-targetable, ratiometric probe that reports lumenal Na+. It is a DNA nanodevice containing a Na+-sensitive fluorophore, a reference dye and an organelle-targeting domain. By measuring Na+ at single endosome resolution in mammalian cells and Caenorhabditis elegans, we discovered that lumenal Na+ levels in each stage of the endolysosomal pathway exceed cytosolic levels and decrease as endosomes mature. Further, we find that lysosomal Na+ levels in nematodes are modulated by the Na+/H+ exchanger NHX-5 in response to salt stress. The ability to image subcellular Na+ will unveil mechanisms of Na+ homeostasis at an increased level of cellular detail.
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Affiliation(s)
- Junyi Zou
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA
| | - Koushambi Mitra
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Palapuravan Anees
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Daphne Oettinger
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA
| | - Joseph R Ramirez
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA
| | - Aneesh Tazhe Veetil
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA
| | - Priyanka Dutta Gupta
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA
| | - Rajini Rao
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jayson J Smith
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA
- Department of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Paschalis Kratsios
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA
- Department of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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3
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Wang X, Cui Y, Wang Z, Jiang H, Ma L, Li W, Yang X, Zhang J, Zhao Y, Li G. NhaA: A promising adjuvant target for colistin against resistant Escherichia coli. Int J Biol Macromol 2024; 268:131833. [PMID: 38663703 DOI: 10.1016/j.ijbiomac.2024.131833] [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: 03/03/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 04/30/2024]
Abstract
The emergence and widespread of multidrug-resistant Gram-negative bacteria have posed a severe threat to human health and environmental safety, escalating into a global medical crisis. Utilization of antibiotic adjuvants is a rapid approach to combat bacterial resistance effectively since the development of new antimicrobial agents is a formidable challenge. NhaA, driven by proton motive force, is a crucial secondary transporter on the cytoplasmic membrane of Escherichia coli. We found that 2-Aminoperimidine (2-AP), which is a specific inhibitor of NhaA, could enhance the activity of colistin against sensitive E. coli and reverse the resistance in mcr-1 positive E. coli. Mechanistic studies indicated that 2-AP induced dysfunction in cytoplasmic membrane through the suppression of NhaA, leading to metabolic inhibition and ultimately enhancing the sensitivity of E. coli to colistin. Moreover, 2-AP restored the efficacy of colistin against resistant E. coli in two animal infection models. Our findings reveal the potential of NhaA as a novel target for colistin adjuvants, providing new possibilities for the clinical application of colistin.
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Affiliation(s)
- Xuelin Wang
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Yong Cui
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zhaohui Wang
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Huilin Jiang
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Lei Ma
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Wenwen Li
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Xinyi Yang
- Beijing Key Laboratory of Antimicrobial Agents, Laboratory of Pharmacology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; Division for Medicinal Microorganisms Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing 100050, China; State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jinghai Zhang
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Yongshan Zhao
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China.
| | - Guoqing Li
- Beijing Key Laboratory of Antimicrobial Agents, Laboratory of Pharmacology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; Division for Medicinal Microorganisms Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing 100050, China; State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
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4
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Yadav A, Kumar D, Dwivedi M. Site-directed mutagenesis at the Glu78 in Ec-NhaA transporter impacting ion exchange: a biophysical study. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:193-203. [PMID: 38647543 DOI: 10.1007/s00249-024-01709-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024]
Abstract
Na+/H+ antiporters facilitate the exchange of Na+ for H+ across the cytoplasmic membrane in prokaryotic and eukaryotic cells. These transporters are crucial to maintain the homeostasis of sodium ions, consequently pH, and volume of the cells. Therefore, sodium/proton antiporters are considered promising therapeutic targets in humans. The Na+/H+ antiporter in Escherichia coli (Ec-NhaA), a prototype of cation-proton antiporter (CPA) family, transports two protons and one sodium (or Li+) in opposite direction. Previous mutagenesis experiments on Ec-NhaA have proposed Asp164, Asp163, and Asp133 amino acids with the significant implication in functional and structural integrity and create site for ion-binding. However, the mechanism and the sites for the binding of the two protons remain unknown and controversial which could be critical for pH regulation. In this study, we have explored the role of Glu78 in the regulation of pH by Ec-NhaA. Although we have created various mutants, E78C has shown a considerable effect on the stoichiometry of NhaA and presented comparable phenotypes. The ITC experiment has shown the binding of ~ 5 protons in response to the transport of one lithium ion. The phenotype analysis on selective medium showed a significant expression compared to WT Ec-NhaA. This represents the importance of Glu78 in transporting the H+ across the membrane where a single mutation with Cys amino acid alters the number of H+ significantly maintaining the activity of the protein.
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Affiliation(s)
- Anuradha Yadav
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Dinesh Kumar
- Center of Biomedical Research, SGPGIMS Campus, Lucknow, 226014, India
| | - Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India.
- Research Cell, Amity University Uttar Pradesh, Lucknow, 226028, India.
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5
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Drew D, Boudker O. Ion and lipid orchestration of secondary active transport. Nature 2024; 626:963-974. [PMID: 38418916 DOI: 10.1038/s41586-024-07062-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024]
Abstract
Transporting small molecules across cell membranes is an essential process in cell physiology. Many structurally diverse, secondary active transporters harness transmembrane electrochemical gradients of ions to power the uptake or efflux of nutrients, signalling molecules, drugs and other ions across cell membranes. Transporters reside in lipid bilayers on the interface between two aqueous compartments, where they are energized and regulated by symported, antiported and allosteric ions on both sides of the membrane and the membrane bilayer itself. Here we outline the mechanisms by which transporters couple ion and solute fluxes and discuss how structural and mechanistic variations enable them to meet specific physiological needs and adapt to environmental conditions. We then consider how general bilayer properties and specific lipid binding modulate transporter activity. Together, ion gradients and lipid properties ensure the effective transport, regulation and distribution of small molecules across cell membranes.
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Affiliation(s)
- David Drew
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY, USA.
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6
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Bailoni E, Partipilo M, Coenradij J, Grundel DAJ, Slotboom DJ, Poolman B. Minimal Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane Perspective. ACS Synth Biol 2023; 12:922-946. [PMID: 37027340 PMCID: PMC10127287 DOI: 10.1021/acssynbio.3c00062] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Indexed: 04/08/2023]
Abstract
Life-like systems need to maintain a basal metabolism, which includes importing a variety of building blocks required for macromolecule synthesis, exporting dead-end products, and recycling cofactors and metabolic intermediates, while maintaining steady internal physical and chemical conditions (physicochemical homeostasis). A compartment, such as a unilamellar vesicle, functionalized with membrane-embedded transport proteins and metabolic enzymes encapsulated in the lumen meets these requirements. Here, we identify four modules designed for a minimal metabolism in a synthetic cell with a lipid bilayer boundary: energy provision and conversion, physicochemical homeostasis, metabolite transport, and membrane expansion. We review design strategies that can be used to fulfill these functions with a focus on the lipid and membrane protein composition of a cell. We compare our bottom-up design with the equivalent essential modules of JCVI-syn3a, a top-down genome-minimized living cell with a size comparable to that of large unilamellar vesicles. Finally, we discuss the bottlenecks related to the insertion of a complex mixture of membrane proteins into lipid bilayers and provide a semiquantitative estimate of the relative surface area and lipid-to-protein mass ratios (i.e., the minimal number of membrane proteins) that are required for the construction of a synthetic cell.
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Affiliation(s)
- Eleonora Bailoni
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Michele Partipilo
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Jelmer Coenradij
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Douwe A. J. Grundel
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Dirk J. Slotboom
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
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7
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Li Y, Li H, Gao J, Niu B, Wang H, Wang W. Visualizing the Intermittent Gating of Na + /H + Antiporters in Single Native Bioluminescent Bacteria. Angew Chem Int Ed Engl 2023; 62:e202215800. [PMID: 36562656 DOI: 10.1002/anie.202215800] [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: 10/27/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/24/2022]
Abstract
While the intermittent gating of ion channels has been well studied for decades, dynamics of the action of secondary transporters, another major pathway for ion transmembrane transports, remains largely unexplored in living cells. Herein, intermittent blinking of the spontaneous bioluminescence (BL) from single native bacteria, P. phosphoreum, was reported, investigated and attributed to the intermittent gating of sodium/proton antiporters (NhaA) between the active and inactive conformations. Each gating event caused the rapid depolarization and recovery of membrane potential within several seconds, accompanying with the apparent BL blinking due to the transient inhibitions on the activity of the respiratory chain. Temperature-dependent measurements further obtained an activation energy barrier of the conformational change of 20.3 kJ mol-1 .
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Affiliation(s)
- Yaohua Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
| | - Haoran Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
| | - Jia Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
| | - Ben Niu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
| | - Huan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
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8
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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.
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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
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9
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Prokaryotic Na+/H+ Exchangers—Transport Mechanism and Essential Residues. Int J Mol Sci 2022; 23:ijms23169156. [PMID: 36012428 PMCID: PMC9408914 DOI: 10.3390/ijms23169156] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
Na+/H+ exchangers are essential for Na+ and pH homeostasis in all organisms. Human Na+/H+ exchangers are of high medical interest, and insights into their structure and function are aided by the investigation of prokaryotic homologues. Most prokaryotic Na+/H+ exchangers belong to either the Cation/Proton Antiporter (CPA) superfamily, the Ion Transport (IT) superfamily, or the Na+-translocating Mrp transporter superfamily. Several structures have been solved so far for CPA and Mrp members, but none for the IT members. NhaA from E. coli has served as the prototype of Na+/H+ exchangers due to the high amount of structural and functional data available. Recent structures from other CPA exchangers, together with diverse functional information, have allowed elucidation of some common working principles shared by Na+/H+ exchangers from different families, such as the type of residues involved in the substrate binding and even a simple mechanism sufficient to explain the pH regulation in the CPA and IT superfamilies. Here, we review several aspects of prokaryotic Na+/H+ exchanger structure and function, discussing the similarities and differences between different transporters, with a focus on the CPA and IT exchangers. We also discuss the proposed transport mechanisms for Na+/H+ exchangers that explain their highly pH-regulated activity profile.
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10
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Lv P, Li Y, Wang R, Zhang Y, Wang W, Liu Y, Shang Y, Su D, Wang W, Yang C. The pH sensor and ion binding of NhaD Na
+
/H
+
antiporter from IT superfamily. Mol Microbiol 2022; 118:244-257. [DOI: 10.1111/mmi.14965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Peiwen Lv
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Yaru Li
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Ruimin Wang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Ye Zhang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Wenkai Wang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Yuanxiang Liu
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Yan Shang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Dandan Su
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Wei Wang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Chunyu Yang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
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11
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Beckstein O, Naughton F. General principles of secondary active transporter function. BIOPHYSICS REVIEWS 2022; 3:011307. [PMID: 35434715 PMCID: PMC8984959 DOI: 10.1063/5.0047967] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/23/2022] [Indexed: 04/13/2023]
Abstract
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported substrate. Secondary active transporters couple the spontaneous influx of a "driving" ion such as Na+ or H+ to the flux of the substrate. The thermodynamics of such cyclical non-equilibrium systems are well understood, and recent work has focused on the molecular mechanism of secondary active transport. The fact that these transporters change their conformation between an inward-facing and outward-facing conformation in a cyclical fashion, called the alternating access model, is broadly recognized as the molecular framework in which to describe transporter function. However, only with the advent of high resolution crystal structures and detailed computer simulations, it has become possible to recognize common molecular-level principles between disparate transporter families. Inverted repeat symmetry in secondary active transporters has shed light onto how protein structures can encode a bi-stable two-state system. Based on structural data, three broad classes of alternating access transitions have been described as rocker-switch, rocking-bundle, and elevator mechanisms. More detailed analysis indicates that transporters can be understood as gated pores with at least two coupled gates. These gates are not just a convenient cartoon element to illustrate a putative mechanism but map to distinct parts of the transporter protein. Enumerating all distinct gate states naturally includes occluded states in the alternating access picture and also suggests what kind of protein conformations might be observable. By connecting the possible conformational states and ion/substrate bound states in a kinetic model, a unified picture emerges in which the symporter, antiporter, and uniporter functions are extremes in a continuum of functionality. As usual with biological systems, few principles and rules are absolute and exceptions are discussed as well as how biological complexity may be integrated in quantitative kinetic models that may provide a bridge from the structure to function.
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Affiliation(s)
- Oliver Beckstein
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
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12
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Köhler S, Fragneto G, Alcaraz JP, Nelson A, Martin DK, Maccarini M. Nanostructural Characterization of Cardiolipin-Containing Tethered Lipid Bilayers Adsorbed on Gold and Silicon Substrates for Protein Incorporation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:8908-8923. [PMID: 34286589 DOI: 10.1021/acs.langmuir.1c00119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A key to the development of lipid membrane-based devices is a fundamental understanding of how the molecular structure of the lipid bilayer membrane is influenced by the type of lipids used to build the membrane. This is particularly important when membrane proteins are included in these devices since the precise lipid environment affects the ability to incorporate membrane proteins and their functionality. Here, we used neutron reflectometry to investigate the structure of tethered bilayer lipid membranes and to characterize the incorporation of the NhaA sodium proton exchanger in the bilayer. The lipid membranes were composed of two lipids, dioleoyl phosphatidylcholine and cardiolipin, and were adsorbed on gold and silicon substrates using two different tethering architectures based on functionalized oligoethylene glycol molecules of different lengths. In all of the investigated samples, the addition of cardiolipin caused distinct structural rearrangement including crowding of ethylene glycol groups of the tethering molecules in the inner head region and a thinning of the lipid tail region. The incorporation of NhaA in the tethered bilayers following two different protocols is quantified, and the way protein incorporation modulates the structural properties of these membranes is detailed.
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Affiliation(s)
- Sebastian Köhler
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC/SyNaBi, 38000 Grenoble, France
- Institut Laue-Langevin, 38042 Grenoble, France
| | | | - Jean-Pierre Alcaraz
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC/SyNaBi, 38000 Grenoble, France
| | - Andrew Nelson
- ANSTO-Sydney, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Donald K Martin
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC/SyNaBi, 38000 Grenoble, France
| | - Marco Maccarini
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC/SyNaBi, 38000 Grenoble, France
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13
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Quick M, Dwivedi M, Padan E. Insight into the direct interaction of Na + with NhaA and mechanistic implications. Sci Rep 2021; 11:7045. [PMID: 33782459 PMCID: PMC8007835 DOI: 10.1038/s41598-021-86318-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/05/2021] [Indexed: 11/21/2022] Open
Abstract
Na+/H+ antiporters comprise a family of membrane proteins evolutionarily conserved in all kingdoms of life that are essential in cellular ion homeostasis. While several human homologues have long been drug targets, NhaA of Escherichia coli has become the paradigm for this class of secondary active transporters as NhaA crystals provided insight in the structure of this molecular machine. However, structural data revealing the composition of the binding site for Na+ (or its surrogate Li+) is missing, representing a bottleneck in our understanding of the correlation between the structure and function of NhaA. Here, by adapting the scintillation proximity assay (SPA) for direct determination of Na+ binding to NhaA, we revealed that (i) NhaA is well adapted as the main antiporter for Na+ homeostasis in Escherichia coli and possibly in other bacteria as the cytoplasmic Na+ concentration is similar to the Na+ binding affinity of NhaA, (ii) experimental conditions affect NhaA-mediated cation binding, (iii) in addition to Na+ and Li+, the halide Tl+ interacts with NhaA, (iv) whereas acidic pH inhibits maximum binding of Na+ to NhaA, partial Na+ binding by NhaA is independent of the pH, an important novel insight into the effect of pH on NhaA cation binding.
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Affiliation(s)
- Matthias Quick
- Department of Psychiatry and Center for Molecular Recognition, Columbia University Vagelos College of Physicians and Surgeons, and New York State Psychiatric Institute, New York, NY, 10032, USA.
| | - Manish Dwivedi
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel.,Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Etana Padan
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel.
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14
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He N, Fang C, Qiu Z, Bao J. Increasing sodium lactate production by enhancement of Na + transmembrane transportation in Pediococcus acidilactici. BIORESOURCE TECHNOLOGY 2021; 323:124562. [PMID: 33360114 DOI: 10.1016/j.biortech.2020.124562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Fermentative production of sodium lactate generally is a low efficient process because of the high Na+ osmatic stress on lactic acid bacterium cells. In this study, the homogeneous genes encoding Na+/H+ antiporters were screened and overexpressed in Pediococcus acidilactici for the enhancement of Na+ transmembrane transportation. The function of the gene RS02775 was identified and its overexpressing in P. acidilactici resulted in the significantly improved sodium lactate production. The recombinant not only accelerated the sugar consumption, but also achieved the record high titer of sodium lactate by 121.1 g/L using pure sugars and 132.4 g/L using wheat straw. The transcription analysis shows that the overexpression of Na+/H+ antiporter significantly upregulated the transcription of the sugar phosphorylation genes of P. acidilactici under high Na+ stress. This study provides an effective method for high titer production of sodium lactate using both pure sugars and lignocellulose feedstocks.
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Affiliation(s)
- Niling He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Chun Fang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhongyang Qiu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, 111 West Changjiang Road, Huaian, Jiangsu 223300, China
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
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15
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Huang Y, Henderson JA, Shen J. Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins. Methods Mol Biol 2021; 2302:275-287. [PMID: 33877633 PMCID: PMC8062021 DOI: 10.1007/978-1-0716-1394-8_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many membrane channels, transporters, and receptors utilize a pH gradient or proton coupling to drive functionally relevant conformational transitions. Conventional molecular dynamics simulations employ fixed protonation states, thus neglecting the coupling between protonation and conformational equilibria. Here we describe the membrane-enabled hybrid-solvent continuous constant pH molecular dynamics method for capturing atomic details of proton-coupled conformational dynamics of transmembrane proteins. Example protocols from our recent application studies of proton channels and ion/substrate transporters are discussed.
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Affiliation(s)
- Yandong Huang
- College of Computer Engineering, Jimei University, Xiamen, Fujian, China
| | | | - Jana Shen
- University of Maryland School of Pharmacy, Baltimore, MD, USA.
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16
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Dwivedi M. Site-directed mutations reflecting functional and structural properties of Ec-NhaA. Biochimie 2020; 180:79-89. [PMID: 33129932 DOI: 10.1016/j.biochi.2020.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 11/20/2022]
Abstract
NhaA antiporters are secondary integral membrane protein critical for maintaining the Na+/H+ cell homeostasis, as a result, they regulate fundamental processes like cell volume and intracellular pH. Exploration of the structural and functional properties can assist to make them effective human drug targets and mechanisms of salt-resistance in plants. NhaA proteins are integrated into cytoplasmic and intracellular membranes, transport 2H+/Na + across the membrane by the canonical alternating access mechanism. There are mutagenesis studies have done on Ec-NhaA predicting residues crucial for function and structure. The unique NhaA structural fold is formed in the middle of the membrane by two transmembrane segments (TMs), TM IV and XI which cross each other creating a delicate electrostatically balanced environment for the binding of Na+/H+. Previously, Asp164, Asp163 and Asp133 residues have been proposed as crucial for Na+/Li + binding on the based on crystal structure and mutation-based studies. However, the pathway and the binding sites for the two protons are still elusive and debatable. This review will provide comprehensive details on various mutations constructed in Ec-NhaA by different research groups using site-directed or random mutagenesis techniques. The selected residues for mutations are located on the sites which are more suspected to have a crucial role in function and structure on NhaA. This information on the single platform would accelerate further studies on the structure-function relationship on NhaA as well as will facilitate to predict the role of Na+/H+ antiporters in human diseases.
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Affiliation(s)
- Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Gomtinagar Ext., Lucknow, 226028, India.
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17
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Alternative proton-binding site and long-distance coupling in Escherichia coli sodium-proton antiporter NhaA. Proc Natl Acad Sci U S A 2020; 117:25517-25522. [PMID: 32973095 DOI: 10.1073/pnas.2005467117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli NhaA is a prototypical sodium-proton antiporter responsible for maintaining cellular ion and volume homeostasis by exchanging two protons for one sodium ion; despite two decades of research, the transport mechanism of NhaA remains poorly understood. Recent crystal structure and computational studies suggested Lys300 as a second proton-binding site; however, functional measurements of several K300 mutants demonstrated electrogenic transport, thereby casting doubt on the role of Lys300. To address the controversy, we carried out state-of-the-art continuous constant pH molecular dynamics simulations of NhaA mutants K300A, K300R, K300Q/D163N, and K300Q/D163N/D133A. Simulations suggested that K300 mutants maintain the electrogenic transport by utilizing an alternative proton-binding residue Asp133. Surprisingly, while Asp133 is solely responsible for binding the second proton in K300R, Asp133 and Asp163 jointly bind the second proton in K300A, and Asp133 and Asp164 jointly bind two protons in K300Q/D163N. Intriguingly, the coupling between Asp133 and Asp163 or Asp164 is enabled through the proton-coupled hydrogen-bonding network at the flexible intersection of two disrupted helices. These data resolve the controversy and highlight the intricacy of the compensatory transport mechanism of NhaA mutants. Alternative proton-binding site and proton sharing between distant aspartates may represent important general mechanisms of proton-coupled transport in secondary active transporters.
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18
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Markones M, Fippel A, Kaiser M, Drechsler C, Hunte C, Heerklotz H. Stairway to Asymmetry: Five Steps to Lipid-Asymmetric Proteoliposomes. Biophys J 2020; 118:294-302. [PMID: 31843262 PMCID: PMC6976795 DOI: 10.1016/j.bpj.2019.10.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/09/2019] [Accepted: 10/28/2019] [Indexed: 12/15/2022] Open
Abstract
Membrane proteins are embedded in a complex lipid environment that influences their structure and function. One key feature of nearly all biological membranes is a distinct lipid asymmetry. However, the influence of membrane asymmetry on proteins is poorly understood, and novel asymmetric proteoliposome systems are beneficial. To our knowledge, we present the first study on a multispanning protein incorporated in large unilamellar liposomes showing a stable lipid asymmetry. These asymmetric proteoliposomes contain the Na+/H+ antiporter NhaA from Salmonella Typhimurium. Asymmetry was introduced by partial, outside-only exchange of anionic phosphatidylglycerol (PG), mimicking this key asymmetry of bacterial membranes. Outer-leaflet and total fractions of PG were determined via ζ-potential (ζ) measurements after lipid exchange and after scrambling of asymmetry. ζ-Values were in good agreement with exclusive outside localization of PG. The electrogenic Na+/H+ antiporter was active in asymmetric liposomes, and it can be concluded that reconstitution and generation of asymmetry were successful. Lipid asymmetry was stable for more than 7 days at 23°C and thus enabled characterization of the Na+/H+ antiporter in an asymmetric lipid environment. We present and validate a simple five-step protocol that addresses key steps to be taken and pitfalls to be avoided for the preparation of asymmetric proteoliposomes: 1) optimization of desired lipid composition, 2) detergent-mediated protein reconstitution with subsequent detergent removal, 3) generation of lipid asymmetry by partial exchange of outer-leaflet lipid, 4) verification of lipid asymmetry and stability, and 5) determination of protein activity in the asymmetric lipid environment. This work offers guidance in designing asymmetric proteoliposomes that will enable researchers to compare functional and structural properties of membrane proteins in symmetric and asymmetric lipid environments.
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Affiliation(s)
- Marie Markones
- Institute for Pharmaceutical Sciences, University of Freiburg, Breisgau, Germany; Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Breisgau, Germany; HSGS Hermann Staudinger Graduate School, University of Freiburg, Breisgau, Germany.
| | - Anika Fippel
- Institute for Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Breisgau, Germany; HSGS Hermann Staudinger Graduate School, University of Freiburg, Breisgau, Germany
| | - Michael Kaiser
- Institute for Pharmaceutical Sciences, University of Freiburg, Breisgau, Germany; HSGS Hermann Staudinger Graduate School, University of Freiburg, Breisgau, Germany
| | - Carina Drechsler
- Institute for Pharmaceutical Sciences, University of Freiburg, Breisgau, Germany; Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Breisgau, Germany
| | - Carola Hunte
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Breisgau, Germany; Institute for Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Breisgau, Germany
| | - Heiko Heerklotz
- Institute for Pharmaceutical Sciences, University of Freiburg, Breisgau, Germany; Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Breisgau, Germany; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
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19
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Abstract
Here, we present a protocol for the functional characterization of the H+-coupled human peptide transporter PepT1 and sufficient notes to transfer the protocol to the Na+-coupled sugar transporter SGLT1, the organic cation transporter OCT2, the Na+/Ca2+ exchanger NCX, and the neuronal glutamate transporter EAAT3.The assay was developed for the commercially available SURFE2R N1 instrument (Nanion Technologies GmbH) which applies solid supported membrane (SSM)-based electrophysiology. This technique is widely used for the functional characterization of membrane transporters with more than 100 different transporters characterized so far. The technique is cost-effective, easy to use, and capable of high-throughput measurements.SSM-based electrophysiology utilizes SSM-coated gold sensors to physically adsorb membrane vesicles containing the protein of interest. A fast solution exchange provides the substrate and activates transport. For the measurement of PepT1 activity, we applied a peptide concentration jump to activate H+/peptide symport. Proton influx charges the sensor. A capacitive current is measured reflecting the transport activity of PepT1 . Multiple measurements on the same sensor allow for comparison of transport activity under different conditions. Here, we determine EC50 for PepT1-mediated glycylglycine transport and perform an inhibition experiment using the specific peptide inhibitor Lys[Z(NO2)]-Val.
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20
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Mutation of two key aspartate residues alters stoichiometry of the NhaB Na +/H + exchanger from Klebsiella pneumoniae. Sci Rep 2019; 9:15390. [PMID: 31659210 PMCID: PMC6817889 DOI: 10.1038/s41598-019-51887-2] [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: 09/05/2019] [Accepted: 10/08/2019] [Indexed: 12/02/2022] Open
Abstract
Bacterial NhaB Na+/H+ exchangers belonging to the Ion Transporter superfamily are poorly characterized in contrast to Na+/H+ exchangers of the Cation Proton Antiporter superfamily which have NhaA from Escherichia coli as a prominent member. For a more detailed understanding of the intricacies of the exchanger’s transport mechanism, mutational studies are essential. Therefore, we mutated two protonatable residues present in the putative transmembrane region of NhaB from Klebsiella pneumoniae (KpNhaB), which could serve as substrate binding sites, Asp146 and Asp404, to either glutamate or alanine and analyzed transport function and stability of the mutants using electrophysiological and fluorimetric techniques. While mutation of either Asp residue to Glu only had slight to moderate effects on the transport activity of the exchanger, the mutations D404A and D146A, in particular, had more profound effects on the transport function. Furthermore, a double mutant, D146A/D404A, exhibited a remarkable behavior at alkaline pH, where recorded electrical currents changed polarity, showing steady-state transport with a stoichiometry of H+:Na+ < 1, as opposed to the H+:Na+ > 1 stoichiometry of the WT. Thus, we showed that Asp146 and Asp404 are part of the substrate binding site(s) of KpNhaB and engineered a Na+/H+ exchanger with a variable stoichiometry.
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21
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Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting. Nat Commun 2019; 10:1742. [PMID: 30988359 PMCID: PMC6465308 DOI: 10.1038/s41467-019-09739-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 03/26/2019] [Indexed: 11/26/2022] Open
Abstract
Na+/H+ antiporters exchange sodium ions and protons on opposite sides of lipid membranes. The electroneutral Na+/H+ antiporter NhaP from archaea Pyrococcus abyssi (PaNhaP) is a functional homolog of the human Na+/H+ exchanger NHE1, which is an important drug target. Here we resolve the Na+ and H+ transport cycle of PaNhaP by transition-path sampling. The resulting molecular dynamics trajectories of repeated ion transport events proceed without bias force, and overcome the enormous time-scale gap between seconds-scale ion exchange and microseconds simulations. The simulations reveal a hydrophobic gate to the extracellular side that opens and closes in response to the transporter domain motion. Weakening the gate by mutagenesis makes the transporter faster, suggesting that the gate balances competing demands of fidelity and efficiency. Transition-path sampling and a committor-based reaction coordinate optimization identify the essential motions and interactions that realize conformational alternation between the two access states in transporter function. Cation-proton antiporters mediate selective ion exchange across cellular membranes to control pH, salt concentration and cell volume. Here the authors present a transition-path sampling method that overcomes the timescale gap between simulations (µs) and transport processes (s), which allows them to resolve the Na+ and H+ transport cycle of the Na+/H+ antiporter NhaP from Pyrococcus abyssi.
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22
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Dupree DE, Price RE, Burgess BA, Andress EL, Breidt F. Effects of Sodium Chloride or Calcium Chloride Concentration on the Growth and Survival of Escherichia coli O157:H7 in Model Vegetable Fermentations. J Food Prot 2019; 82:570-578. [PMID: 30907663 DOI: 10.4315/0362-028x.jfp-18-468] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
HIGHLIGHTS NaCl and CaCl2 concentrations affected LAB and STEC strains differently. Growth rates at 6% NaCl were reduced for STEC more than LAB in vegetable broth. Extent of growth was reduced for STEC versus LAB for most vegetable fermentations. Death rates were minimally affected by salt type or concentration with lactic acid. Correlations between salt and STEC die-off were inconsistent for fermentation.
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Affiliation(s)
- Dorothy E Dupree
- 1 Department of Foods and Nutrition, University of Georgia, 305 Sanford Drive, Athens, Georgia 30602
| | - Robert E Price
- 2 U.S. Department of Agriculture, Agricultural Research Service, Food Science Research Unit, 322 Schaub Hall, Box 7624, North Carolina State University, Raleigh, North Carolina 27695
| | - Breanne A Burgess
- 3 Department of Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Box 7622, Raleigh, North Carolina 27695, USA
| | - Elizabeth L Andress
- 1 Department of Foods and Nutrition, University of Georgia, 305 Sanford Drive, Athens, Georgia 30602
| | - Frederick Breidt
- 2 U.S. Department of Agriculture, Agricultural Research Service, Food Science Research Unit, 322 Schaub Hall, Box 7624, North Carolina State University, Raleigh, North Carolina 27695
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23
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Patiño-Ruiz M, Dwivedi M, Călinescu O, Karabel M, Padan E, Fendler K. Replacement of Lys-300 with a glutamine in the NhaA Na +/H + antiporter of Escherichia coli yields a functional electrogenic transporter. J Biol Chem 2019; 294:246-256. [PMID: 30409911 PMCID: PMC6322889 DOI: 10.1074/jbc.ra118.004903] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/06/2018] [Indexed: 01/28/2023] Open
Abstract
Much of the research on Na+/H+ exchange has been done in prokaryotic models, mainly on the NhaA Na+/H+-exchanger from Escherichia coli (EcNhaA). Two conserved aspartate residues, Asp-163 and Asp-164, are essential for transport and are candidates for possible binding sites for the two H+ that are exchanged for one Na+ to make the overall transport process electrogenic. More recently, a proposed mechanism of transport for EcNhaA has suggested direct binding of one of the transported H+ to the conserved Lys-300 residue, a salt bridge partner of Asp-163. This contention is supported by a study reporting that substitution of the equivalent residue, Lys-305, of a related Na+/H+ antiporter, NapA from Thermus thermophilus, renders the transporter electroneutral. In this work, we sought to establish whether the Lys-300 residue and its partner Asp-163 are essential for the electrogenicity of EcNhaA. To that end, we replaced Lys-300 with Gln, either alone or together with the simultaneous substitution of Asp-163 with Asn, and characterized these transporter variants in electrophysiological experiments combined with H+ transport measurements and stability analysis. We found that K300Q EcNhaA can still support electrogenic Na+/H+ antiport in EcNhaA, but has reduced thermal stability. A parallel electrophysiological investigation of the K305Q variant of TtNapA revealed that it is also electrogenic. Furthermore, replacement of both salt bridge partners in the ion-binding site of EcNhaA produced an electrogenic variant (D163N/K300Q). Our findings indicate that alternative mechanisms sustain EcNhaA activity in the absence of canonical ion-binding residues and that the conserved lysines confer structural stability.
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Affiliation(s)
- Miyer Patiño-Ruiz
- Max-Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Manish Dwivedi
- Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Octavian Călinescu
- Max-Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Department of Biophysics, "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Mehmet Karabel
- Max-Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Etana Padan
- Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Klaus Fendler
- Max-Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.
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24
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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.
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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.
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25
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Hollingsworth SA, Dror RO. Molecular Dynamics Simulation for All. Neuron 2018; 99:1129-1143. [PMID: 30236283 PMCID: PMC6209097 DOI: 10.1016/j.neuron.2018.08.011] [Citation(s) in RCA: 993] [Impact Index Per Article: 165.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/17/2018] [Accepted: 08/07/2018] [Indexed: 12/12/2022]
Abstract
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery has expanded dramatically in recent years. These simulations capture the behavior of proteins and other biomolecules in full atomic detail and at very fine temporal resolution. Major improvements in simulation speed, accuracy, and accessibility, together with the proliferation of experimental structural data, have increased the appeal of biomolecular simulation to experimentalists-a trend particularly noticeable in, although certainly not limited to, neuroscience. Simulations have proven valuable in deciphering functional mechanisms of proteins and other biomolecules, in uncovering the structural basis for disease, and in the design and optimization of small molecules, peptides, and proteins. Here we describe, in practical terms, the types of information MD simulations can provide and the ways in which they typically motivate further experimental work.
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Affiliation(s)
- Scott A Hollingsworth
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.
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26
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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.
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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
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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]
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28
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Bazzone A, Zabadne AJ, Salisowski A, Madej MG, Fendler K. A Loose Relationship: Incomplete H +/Sugar Coupling in the MFS Sugar Transporter GlcP. Biophys J 2018; 113:2736-2749. [PMID: 29262366 PMCID: PMC5770559 DOI: 10.1016/j.bpj.2017.09.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/11/2017] [Accepted: 09/29/2017] [Indexed: 11/26/2022] Open
Abstract
The glucose transporter from Staphylococcus epidermidis, GlcPSe, is a homolog of the human GLUT sugar transporters of the major facilitator superfamily. Together with the xylose transporter from Escherichia coli, XylEEc, the other prominent prokaryotic GLUT homolog, GlcPSe, is equipped with a conserved proton-binding site arguing for an electrogenic transport mode. However, the electrophysiological analysis of GlcPSe presented here reveals important differences between the two GLUT homologs. GlcPSe, unlike XylEEc, does not perform steady-state electrogenic transport at symmetrical pH conditions. Furthermore, when a pH gradient is applied, partially uncoupled transport modes can be generated. In contrast to other bacterial sugar transporters analyzed so far, in GlcPSe sugar binding, translocation and release are also accomplished by the deprotonated transporter. Based on these experimental results, we conclude that coupling of sugar and H+ transport is incomplete in GlcPSe. To verify the viability of the observed partially coupled GlcPSe transport modes, we propose a universal eight-state kinetic model in which any degree of coupling is realized and H+/sugar symport represents only a specific instance. Furthermore, using sequence comparison with strictly coupled XylEEc and similar sugar transporters, we identify an additional charged residue that may be essential for effective H+/sugar symport.
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Affiliation(s)
- Andre Bazzone
- Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | | | | | - M Gregor Madej
- Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Klaus Fendler
- Max Planck Institute of Biophysics, Frankfurt/Main, Germany.
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29
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Dibrov P, Dibrov E, Pierce GN. Na+-NQR (Na+-translocating NADH:ubiquinone oxidoreductase) as a novel target for antibiotics. FEMS Microbiol Rev 2017; 41:653-671. [PMID: 28961953 DOI: 10.1093/femsre/fux032] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/17/2017] [Indexed: 01/08/2023] Open
Abstract
The recent breakthrough in structural studies on Na+-translocating NADH:ubiquinone oxidoreductase (Na+-NQR) from the human pathogen Vibrio cholerae creates a perspective for the systematic design of inhibitors for this unique enzyme, which is the major Na+ pump in aerobic pathogens. Widespread distribution of Na+-NQR among pathogenic species, its key role in energy metabolism, its relation to virulence in different species as well as its absence in eukaryotic cells makes this enzyme especially attractive as a target for prospective antibiotics. In this review, the major biochemical, physiological and, especially, the pharmacological aspects of Na+-NQR are discussed to assess its 'target potential' for drug development. A comparison to other primary bacterial Na+ pumps supports the contention that NQR is a first rate prospective target for a new generation of antimicrobials. A new, narrowly targeted furanone inhibitor of NQR designed in our group is presented as a molecular platform for the development of anti-NQR remedies.
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Affiliation(s)
- Pavel Dibrov
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Elena Dibrov
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St. Boniface Hospital, Winnipeg, Canada.,Department of Physiology and Pathophysiology, Colleges of Medicine and Pharmacy, Faculty of Health Sciences, Winnipeg, Canada
| | - Grant N Pierce
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St. Boniface Hospital, Winnipeg, Canada.,Department of Physiology and Pathophysiology, Colleges of Medicine and Pharmacy, Faculty of Health Sciences, Winnipeg, Canada
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30
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Ligand-induced conformational dynamics of the Escherichia coli Na +/H + antiporter NhaA revealed by hydrogen/deuterium exchange mass spectrometry. Proc Natl Acad Sci U S A 2017; 114:11691-11696. [PMID: 29078272 DOI: 10.1073/pnas.1703422114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Na+/H+ antiporters comprise a family of membrane proteins evolutionarily conserved in all kingdoms of life and play an essential role in cellular ion homeostasis. The NhaA crystal structure of Escherichia coli has become the paradigm for this class of secondary active transporters. However, structural data are only available at low pH, where NhaA is inactive. Here, we adapted hydrogen/deuterium-exchange mass spectrometry (HDX-MS) to analyze conformational changes in NhaA upon Li+ binding at physiological pH. Our analysis revealed a global conformational change in NhaA with two sets of movements around an immobile binding site. Based on these results, we propose a model for the ion translocation mechanism that explains previously controversial data for this antiporter. Furthermore, these findings contribute to our understanding of related human transporters that have been linked to various diseases.
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31
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Patiño-Ruiz M, Ganea C, Fendler K, Călinescu O. Competition is the basis of the transport mechanism of the NhaB Na+/H+ exchanger from Klebsiella pneumoniae. PLoS One 2017; 12:e0182293. [PMID: 28750048 PMCID: PMC5531510 DOI: 10.1371/journal.pone.0182293] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/14/2017] [Indexed: 11/18/2022] Open
Abstract
Na+/H+ exchange is essential for survival of all organisms, having a role in the regulation of the intracellular Na+ concentration, pH and cell volume. Furthermore, Na+/H+ exchangers were shown to be involved in the virulence of the bacterium Yersinia pestis, indicating they might be potential targets for novel antibiotic treatments. The model system for Na+/H+ exchangers is the NhaA transporter from Escherichia coli, EcNhaA. Therefore, the general transport mechanism of NhaA exchangers is currently well characterized. However, much less is known about NhaB exchangers, with only a limited number of studies available. The pathogen Klebsiella pneumoniae, which is a major source of nosocomial infection, possesses three electrogenic Na+/H+ exchangers, KpNhaA1, KpNhaA2 and KpNhaB, none of which have been previously investigated. Our aim in this study was to functionally characterize KpNhaB using solid supported membrane-based electrophysiology as the main investigation technique, and thus provide the first electrophysiological investigation of an NhaB Na+/H+ exchanger. We found that NhaB can be described by the same competition-based mechanism that was shown to be valid for electrogenic NhaA and NapA, and for electroneutral NhaP Na+/H+ exchangers. For comparison we also characterized the activity of KpNhaA1 and KpNhaA2 and found that the three exchangers have complementary activity profiles, which is likely a survival advantage for K. pneumoniae when faced with environments of different salinity and pH. This underlines their importance as potential antibiotic drug targets.
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Affiliation(s)
- Miyer Patiño-Ruiz
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Constanța Ganea
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Department of Biophysics, “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
| | - Klaus Fendler
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Octavian Călinescu
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Department of Biophysics, “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
- * E-mail:
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32
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Abstract
Functional characterization of transport proteins using conventional electrophysiology can be challenging, especially for low turnover transporters or transporters from bacteria and intracellular compartments. Solid-supported membrane (SSM)-based electrophysiology is a sensitive and cell-free assay technique for the characterization of electrogenic membrane proteins. Purified proteins reconstituted into proteoliposomes or membrane vesicles from cell culture or native tissues are adsorbed to the sensor holding an SSM. A substrate or a ligand is applied via rapid solution exchange. The electrogenic transporter activity charges the sensor, which is recorded as a transient current. The high stability of the SSM allows cumulative measurements on the same sensor using different experimental conditions. This allows the determination of kinetic properties including EC50, IC50, Km, KD, and rate constants of electrogenic reactions. About 100 different transporters have been measured so far using this technique, among them symporters, exchangers, uniporters, ATP-, redox-, and light-driven ion pumps, as well as receptors and ion channels. Different instruments apply this technique: the laboratory setups use a closed flow-through arrangement, while the commercially available SURFE2R N1 resembles a pipetting robot. For drug screening purposes high-throughput systems, such as the SURFE2R 96SE enable the simultaneous measurement of up to 96 sensors.
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Affiliation(s)
- Andre Bazzone
- Max Planck Institute of Biophysics, Frankfurt/Main, Germany; Nanion Technologies GmbH, Munich, Germany
| | | | - Klaus Fendler
- Max Planck Institute of Biophysics, Frankfurt/Main, Germany.
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33
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Functional Interaction between the N and C Termini of NhaD Antiporters from Halomonas sp. Strain Y2. J Bacteriol 2017; 199:JB.00302-17. [PMID: 28559301 DOI: 10.1128/jb.00302-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 05/23/2017] [Indexed: 02/04/2023] Open
Abstract
Two NhaD-type antiporters, NhaD1 and NhaD2, from the halotolerant and alkaliphilic Halomonas sp. strain Y2, exhibit different physiological functions in regard to Na+ and Li+ resistance, although they share high sequence identity. In the present study, the truncation of an additional 4 C-terminal residues from NhaD2 or an exchange of 39 N-terminal residues between these proteins resulted in the complete loss of antiporter activity. Interestingly, combining 39 N-terminal residues and 7 C-terminal residues of NhaD2 (N39D2-C7) partially recovered the activity for Na+ and Li+ expulsion, as well as complementary growth following exposure to 300 mM Na+ and 100 mM Li+ stress. The recovered activity of chimera N39D2-C7 indicated that the N and C termini are structurally dependent on each other and function synergistically. Furthermore, fluorescence resonance energy transfer (FRET) analysis suggested that the N and C termini are relatively close in proximity which may account for their synergistic function in ion translocation. In the N-terminal region of N39D2-C7, the replacement of Glu38 with Pro abolished the recovered complementary and transport activities. In addition, this amino acid substitution in NhaD2 resulted in a drastically decreased complementation ability in Escherichia coli KNabc (level identical to that of NhaD1), as well as decreased activity and an altered pH profile.IMPORTANCE Limited information on NhaD antiporters supports speculation that these antiporters are important for resistance to high salinity and alkalinity. Moreover, only a few functional residues have been identified in NhaD antiporters, and there is limited literature on the molecular mechanisms of NhaD antiporter activity. The altered antiporter abilities of chimeras and mutants in this study implicate the functions of the N and C termini, especially Glu38, in pH regulation and ion translocation, and, most importantly, the essential roles of this negatively charged residue in maintaining the physiological function of NhaD2. These findings further our understanding of the molecular mechanism of NhaD antiporters for ion transport.
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34
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Călinescu O, Dwivedi M, Patiño-Ruiz M, Padan E, Fendler K. Lysine 300 is essential for stability but not for electrogenic transport of the Escherichia coli NhaA Na +/H + antiporter. J Biol Chem 2017; 292:7932-7941. [PMID: 28330875 PMCID: PMC5427271 DOI: 10.1074/jbc.m117.778175] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/09/2017] [Indexed: 11/06/2022] Open
Abstract
Na+/H+ antiporters are located in the cytoplasmic and intracellular membranes and play crucial roles in regulating intracellular pH, Na+, and volume. The NhaA antiporter of Escherichia coli is the best studied member of the Na+/H+ exchanger family and a model system for all related Na+/H+ exchangers, including eukaryotic representatives. Several amino acid residues are important for the transport activity of NhaA, including Lys-300, a residue that has recently been proposed to carry one of the two H+ ions that NhaA exchanges for one Na+ ion during one transport cycle. Here, we sought to characterize the effects of mutating Lys-300 of NhaA to amino acid residues containing side chains of different polarity and length (i.e. Ala, Arg, Cys, His, Glu, and Leu) on transporter stability and function. Salt resistance assays, acridine-orange fluorescence dequenching, solid supported membrane-based electrophysiology, and differential scanning fluorometry were used to characterize Na+ and H+ transport, charge translocation, and thermal stability of the different variants. These studies revealed that NhaA could still perform electrogenic Na+/H+ exchange even in the absence of a protonatable residue at the Lys-300 position. However, all mutants displayed lower thermal stability and reduced ion transport activity compared with the wild-type enzyme, indicating the critical importance of Lys-300 for optimal NhaA structural stability and function. On the basis of these experimental data, we propose a tentative mechanism integrating the functional and structural role of Lys-300.
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Affiliation(s)
- Octavian Călinescu
- From the Max-Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- the "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania, and
| | - Manish Dwivedi
- the Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Miyer Patiño-Ruiz
- From the Max-Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Etana Padan
- the Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Klaus Fendler
- From the Max-Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany,
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35
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Cultivation of Pichia pastoris carrying the scFv anti LDL (-) antibody fragment. Effect of preculture carbon source. Braz J Microbiol 2017; 48:419-426. [PMID: 28237678 PMCID: PMC5498413 DOI: 10.1016/j.bjm.2016.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 11/11/2016] [Accepted: 11/28/2016] [Indexed: 12/27/2022] Open
Abstract
Antibodies and antibody fragments are nowadays among the most important biotechnological products, and Pichia pastoris is one of the most important vectors to produce them as well as other recombinant proteins. The conditions to effectively cultivate a P. pastoris strain previously genetically modified to produce the single-chain variable fragment anti low density lipoprotein (−) under the control of the alcohol oxidase promoter have been investigated in this study. In particular, it was evaluated if, and eventually how, the carbon source (glucose or glycerol) used in the preculture preceding cryopreservation in 20% glycerol influences both cell and antibody fragment productions either in flasks or in bioreactor. Although in flasks the volumetric productivity of the antibody fragment secreted by cells precultured, cryopreserved and reactivated in glycerol was 42.9% higher compared with cells precultured in glucose, the use of glycerol in bioreactor led to a remarkable shortening of the lag phase, thereby increasing it by no less than thrice compared to flasks. These results are quite promising in comparison with those reported in the literature for possible future industrial applications of this cultivation, taking into account that the overall process time was reduced by around 8 h.
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36
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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.
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37
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Călinescu O, Linder M, Wöhlert D, Yildiz Ö, Kühlbrandt W, Fendler K. Electrogenic Cation Binding in the Electroneutral Na+/H+ Antiporter of Pyrococcus abyssi. J Biol Chem 2016; 291:26786-26793. [PMID: 27821589 PMCID: PMC5207186 DOI: 10.1074/jbc.m116.761080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/02/2016] [Indexed: 01/04/2023] Open
Abstract
Na+/H+ antiporters in the CPA1 branch of the cation proton antiporter family drive the electroneutral exchange of H+ against Na+ ions and ensure pH homeostasis in eukaryotic and prokaryotic organisms. Although their transport cycle is overall electroneutral, specific partial reactions are electrogenic. Here, we present an electrophysiological study of the PaNhaP Na+/H+ antiporter from Pyrococcus abyssi reconstituted into liposomes. Positive transient currents were recorded upon addition of Na+ to PaNhaP proteoliposomes, indicating a reaction where positive charge is rapidly displaced into the proteoliposomes with a rate constant of k >200 s-1 We attribute the recorded currents to an electrogenic reaction that includes Na+ binding and possibly occlusion. Subsequently, positive charge is transported out of the cell associated with H+ binding, so that the overall reaction is electroneutral. We show that the differences in pH profile and Na+ affinity of PaNhaP and the related MjNhaP1 from Methanocaldococcus jannaschii can be attributed to an additional negatively charged glutamate residue in PaNhaP. The results are discussed in the context of the physiological function of PaNhaP and other microbial Na+/H+ exchangers. We propose that both, electroneutral and electrogenic Na+/H+ antiporters, represent a carefully tuned self-regulatory system, which drives the cytoplasmic pH back to neutral after any deviation.
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Affiliation(s)
- Octavian Călinescu
- From the Departments of Biological Chemistry and.,the Department of Biophysics, "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Mark Linder
- From the Departments of Biological Chemistry and.,Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany and
| | - David Wöhlert
- Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany and
| | - Özkan Yildiz
- Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany and
| | - Werner Kühlbrandt
- Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany and
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38
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Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA. Nat Commun 2016; 7:12940. [PMID: 27708266 PMCID: PMC5059715 DOI: 10.1038/ncomms12940] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 08/17/2016] [Indexed: 11/08/2022] Open
Abstract
Escherichia coli NhaA is a prototype sodium-proton antiporter, which has been extensively characterized by X-ray crystallography, biochemical and biophysical experiments. However, the identities of proton carriers and details of pH-regulated mechanism remain controversial. Here we report constant pH molecular dynamics data, which reveal that NhaA activation involves a net charge switch of a pH sensor at the entrance of the cytoplasmic funnel and opening of a hydrophobic gate at the end of the funnel. The latter is triggered by charging of Asp164, the first proton carrier. The second proton carrier Lys300 forms a salt bridge with Asp163 in the inactive state, and releases a proton when a sodium ion binds Asp163. These data reconcile current models and illustrate the power of state-of-the-art molecular dynamics simulations in providing atomic details of proton-coupled transport across membrane which is challenging to elucidate by experimental techniques. The pH dependence of the activity of Escherichia coli main sodium-proton antiporter NhaA is still not fully understood. Here, the authors use continuous constant pH molecular dynamics simulations to identify NhaA proton carrier residues and elucidate its gating and ion transport processes.
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39
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Khan S, Li M, Muench SP, Jeuken LJC, Beales PA. Durable proteo-hybrid vesicles for the extended functional lifetime of membrane proteins in bionanotechnology. Chem Commun (Camb) 2016; 52:11020-3. [PMID: 27540604 PMCID: PMC5048396 DOI: 10.1039/c6cc04207d] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Significant enhancement of membrane protein functional durability is demonstrated when reconstituted in hybrid lipid–block copolymer vesicles compared to conventional proteoliposomes.
The full capabilities of membrane proteins in bionanotechnology can only be realised through improvements in their reconstitution environments that combine biocompatibility to support function and durability for long term stability. We demonstrate that hybrid vesicles composed of natural phospholipids and synthetic diblock copolymers have the potential to achieve these criteria.
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Affiliation(s)
- Sanobar Khan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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40
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The Ec-NhaA antiporter switches from antagonistic to synergistic antiport upon a single point mutation. Sci Rep 2016; 6:23339. [PMID: 27021484 PMCID: PMC4810432 DOI: 10.1038/srep23339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/04/2016] [Indexed: 12/14/2022] Open
Abstract
The Na+, Li+/H+ antiporter of Escherichia coli (Ec-NhaA) maintains pH, Na+ homeostasis in enterobacteria. We used isothermal titration calorimetry to perform a detailed thermodynamic analysis of Li+ binding to Ec-NhaA and several of its mutants. We found that, in line with the canonical alternative access mechanistic model of secondary transporters, Li+/H+ binding to the antiporter is antagonistically coupled. Binding of Li+ displaces 2 H+ from the binding site. The process is enthalpically driven, the enthalpic gain just compensating for an entropic loss and the buffer-associated enthalpic changes dominate the overall free-energy change. Li+ binding, H+ release and antiporter activity were all affected to the same extent by mutations in the Li+ binding site (D163E, D163N, D164N, D164E), while D133C changed the H+/Li+ stoichiometry to 4. Most striking, however, was the mutation, A167P, which converted the Ec-NhaA antagonistic binding into synergistic binding which is only known to occur in Cl−/H+ antiporter.
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41
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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.
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42
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Wu W, Huang H, Ling Z, Yu Z, Jiang Y, Liu P, Li X. Genome sequencing reveals mechanisms for heavy metal resistance and polycyclic aromatic hydrocarbon degradation in Delftia lacustris strain LZ-C. ECOTOXICOLOGY (LONDON, ENGLAND) 2016; 25:234-247. [PMID: 26589947 DOI: 10.1007/s10646-015-1583-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/30/2015] [Indexed: 06/05/2023]
Abstract
Strain LZ-C, isolated from a petrochemical wastewater discharge site, was found to be resistant to heavy metals and to degrade various aromatic compounds, including naphenol, naphthalene, 2-methylnaphthalene and toluene. Data obtained from 16S rRNA gene sequencing showed that this strain was closely related to Delftia lacustris. The 5,889,360 bp genome of strain LZ-C was assembled into 239 contigs and 197 scaffolds containing 5855 predicted open reading frames (ORFs). Among these predicted ORFs, 464 were different from the type strain of Delftia. The minimal inhibitory concentrations were 4 mM, 30 µM, 2 mM and 1 mM for Cr(VI), Hg(II), Cd(II) and Pb(II), respectively. Both genome sequencing and quantitative real-time PCR data revealed that genes related to Chr, Czc and Mer family genes play important roles in heavy metal resistance in strain LZ-C. In addition, the Na(+)/H(+) antiporter NhaA is important for adaptation to high salinity resistance (2.5 M NaCl). The complete pathways of benzene and benzoate degradation were identified through KEGG analysis. Interestingly, strain LZ-C also degrades naphthalene but lacks the key naphthalene degradation gene NahA. Thus, we propose that strain LZ-C exhibits a novel protein with a function similar to NahA. This study is the first to reveal the mechanisms of heavy metal resistance and salinity tolerance in D. lacustris and to identify a potential 2-methylnaphthalene degradation protein in this strain. Through whole-genome sequencing analysis, strain LZ-C might be a good candidate for the bioremediation of heavy metals and polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Wenyang Wu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Haiying Huang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Zhenmin Ling
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Zhengsheng Yu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Yiming Jiang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Pu Liu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Xiangkai Li
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China.
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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]
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Morrison EA, Robinson AE, Liu Y, Henzler-Wildman KA. Asymmetric protonation of EmrE. J Gen Physiol 2015; 146:445-61. [PMID: 26573622 PMCID: PMC4664823 DOI: 10.1085/jgp.201511404] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 10/13/2015] [Indexed: 01/26/2023] Open
Abstract
The small multidrug resistance transporter EmrE is a homodimer that uses energy provided by the proton motive force to drive the efflux of drug substrates. The pKa values of its "active-site" residues--glutamate 14 (Glu14) from each subunit--must be poised around physiological pH values to efficiently couple proton import to drug export in vivo. To assess the protonation of EmrE, pH titrations were conducted with (1)H-(15)N TROSY-HSQC nuclear magnetic resonance (NMR) spectra. Analysis of these spectra indicates that the Glu14 residues have asymmetric pKa values of 7.0 ± 0.1 and 8.2 ± 0.3 at 45°C and 6.8 ± 0.1 and 8.5 ± 0.2 at 25°C. These pKa values are substantially increased compared with typical pKa values for solvent-exposed glutamates but are within the range of published Glu14 pKa values inferred from the pH dependence of substrate binding and transport assays. The active-site mutant, E14D-EmrE, has pKa values below the physiological pH range, consistent with its impaired transport activity. The NMR spectra demonstrate that the protonation states of the active-site Glu14 residues determine both the global structure and the rate of conformational exchange between inward- and outward-facing EmrE. Thus, the pKa values of the asymmetric active-site Glu14 residues are key for proper coupling of proton import to multidrug efflux. However, the results raise new questions regarding the coupling mechanism because they show that EmrE exists in a mixture of protonation states near neutral pH and can interconvert between inward- and outward-facing forms in multiple different protonation states.
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Affiliation(s)
- Emma A Morrison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Anne E Robinson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Yongjia Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Katherine A Henzler-Wildman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
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Abstract
The molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function. This work explores the molecular origin of the function of the bacterial Na+/H+ antiporter NhaA by evaluating the energetics of the Na+ and H+ movement and then using the resulting landscape in Monte Carlo simulations that examine two transport models and explore which model can reproduce the relevant experimental results. The simulations reproduce the observed transport features by a relatively simple model that relates the protein structure to its transporting function. Focusing on the two key aspartic acid residues of NhaA, D163 and D164, shows that the fully charged state acts as an Na+ trap and that the fully protonated one poses an energetic barrier that blocks the transport of Na+. By alternating between the former and latter states, mediated by the partially protonated protein, protons, and Na+ can be exchanged across the membrane at 2:1 stoichiometry. Our study provides a numerical validation of the need of large conformational changes for effective transport. Furthermore, we also yield a reasonable explanation for the observation that some mammalian transporters have 1:1 stoichiometry. The present coarse-grained model can provide a general way for exploring the function of transporters on a molecular level.
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Lee C, Yashiro S, Dotson DL, Uzdavinys P, Iwata S, Sansom MSP, von Ballmoos C, Beckstein O, Drew D, Cameron AD. Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights. ACTA ACUST UNITED AC 2015; 144:529-44. [PMID: 25422503 PMCID: PMC4242812 DOI: 10.1085/jgp.201411219] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A dimeric structure of the sodium–proton antiporter NhaA provides insight into the roles of Asp163 and Lys300 in the transport mechanism. Sodium–proton antiporters rapidly exchange protons and sodium ions across the membrane to regulate intracellular pH, cell volume, and sodium concentration. How ion binding and release is coupled to the conformational changes associated with transport is not clear. Here, we report a crystal form of the prototypical sodium–proton antiporter NhaA from Escherichia coli in which the protein is seen as a dimer. In this new structure, we observe a salt bridge between an essential aspartic acid (Asp163) and a conserved lysine (Lys300). An equivalent salt bridge is present in the homologous transporter NapA, but not in the only other known crystal structure of NhaA, which provides the foundation of most existing structural models of electrogenic sodium–proton antiport. Molecular dynamics simulations show that the stability of the salt bridge is weakened by sodium ions binding to Asp164 and the neighboring Asp163. This suggests that the transport mechanism involves Asp163 switching between forming a salt bridge with Lys300 and interacting with the sodium ion. pKa calculations suggest that Asp163 is highly unlikely to be protonated when involved in the salt bridge. As it has been previously suggested that Asp163 is one of the two residues through which proton transport occurs, these results have clear implications to the current mechanistic models of sodium–proton antiport in NhaA.
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Affiliation(s)
- Chiara Lee
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, England, UK
| | - Shoko Yashiro
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, England, UK Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, England, UK
| | - David L Dotson
- Department of Physics, Arizona State University, Tempe, AZ 85287
| | - Povilas Uzdavinys
- Department of Biochemistry and Biophysics, Centre for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - So Iwata
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, England, UK Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, England, UK Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire OX11 0FA, England, UK Japan Science and Technology Agency, ERATO, Human Crystallography Project, Sakyo-ku, Kyoto 606-851, Japan Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, England, UK
| | - Christoph von Ballmoos
- Department of Biochemistry and Biophysics, Centre for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Oliver Beckstein
- Department of Physics, Arizona State University, Tempe, AZ 85287 Department of Biochemistry, University of Oxford, Oxford OX1 3QU, England, UK
| | - David Drew
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, England, UK Department of Biochemistry and Biophysics, Centre for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Alexander D Cameron
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, England, UK Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, England, UK Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire OX11 0FA, England, UK School of Life Sciences, University of Warwick, Coventry CV4 7AL, England, UK
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Rycovska-Blume A, Lü W, Andrade S, Fendler K, Einsle O. Structural and Functional Studies of NirC from Salmonella typhimurium. Methods Enzymol 2015; 556:475-97. [PMID: 25857796 DOI: 10.1016/bs.mie.2014.12.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
NirC is a pentameric transport system for monovalent anions that is expressed in the context of assimilatory nitrite reductase NirBD in a wide variety of enterobacterial species. A NirC pentamer contains individual pores in each protomer that mediate the passage of at least the nitrite [Formula: see text] and nitrate [Formula: see text] anions. As a member of the formate/nitrite transporter family of membrane transport proteins, NirC shares a range of structural and functional features with the formate channel FocA and the hydrosulfide channel AsrD (HSC). NirC from the enteropathogen Salmonella typhimurium has been studied by X-ray crystallography, proton uptake assays, and different electrophysiological techniques, and the picture that has emerged shows a fast and versatile transport system for nitrite that doubles as a defense system during the enteric life of the bacterium. Structural and functional assays are described, which shed light on the transport mechanism of this important molecular machine.
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Affiliation(s)
- Adriana Rycovska-Blume
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Wei Lü
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Freiburg im Breisgau, Germany
| | - Susana Andrade
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Freiburg im Breisgau, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg im Breisgau, Germany
| | - Klaus Fendler
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Freiburg im Breisgau, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg im Breisgau, Germany
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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.
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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
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