101
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Giladi M, Shor R, Lisnyansky M, Khananshvili D. Structure-Functional Basis of Ion Transport in Sodium-Calcium Exchanger (NCX) Proteins. Int J Mol Sci 2016; 17:E1949. [PMID: 27879668 PMCID: PMC5133943 DOI: 10.3390/ijms17111949] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/13/2016] [Accepted: 11/14/2016] [Indexed: 01/19/2023] Open
Abstract
The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α₁ and α₂ repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na⁺ or Ca2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca2+/cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 699780, Israel.
- Tel-Aviv Sourasky Medical Center, Tel-Aviv 6423906, Israel.
| | - Reut Shor
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 699780, Israel.
| | - Michal Lisnyansky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 699780, Israel.
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 699780, Israel.
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102
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Zhekova H, Zhao C, Schnetkamp PPM, Noskov SY. Characterization of the Cation Binding Sites in the NCKX2 Na +/Ca 2+-K + Exchanger. Biochemistry 2016; 55:6445-6455. [PMID: 27805378 DOI: 10.1021/acs.biochem.6b00591] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
NCKX1-5 are proteins involved in K+-dependent Na+/Ca2+ exchange in various signal tissues. Here we present a homology model of NCKX2 based on the crystal structure of the NCX_Mj transporter found in Methanoccocus jannaschii. Molecular dynamics simulations were performed on the resultant wild-type NCKX2 model and two mutants (D548N and D575N) loaded with either four Na+ ions or one Ca2+ ion and one K+ ion, in line with the experimentally observed transport stoichiometry. The selectivity of the active site in wild-type NCKX2 for Na+, K+, and Li+ and the electrostatic interactions of the positive Na+ ions in the negatively charged active site of wild-type NCKX2 and the two mutants were evaluated from free energy perturbation calculations. For validation of the homology model, our computational results were compared to available experimental data obtained from numerous prior functional studies. The NCKX2 homology model is in good agreement with the discussed experimental data and provides valuable insights into the structure of the active site, which is lined with acidic and polar residues. The binding of the potassium and calcium ions is accomplished via Asp 575 and 548, respectively. Mutation of these residues to Asn alters the functionality of NCKX2 because of the elimination of the favorable carboxylate-cation interactions. The knowledge obtained from the NCKX2 model can be transferred to other isoforms of the NCKX family: newly discovered pathological mutations in NCKX4 and NCKX5 affect residues that are involved in ion binding and/or transport according to our homology model.
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Affiliation(s)
- Hristina Zhekova
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary , Calgary, AB, Canada T2N 1N4
| | - Chunfeng Zhao
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary , Calgary, AB, Canada T2N 1N4
| | - Paul P M Schnetkamp
- Department of Physiology & Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary , Calgary, AB T2N 4N1, Canada
| | - Sergei Yu Noskov
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary , Calgary, AB, Canada T2N 1N4
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103
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Leucine zipper-EF-hand containing transmembrane protein 1 (LETM1) forms a Ca 2+/H + antiporter. Sci Rep 2016; 6:34174. [PMID: 27669901 PMCID: PMC5037442 DOI: 10.1038/srep34174] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/08/2016] [Indexed: 02/06/2023] Open
Abstract
Leucine zipper-EF-hand-containing transmembrane protein1 (LETM1) is located in the mitochondrial inner membrane and is defective in Wolf-Hirschhorn syndrome. LETM1 contains only one transmembrane helix, but it behaves as a putative transporter. Our data shows that LETM1 knockdown or overexpression robustly increases or decreases mitochondrial Ca2+ level in HeLa cells, respectively. Also the residue Glu221 of mouse LETM1 is identified to be necessary for Ca2+ flux. The mutation of Glu221 to glutamine abolishes the Ca2+-transport activity of LETM1 in cells. Furthermore, the purified LETM1 exhibits Ca2+/H+ anti-transport activity, and the activity is enhanced as the proton gradient is increased. More importantly, electron microscopy studies reveal a hexameric LETM1 with a central cavity, and also, observe two different conformational states under alkaline and acidic conditions, respectively. Our results indicate that LETM1 is a Ca2+/H+ antiporter and most likely responsible for mitochondrial Ca2+ output.
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104
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Affiliation(s)
- David Drew
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065;
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105
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Structural basis for amino acid export by DMT superfamily transporter YddG. Nature 2016; 534:417-20. [DOI: 10.1038/nature17991] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 04/08/2016] [Indexed: 01/29/2023]
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106
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Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger. Nat Struct Mol Biol 2016; 23:590-599. [PMID: 27183196 PMCID: PMC4918766 DOI: 10.1038/nsmb.3230] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 04/18/2016] [Indexed: 12/21/2022]
Abstract
Na+/Ca2+ exchangers utilize the Na+ electrochemical gradient across the plasma membrane to extrude intracellular Ca2+, and play a central role in Ca2+ homeostasis. Here, we elucidate their mechanisms of extracellular ion recognition and exchange through a structural analysis of the exchanger from Methanococcus jannaschii (NCX_Mj) bound to Na+, Ca2+ or Sr2+ in various occupancies and in an apo state. This analysis defines the binding mode and relative affinity of these ions, establishes the structural basis for the anticipated 3Na+:1Ca2+ exchange stoichiometry, and reveals the conformational changes at the onset of the alternating-access transport mechanism. An independent analysis of the dynamics and conformational free-energy landscape of NCX_Mj in different ion-occupancy states, based on enhanced-sampling molecular-dynamics simulations, demonstrates that the crystal structures reflect mechanistically relevant, interconverting conformations. These calculations also reveal the mechanism by which the outward-to-inward transition is controlled by the ion-occupancy state, thereby explaining the emergence of strictly-coupled Na+/Ca2+ antiport.
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107
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Abstract
In the last 5 years, most of the molecules that control mitochondrial Ca(2+) homeostasis have been finally identified. Mitochondrial Ca(2+) uptake is mediated by the Mitochondrial Calcium Uniporter (MCU) complex, a macromolecular structure that guarantees Ca(2+) accumulation inside mitochondrial matrix upon increases in cytosolic Ca(2+). Conversely, Ca(2+) release is under the control of the Na(+)/Ca(2+) exchanger, encoded by the NCLX gene, and of a H(+)/Ca(2+) antiporter, whose identity is still debated. The low affinity of the MCU complex, coupled to the activity of the efflux systems, protects cells from continuous futile cycles of Ca(2+) across the inner mitochondrial membrane and consequent massive energy dissipation. In this review, we discuss the basic principles that govern mitochondrial Ca(2+) homeostasis and the methods used to investigate the dynamics of Ca(2+) concentration within the organelles. We discuss the functional and structural role of the different molecules involved in mitochondrial Ca(2+) handling and their pathophysiological role.
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Affiliation(s)
- Diego De Stefani
- Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy; , ,
| | - Rosario Rizzuto
- Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy; , , .,National Research Council (CNR) Neuroscience Institute, 35121 Padova, Italy
| | - Tullio Pozzan
- Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy; , , .,National Research Council (CNR) Neuroscience Institute, 35121 Padova, Italy.,Venetian Institute of Molecular Medicine, 35121 Padova, Italy
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108
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Martin-Garcia JM, Conrad CE, Coe J, Roy-Chowdhury S, Fromme P. Serial femtosecond crystallography: A revolution in structural biology. Arch Biochem Biophys 2016; 602:32-47. [PMID: 27143509 DOI: 10.1016/j.abb.2016.03.036] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 10/21/2022]
Abstract
Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein.
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Affiliation(s)
- Jose M Martin-Garcia
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Chelsie E Conrad
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Jesse Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA.
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109
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Jalloul AH, Rogasevskaia TP, Szerencsei RT, Schnetkamp PPM. A Functional Study of Mutations in K+-dependent Na+-Ca2+ Exchangers Associated with Amelogenesis Imperfecta and Non-syndromic Oculocutaneous Albinism. J Biol Chem 2016; 291:13113-23. [PMID: 27129268 DOI: 10.1074/jbc.m116.728824] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 12/20/2022] Open
Abstract
K(+)-dependent Na(+)/Ca(2+) exchangers belong to the solute carrier 24 (SLC24A1-5) gene family of membrane transporters. Five different gene products (NCKX1-5) have been identified in humans, which play key roles in biological processes including vision, olfaction, and skin pigmentation. NCKXs are bi-directional membrane transporters that transport 1 Ca(2+)+K(+) ions in exchange for 4 Na(+) ions. Recent studies have linked mutations in the SLC24A4 (NCKX4) and SLC24A5 (NCKX5) genes to amylogenesis imperfecta (AI) and non-syndromic oculocutaneous albinism (OCA6), respectively. Here, we introduced mutations found in patients with AI and OCA6 into human SLC24A4 (NCKX4) cDNA leading to single residue substitutions in the mutant NCKX4 proteins. We measured NCKX-mediated Ca(2+) transport activity of WT and mutant NCKX4 proteins expressed in HEK293 cells. Three mutant NCKX4 cDNAs represent mutations found in the SCL24A4 gene and three represent mutations found in the SCL24A5 gene involving residues conserved between NCKX4 and NCKX5. Five mutant proteins had no observable NCKX activity, whereas one mutation resulted in a 78% reduction in transport activity. Total protein expression and trafficking to the plasma membrane (the latter with one exception) were not affected in the HEK293 cell expression system. We also analyzed two mutations in a Drosophila NCKX gene that have been reported to result in an increased susceptibility for seizures, and found that both resulted in mutant proteins with significantly reduced but observable NCKX activity. The data presented here support the genetic analyses that mutations in SLC24A4 and SLC24A5 are responsible for the phenotypic defects observed in human patients.
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Affiliation(s)
- Ali H Jalloul
- From the Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Tatiana P Rogasevskaia
- From the Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Robert T Szerencsei
- From the Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Paul P M Schnetkamp
- From the Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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110
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Yeast Gdt1 is a Golgi-localized calcium transporter required for stress-induced calcium signaling and protein glycosylation. Sci Rep 2016; 6:24282. [PMID: 27075443 PMCID: PMC4830978 DOI: 10.1038/srep24282] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/22/2016] [Indexed: 11/30/2022] Open
Abstract
Calcium signaling depends on a tightly regulated set of pumps, exchangers, and channels that are responsible for controlling calcium fluxes between the different subcellular compartments of the eukaryotic cell. We have recently reported that two members of the highly-conserved UPF0016 family, human TMEM165 and budding yeast Gdt1p, are functionally related and might form a new group of Golgi-localized cation/Ca2+ exchangers. Defects in the human protein TMEM165 are known to cause a subtype of Congenital Disorders of Glycosylation. Using an assay based on the heterologous expression of GDT1 in the bacterium Lactococcus lactis, we demonstrated the calcium transport activity of Gdt1p. We observed a Ca2+ uptake activity in cells expressing GDT1, which was dependent on the external pH, indicating that Gdt1p may act as a Ca2+/H+ antiporter. In yeast, we found that Gdt1p controls cellular calcium stores and plays a major role in the calcium response induced by osmotic shock when the Golgi calcium pump, Pmr1p, is absent. Importantly, we also discovered that, in the presence of a high concentration of external calcium, Gdt1p is required for glycosylation of carboxypeptidase Y and the glucanosyltransferase Gas1p. Finally we showed that glycosylation process is restored by providing more Mn2+ to the cells.
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111
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Abiko LA, Vitale PM, Favaro DC, Hauk P, Li DW, Yuan J, Bruschweiler-Li L, Salinas RK, Brüschweiler R. Model for the allosteric regulation of the Na+/Ca2+exchanger NCX. Proteins 2016; 84:580-90. [DOI: 10.1002/prot.25003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/21/2016] [Accepted: 01/25/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Layara Akemi Abiko
- Institute of Chemistry; University of São Paulo; São Paulo SP 05508-000 Brazil
| | - Phelipe M. Vitale
- Institute of Chemistry; University of São Paulo; São Paulo SP 05508-000 Brazil
| | - Denize C. Favaro
- Institute of Chemistry; University of São Paulo; São Paulo SP 05508-000 Brazil
| | - Pricila Hauk
- Institute of Chemistry; University of São Paulo; São Paulo SP 05508-000 Brazil
| | - Da-Wei Li
- Campus Chemical Instrument Center; The Ohio State University; Columbus Ohio 43210
| | - Jiaqi Yuan
- Department of Chemistry & Biochemistry; The Ohio State University; Columbus Ohio 43210
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center; The Ohio State University; Columbus Ohio 43210
| | - Roberto K. Salinas
- Institute of Chemistry; University of São Paulo; São Paulo SP 05508-000 Brazil
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center; The Ohio State University; Columbus Ohio 43210
- Department of Chemistry & Biochemistry; The Ohio State University; Columbus Ohio 43210
- Department of Biological Chemistry and Pharmacology; The Ohio State University; Columbus Ohio 43210
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112
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Refaeli B, Giladi M, Hiller R, Khananshvili D. Structure-Based Engineering of Lithium-Transport Capacity in an Archaeal Sodium–Calcium Exchanger. Biochemistry 2016; 55:1673-6. [DOI: 10.1021/acs.biochem.6b00119] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bosmat Refaeli
- Department of Physiology
and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
| | - Moshe Giladi
- Department of Physiology
and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
| | - Reuben Hiller
- Department of Physiology
and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
| | - Daniel Khananshvili
- Department of Physiology
and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
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113
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Liu JL, Hsieh HJ, Eisenberg B. Poisson–Fermi Modeling of the Ion Exchange Mechanism of the Sodium/Calcium Exchanger. J Phys Chem B 2016; 120:2658-69. [DOI: 10.1021/acs.jpcb.5b11515] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jinn-Liang Liu
- Department of Applied Mathematics, National Hsinchu University of Education, Hsinchu 300, Taiwan
| | - Hann-jeng Hsieh
- Department
of Applied Mathematics, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Bob Eisenberg
- Department of Molecular Biophysics
and Physiology, Rush University, Chicago, Illinois 60612, United States
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114
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Giladi M, Almagor L, van Dijk L, Hiller R, Man P, Forest E, Khananshvili D. Asymmetric Preorganization of Inverted Pair Residues in the Sodium-Calcium Exchanger. Sci Rep 2016; 6:20753. [PMID: 26876271 PMCID: PMC4753433 DOI: 10.1038/srep20753] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/07/2016] [Indexed: 01/22/2023] Open
Abstract
In analogy with many other proteins, Na+/Ca2+ exchangers (NCX) adapt an inverted twofold symmetry of repeated structural elements, while exhibiting a functional asymmetry by stabilizing an outward-facing conformation. Here, structure-based mutant analyses of the Methanococcus jannaschii Na+/Ca2+ exchanger (NCX_Mj) were performed in conjunction with HDX-MS (hydrogen/deuterium exchange mass spectrometry) to identify the structure-dynamic determinants of functional asymmetry. HDX-MS identified hallmark differences in backbone dynamics at ion-coordinating residues of apo-NCX_Mj, whereas Na+or Ca2+ binding to the respective sites induced relatively small, but specific, changes in backbone dynamics. Mutant analysis identified ion-coordinating residues affecting the catalytic capacity (kcat/Km), but not the stability of the outward-facing conformation. In contrast, distinct “noncatalytic” residues (adjacent to the ion-coordinating residues) control the stability of the outward-facing conformation, but not the catalytic capacity. The helix-breaking signature sequences (GTSLPE) on the α1 and α2 repeats (at the ion-binding core) differ in their folding/unfolding dynamics, while providing asymmetric contributions to transport activities. The present data strongly support the idea that asymmetric preorganization of the ligand-free ion-pocket predefines catalytic reorganization of ion-bound residues, where secondary interactions with adjacent residues couple the alternating access. These findings provide a structure-dynamic basis for ion-coupled alternating access in NCX and similar proteins.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Lior Almagor
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Liat van Dijk
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Petr Man
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Eric Forest
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France.,CNRS, IBS, F-38044 Grenoble, France.,CEA, IBS, F-38044 Grenoble, France
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
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115
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Giladi M, Tal I, Khananshvili D. Structural Features of Ion Transport and Allosteric Regulation in Sodium-Calcium Exchanger (NCX) Proteins. Front Physiol 2016; 7:30. [PMID: 26903880 PMCID: PMC4746289 DOI: 10.3389/fphys.2016.00030] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/19/2016] [Indexed: 01/14/2023] Open
Abstract
Na(+)/Ca(2+) exchanger (NCX) proteins extrude Ca(2+) from the cell to maintain cellular homeostasis. Since NCX proteins contribute to numerous physiological and pathophysiological events, their pharmacological targeting has been desired for a long time. This intervention remains challenging owing to our poor understanding of the underlying structure-dynamic mechanisms. Recent structural studies have shed light on the structure-function relationships underlying the ion-transport and allosteric regulation of NCX. The crystal structure of an archaeal NCX (NCX_Mj) along with molecular dynamics simulations and ion flux analyses, have assigned the ion binding sites for 3Na(+) and 1Ca(2+), which are being transported in separate steps. In contrast with NCX_Mj, eukaryotic NCXs contain the regulatory Ca(2+)-binding domains, CBD1 and CBD2, which affect the membrane embedded ion-transport domains over a distance of ~80 Å. The Ca(2+)-dependent regulation is ortholog, isoform, and splice-variant dependent to meet physiological requirements, exhibiting either a positive, negative, or no response to regulatory Ca(2+). The crystal structures of the two-domain (CBD12) tandem have revealed a common mechanism involving a Ca(2+)-driven tethering of CBDs in diverse NCX variants. However, dissociation kinetics of occluded Ca(2+) (entrapped at the two-domain interface) depends on the alternative-splicing segment (at CBD2), thereby representing splicing-dependent dynamic coupling of CBDs. The HDX-MS, SAXS, NMR, FRET, equilibrium (45)Ca(2+) binding and stopped-flow techniques provided insights into the dynamic mechanisms of CBDs. Ca(2+) binding to CBD1 results in a population shift, where more constraint conformational states become highly populated without global conformational changes in the alignment of CBDs. This mechanism is common among NCXs. Recent HDX-MS studies have demonstrated that the apo CBD1 and CBD2 are stabilized by interacting with each other, while Ca(2+) binding to CBD1 rigidifies local backbone segments of CBD2, but not of CBD1. The extent and strength of Ca(2+)-dependent rigidification at CBD2 is splice-variant dependent, showing clear correlations with phenotypes of matching NCX variants. Therefore, diverse NCX variants share a common mechanism for the initial decoding of the regulatory signal upon Ca(2+) binding at the interface of CBDs, whereas the allosteric message is shaped by CBD2, the dynamic features of which are dictated by the splicing segment.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University Tel Aviv, Israel
| | - Inbal Tal
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University Tel Aviv, Israel
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University Tel Aviv, Israel
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116
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Abstract
Symmetry is a common feature among natural systems, including protein structures. A strong propensity toward symmetric architectures has long been recognized for water-soluble proteins, and this propensity has been rationalized from an evolutionary standpoint. Proteins residing in cellular membranes, however, have traditionally been less amenable to structural studies, and thus the prevalence and significance of symmetry in this important class of molecules is not as well understood. In the past two decades, researchers have made great strides in this area, and these advances have provided exciting insights into the range of architectures adopted by membrane proteins. These structural studies have revealed a similarly strong bias toward symmetric arrangements, which were often unexpected and which occurred despite the restrictions imposed by the membrane environment on the possible symmetry groups. Moreover, membrane proteins disproportionately contain internal structural repeats resulting from duplication and fusion of smaller segments. This article discusses the types and origins of symmetry in membrane proteins and the implications of symmetry for protein function.
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Affiliation(s)
- Lucy R Forrest
- Computational Structural Biology Group, Porter Neuroscience Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20852;
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117
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Shattock MJ, Ottolia M, Bers DM, Blaustein MP, Boguslavskyi A, Bossuyt J, Bridge JHB, Chen-Izu Y, Clancy CE, Edwards A, Goldhaber J, Kaplan J, Lingrel JB, Pavlovic D, Philipson K, Sipido KR, Xie ZJ. Na+/Ca2+ exchange and Na+/K+-ATPase in the heart. J Physiol 2015; 593:1361-82. [PMID: 25772291 PMCID: PMC4376416 DOI: 10.1113/jphysiol.2014.282319] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/30/2014] [Indexed: 12/17/2022] Open
Abstract
This paper is the third in a series of reviews published in this issue resulting from the University of California Davis Cardiovascular Symposium 2014: Systems approach to understanding cardiac excitation–contraction coupling and arrhythmias: Na+ channel and Na+ transport. The goal of the symposium was to bring together experts in the field to discuss points of consensus and controversy on the topic of sodium in the heart. The present review focuses on cardiac Na+/Ca2+ exchange (NCX) and Na+/K+-ATPase (NKA). While the relevance of Ca2+ homeostasis in cardiac function has been extensively investigated, the role of Na+ regulation in shaping heart function is often overlooked. Small changes in the cytoplasmic Na+ content have multiple effects on the heart by influencing intracellular Ca2+ and pH levels thereby modulating heart contractility. Therefore it is essential for heart cells to maintain Na+ homeostasis. Among the proteins that accomplish this task are the Na+/Ca2+ exchanger (NCX) and the Na+/K+ pump (NKA). By transporting three Na+ ions into the cytoplasm in exchange for one Ca2+ moved out, NCX is one of the main Na+ influx mechanisms in cardiomyocytes. Acting in the opposite direction, NKA moves Na+ ions from the cytoplasm to the extracellular space against their gradient by utilizing the energy released from ATP hydrolysis. A fine balance between these two processes controls the net amount of intracellular Na+ and aberrations in either of these two systems can have a large impact on cardiac contractility. Due to the relevant role of these two proteins in Na+ homeostasis, the emphasis of this review is on recent developments regarding the cardiac Na+/Ca2+ exchanger (NCX1) and Na+/K+ pump and the controversies that still persist in the field.
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Affiliation(s)
- Michael J Shattock
- King's College London BHF Centre of Excellence, The Rayne Institute, St Thomas' Hospital, London, SE1 7EH, UK
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118
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Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nat Commun 2015; 5:3309. [PMID: 24525480 DOI: 10.1038/ncomms4309] [Citation(s) in RCA: 407] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/24/2014] [Indexed: 01/23/2023] Open
Abstract
Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously renewed source of material for serial femtosecond crystallography. Data collected from sub-10-μm-sized crystals produced with less than 0.5 mg of purified protein yield structural insights regarding cyclopamine binding to the Smoothened receptor.
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119
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Chou AC, Ju YT, Pan CY. Calmodulin Interacts with the Sodium/Calcium Exchanger NCX1 to Regulate Activity. PLoS One 2015; 10:e0138856. [PMID: 26421717 PMCID: PMC4589332 DOI: 10.1371/journal.pone.0138856] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/04/2015] [Indexed: 11/22/2022] Open
Abstract
Changes in intracellular Ca2+ concentrations ([Ca2+]i) are an important signal for various physiological activities. The Na+/Ca2+ exchangers (NCX) at the plasma membrane transport Ca2+ into or out of the cell according to the electrochemical gradients of Na+ and Ca2+ to modulate [Ca2+]i homeostasis. Calmodulin (CaM) senses [Ca2+]i changes and relays Ca2+ signals by binding to target proteins such as channels and transporters. However, it is not clear how calmodulin modulates NCX activity. Using CaM as a bait, we pulled down the intracellular loops subcloned from the NCX1 splice variants NCX1.1 and NCX1.3. This interaction requires both Ca2+ and a putative CaM-binding segment (CaMS). To determine whether CaM modulates NCX activity, we co-expressed NCX1 splice variants with CaM or CaM1234 (a Ca2+-binding deficient mutant) in HEK293T cells and measured the increase in [Ca2+]i contributed by the influx of Ca2+ through NCX. Deleting the CaMS from NCX1.1 and NCX1.3 attenuated exchange activity and decreased membrane localization. Without the mutually exclusive exon, the exchange activity was decreased and could be partially rescued by CaM1234. Point-mutations at any of the 4 conserved a.a. residues in the CaMS had differential effects in NCX1.1 and NCX1.3. Mutating the first two conserved a.a. in NCX1.1 decreased exchange activity; mutating the 3rd or 4th conserved a.a. residues did not alter exchange activity, but CaM co-expression suppressed activity. Mutating the 2nd and 3rd conserved a.a. residues in NCX1.3 decreased exchange activity. Taken together, our results demonstrate that CaM senses changes in [Ca2+]i and binds to the cytoplasmic loop of NCX1 to regulate exchange activity.
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Affiliation(s)
- Ai-Chuan Chou
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Ten Ju
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chien-Yuan Pan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Brain and Mind Sciences, National Taiwan University, Taipei, Taiwan
- * E-mail:
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120
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Vergara-Jaque A, Fenollar-Ferrer C, Kaufmann D, Forrest LR. Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms. Front Pharmacol 2015; 6:183. [PMID: 26388773 PMCID: PMC4560100 DOI: 10.3389/fphar.2015.00183] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/13/2015] [Indexed: 12/04/2022] Open
Abstract
Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to one or other side of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (a)symmetry of these systems has been successfully used as a bioinformatic tool, called “repeat-swap modeling” to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that nucleoside transport also occurs via an elevator-like mechanism.
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Affiliation(s)
- Ariela Vergara-Jaque
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Cristina Fenollar-Ferrer
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Desirée Kaufmann
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Lucy R Forrest
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
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121
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Reilly L, Howie J, Wypijewski K, Ashford MLJ, Hilgemann DW, Fuller W. Palmitoylation of the Na/Ca exchanger cytoplasmic loop controls its inactivation and internalization during stress signaling. FASEB J 2015; 29:4532-43. [PMID: 26174834 PMCID: PMC4608915 DOI: 10.1096/fj.15-276493] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 06/30/2015] [Indexed: 01/02/2023]
Abstract
The electrogenic Na/Ca exchanger (NCX) mediates bidirectional Ca movements that are highly sensitive to changes of Na gradients in many cells. NCX1 is implicated in the pathogenesis of heart failure and a number of cardiac arrhythmias. We measured NCX1 palmitoylation using resin-assisted capture, the subcellular location of yellow fluorescent protein–NCX1 fusion proteins, and NCX1 currents using whole-cell voltage clamping. Rat NCX1 is substantially palmitoylated in all tissues examined. Cysteine 739 in the NCX1 large intracellular loop is necessary and sufficient for NCX1 palmitoylation. Palmitoylation of NCX1 occurs in the Golgi and anchors the NCX1 large regulatory intracellular loop to membranes. Surprisingly, palmitoylation does not influence trafficking or localization of NCX1 to surface membranes, nor does it strongly affect the normal forward or reverse transport modes of NCX1. However, exchangers that cannot be palmitoylated do not inactivate normally (leading to substantial activity in conditions when wild-type exchangers are inactive) and do not promote cargo-dependent endocytosis that internalizes 50% of the cell surface following strong G-protein activation or large Ca transients. The palmitoylated cysteine in NCX1 is found in all vertebrate and some invertebrate NCX homologs. Thus, NCX palmitoylation ubiquitously modulates Ca homeostasis and membrane domain function in cells that express NCX proteins.—Reilly, L., Howie, J., Wypijewski, K., Ashford, M. L. J., Hilgemann, D. W., Fuller, W. Palmitoylation of the Na/Ca exchanger cytoplasmic loop controls its inactivation and internalization during stress signaling.
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Affiliation(s)
- Louise Reilly
- *Division of Cardiovascular and Diabetes Medicine, Medical Research Institute, College of Medicine, Dentistry, and Nursing, University of Dundee, Dundee, United Kingdom; and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jacqueline Howie
- *Division of Cardiovascular and Diabetes Medicine, Medical Research Institute, College of Medicine, Dentistry, and Nursing, University of Dundee, Dundee, United Kingdom; and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Krzysztof Wypijewski
- *Division of Cardiovascular and Diabetes Medicine, Medical Research Institute, College of Medicine, Dentistry, and Nursing, University of Dundee, Dundee, United Kingdom; and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Michael L J Ashford
- *Division of Cardiovascular and Diabetes Medicine, Medical Research Institute, College of Medicine, Dentistry, and Nursing, University of Dundee, Dundee, United Kingdom; and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Donald W Hilgemann
- *Division of Cardiovascular and Diabetes Medicine, Medical Research Institute, College of Medicine, Dentistry, and Nursing, University of Dundee, Dundee, United Kingdom; and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - William Fuller
- *Division of Cardiovascular and Diabetes Medicine, Medical Research Institute, College of Medicine, Dentistry, and Nursing, University of Dundee, Dundee, United Kingdom; and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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122
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Liu JL, Eisenberg B. Numerical methods for a Poisson-Nernst-Planck-Fermi model of biological ion channels. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:012711. [PMID: 26274207 DOI: 10.1103/physreve.92.012711] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Indexed: 05/17/2023]
Abstract
Numerical methods are proposed for an advanced Poisson-Nernst-Planck-Fermi (PNPF) model for studying ion transport through biological ion channels. PNPF contains many more correlations than most models and simulations of channels, because it includes water and calculates dielectric properties consistently as outputs. This model accounts for the steric effect of ions and water molecules with different sizes and interstitial voids, the correlation effect of crowded ions with different valences, and the screening effect of polarized water molecules in an inhomogeneous aqueous electrolyte. The steric energy is shown to be comparable to the electrical energy under physiological conditions, demonstrating the crucial role of the excluded volume of particles and the voids in the natural function of channel proteins. Water is shown to play a critical role in both correlation and steric effects in the model. We extend the classical Scharfetter-Gummel (SG) method for semiconductor devices to include the steric potential for ion channels, which is a fundamental physical property not present in semiconductors. Together with a simplified matched interface and boundary (SMIB) method for treating molecular surfaces and singular charges of channel proteins, the extended SG method is shown to exhibit important features in flow simulations such as optimal convergence, efficient nonlinear iterations, and physical conservation. The generalized SG stability condition shows why the standard discretization (without SG exponential fitting) of NP equations may fail and that divalent Ca(2+) may cause more unstable discrete Ca(2+) fluxes than that of monovalent Na(+). Two different methods-called the SMIB and multiscale methods-are proposed for two different types of channels, namely, the gramicidin A channel and an L-type calcium channel, depending on whether water is allowed to pass through the channel. Numerical methods are first validated with constructed models whose exact solutions are known. The experimental data of both channels are then used to verify and explain novel features of PNPF as compared with previous PNP models. The PNPF currents are in accord with the experimental I-V (V for applied voltages) data of the gramicidin A channel and I-C (C for bath concentrations) data of the calcium channel with 10(-8)-fold bath concentrations that pose severe challenges in theoretical simulations.
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Affiliation(s)
- Jinn-Liang Liu
- Department of Applied Mathematics, National Hsinchu University of Education, Hsinchu 300, Taiwan
| | - Bob Eisenberg
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, Illinois 60612, USA
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123
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Lockless SW. Determinants of cation transport selectivity: Equilibrium binding and transport kinetics. J Gen Physiol 2015; 146:3-13. [PMID: 26078056 PMCID: PMC4485025 DOI: 10.1085/jgp.201511371] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/11/2015] [Indexed: 01/13/2023] Open
Abstract
The crystal structures of channels and transporters reveal the chemical nature of ion-binding sites and, thereby, constrain mechanistic models for their transport processes. However, these structures, in and of themselves, do not reveal equilibrium selectivity or transport preferences, which can be discerned only from various functional assays. In this Review, I explore the relationship between cation transport protein structures, equilibrium binding measurements, and ion transport selectivity. The primary focus is on K(+)-selective channels and nonselective cation channels because they have been extensively studied both functionally and structurally, but the principles discussed are relevant to other transport proteins and molecules.
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Affiliation(s)
- Steve W Lockless
- Department of Biology, Texas A&M University, College Station, TX 77843
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124
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Balaji S. Internal symmetry in protein structures: prevalence, functional relevance and evolution. Curr Opin Struct Biol 2015; 32:156-66. [PMID: 26093245 DOI: 10.1016/j.sbi.2015.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
Abstract
Symmetry has been found at various levels of biological organization in the protein structural universe. Numerous evolutionary studies have proposed connections between internal symmetry within protein tertiary structures, quaternary associations and protein functions. Recent computational methods, such as SymD and CE-Symm, facilitate a large-scale detection of internal symmetry in protein structures. Based on the results from these methods, about 20% of SCOP folds, superfamilies and families are estimated to have structures with internal symmetry (Figure 1d). All-β and membrane proteins fold classes contain a relatively high number of unique instances of internal symmetry. In addition to the axis of symmetry, anecdotal evidence suggests that, the region of connection or contact between symmetric units could coincide with functionally relevant sites within a fold. General principles that underlie protein internal symmetry and their connections to protein structural integrity and functions remain to be elucidated.
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Affiliation(s)
- Santhanam Balaji
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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125
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Shenoda B. The role of Na+/Ca2+ exchanger subtypes in neuronal ischemic injury. Transl Stroke Res 2015; 6:181-90. [PMID: 25860439 DOI: 10.1007/s12975-015-0395-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/09/2015] [Indexed: 01/03/2023]
Abstract
The Na(+)/Ca(2+) exchanger (NCX) plays an important role in the maintenance of Na(+) and Ca(2+) homeostasis in most cells including neurons under physiological and pathological conditions. It exists in three subtypes (NCX1-3) with different tissue distributions but all of them are present in the brain. NCX transports Na(+) and Ca(2+) in either Ca(2+)-efflux (forward) or Ca(2+)-influx (reverse) mode, depending on membrane potential and transmembrane ion gradients. During neuronal ischemia, Na(+) and Ca(2+) ionic disturbances favor NCX to work in reverse mode, giving rise to increased intracellular Ca(2+) levels, while it may regain its forward mode activity on reperfusion. The exact significance of NCX in neuronal ischemic and reperfusion states remains unclear. The differential role of NCX subtypes in ischemic neuronal injury has been extensively investigated using various pharmacological tools as well as genetic models. This review discusses the mode of action of NCX in ischemic and reperfusion states, the differential roles played by NCX subtypes in these states as well as the role of NCX in pre- and postconditioning. NCX subtypes carry variable roles in ischemic injury. Furthermore, the mode of action of each subtype varies in ischemia and reperfusion states. Thus, therapeutic targeting of NCX in stroke should be based on appropriate timing of the administration of NCX subtype-specific strategies.
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Affiliation(s)
- Botros Shenoda
- Department of Pharmacology and Physiology, Drexel University College of Medicine, 245 North 15th Street, Mail Stop #488, Philadelphia, PA, 19102, USA,
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126
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Balasubramaniam SL, Gopalakrishnapillai A, Gangadharan V, Duncan RL, Barwe SP. Sodium-calcium exchanger 1 regulates epithelial cell migration via calcium-dependent extracellular signal-regulated kinase signaling. J Biol Chem 2015; 290:12463-73. [PMID: 25770213 DOI: 10.1074/jbc.m114.629519] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 12/16/2022] Open
Abstract
Na(+)/Ca(2+) exchanger-1 (NCX1) is a major calcium extrusion mechanism in renal epithelial cells enabling the efflux of one Ca(2+) ion and the influx of three Na(+) ions. The gradient for this exchange activity is provided by Na,K-ATPase, a hetero-oligomer consisting of a catalytic α-subunit and a regulatory β-subunit (Na,K-β) that also functions as a motility and tumor suppressor. We showed earlier that mice with heart-specific ablation (KO) of Na,K-β had a specific reduction in NCX1 protein and were ouabain-insensitive. Here, we demonstrate that Na,K-β associates with NCX1 and regulates its localization to the cell surface. Madin-Darby canine kidney cells with Na,K-β knockdown have reduced NCX1 protein and function accompanied by 2.1-fold increase in free intracellular calcium and a corresponding increase in the rate of cell migration. Increased intracellular calcium up-regulated ERK1/2 via calmodulin-dependent activation of PI3K. Both myosin light chain kinase and Rho-associated kinase acted as mediators of ERK1/2-dependent migration. Restoring NCX1 expression in β-KD cells reduced migration rate and ERK1/2 activation, suggesting that NCX1 functions downstream of Na,K-β in regulating cell migration. In parallel, inhibition of NCX1 by KB-R7943 in Madin-Darby canine kidney cells, LLC-PK1, and human primary renal epithelial cells (HREpiC) increased ERK1/2 activation and cell migration. This increased migration was associated with high myosin light chain phosphorylation by PI3K/ERK-dependent mechanism in HREpiC cells. These data confirm the role of NCX1 activity in regulating renal epithelial cell migration.
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Affiliation(s)
- Sona Lakshme Balasubramaniam
- From the Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware 19803 and Department of Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - Anilkumar Gopalakrishnapillai
- From the Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware 19803 and
| | - Vimal Gangadharan
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - Randall L Duncan
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - Sonali P Barwe
- From the Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware 19803 and Department of Biological Sciences, University of Delaware, Newark, Delaware 19716
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127
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Fowler PW, Orwick-Rydmark M, Radestock S, Solcan N, Dijkman PM, Lyons JA, Kwok J, Caffrey M, Watts A, Forrest LR, Newstead S. Gating topology of the proton-coupled oligopeptide symporters. Structure 2015; 23:290-301. [PMID: 25651061 PMCID: PMC4321885 DOI: 10.1016/j.str.2014.12.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/21/2014] [Accepted: 12/03/2014] [Indexed: 01/10/2023]
Abstract
Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport.
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Affiliation(s)
- Philip W Fowler
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | | | - Sebastian Radestock
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, Germany
| | - Nicolae Solcan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Patricia M Dijkman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joseph A Lyons
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Jane Kwok
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Caffrey
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lucy R Forrest
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, Germany
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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128
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Liu W, Wacker D, Wang C, Abola E, Cherezov V. Femtosecond crystallography of membrane proteins in the lipidic cubic phase. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130314. [PMID: 24914147 DOI: 10.1098/rstb.2013.0314] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Despite recent technological advances in heterologous expression, stabilization and crystallization of membrane proteins (MPs), their structural studies remain difficult and require new transformative approaches. During the past two years, crystallization in lipidic cubic phase (LCP) has started gaining a widespread acceptance, owing to the spectacular success in high-resolution structure determination of G protein-coupled receptors (GPCRs) and to the introduction of commercial instrumentation, tools and protocols. The recent appearance of X-ray free-electron lasers (XFELs) has enabled structure determination from substantially smaller crystals than previously possible with minimal effects of radiation damage, offering new exciting opportunities in structural biology. The unique properties of LCP material have been exploited to develop special protocols and devices that have established a new method of serial femtosecond crystallography of MPs in LCP (LCP-SFX). In this method, microcrystals are generated in LCP and streamed continuously inside the same media across the intersection with a pulsed XFEL beam at a flow rate that can be adjusted to minimize sample consumption. Pioneering studies that yielded the first room temperature GPCR structures, using a few hundred micrograms of purified protein, validate the LCP-SFX approach and make it attractive for structure determination of difficult-to-crystallize MPs and their complexes with interacting partners. Together with the potential of femtosecond data acquisition to interrogate unstable intermediate functional states of MPs, LCP-SFX holds promise to advance our understanding of this biomedically important class of proteins.
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Affiliation(s)
- Wei Liu
- Marine Drug Research Institute, Huaihai Institute of Technology, Lianyungang 222005, People's Republic of China Department of Integrated Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel Wacker
- Department of Integrated Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chong Wang
- Department of Integrated Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Enrique Abola
- Department of Integrated Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Vadim Cherezov
- Department of Integrated Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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129
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Towards Understanding the Role of the Na+-Ca2+ Exchanger Isoform 3. Rev Physiol Biochem Pharmacol 2015; 168:31-57. [DOI: 10.1007/112_2015_23] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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130
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Caffrey M. A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:3-18. [PMID: 25615961 PMCID: PMC4304740 DOI: 10.1107/s2053230x14026843] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/05/2014] [Indexed: 01/12/2023]
Abstract
A comprehensive and up-to-date review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes is reported. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The lipid cubic phase or in meso method is a robust approach for crystallizing membrane proteins for structure determination. The uptake of the method is such that it is experiencing what can only be described as explosive growth. This timely, comprehensive and up-to-date review introduces the reader to the practice of in meso crystallogenesis, to the associated challenges and to their solutions. A model of how crystallization comes about mechanistically is presented for a more rational approach to crystallization. The possible involvement of the lamellar and inverted hexagonal phases in crystallogenesis and the application of the method to water-soluble, monotopic and lipid-anchored proteins are addressed. How to set up trials manually and automatically with a robot is introduced with reference to open-access online videos that provide a practical guide to all aspects of the method. These range from protein reconstitution to crystal harvesting from the hosting mesophase, which is noted for its viscosity and stickiness. The sponge phase, as an alternative medium in which to perform crystallization, is described. The compatibility of the method with additive lipids, detergents, precipitant-screen components and materials carried along with the protein such as denaturants and reducing agents is considered. The powerful host and additive lipid-screening strategies are described along with how samples that have low protein concentration and cell-free expressed protein can be used. Assaying the protein reconstituted in the bilayer of the cubic phase for function is an important element of quality control and is detailed. Host lipid design for crystallization at low temperatures and for large proteins and complexes is outlined. Experimental phasing by heavy-atom derivatization, soaking or co-crystallization is routine and the approaches that have been implemented to date are described. An overview and a breakdown by family and function of the close to 200 published structures that have been obtained using in meso-grown crystals are given. Recommendations for conducting the screening process to give a more productive outcome are summarized. The fact that the in meso method also works with soluble proteins should not be overlooked. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The review ends with a view to the future and to the bright prospects for the method, which continues to contribute to our understanding of the molecular mechanisms of some of nature’s most valued proteinaceous robots.
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Affiliation(s)
- Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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131
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Li D, Pye VE, Caffrey M. Experimental phasing for structure determination using membrane-protein crystals grown by the lipid cubic phase method. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:104-22. [PMID: 25615865 PMCID: PMC4304691 DOI: 10.1107/s1399004714010360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/07/2014] [Indexed: 03/02/2023]
Abstract
Despite the marked increase in the number of membrane-protein structures solved using crystals grown by the lipid cubic phase or in meso method, only ten have been determined by SAD/MAD. This is likely to be a consequence of the technical difficulties associated with handling proteins and crystals in the sticky and viscous hosting mesophase that is usually incubated in glass sandwich plates for the purposes of crystallization. Here, a four-year campaign aimed at phasing the in meso structure of the integral membrane diacylglycerol kinase (DgkA) from Escherichia coli is reported. Heavy-atom labelling of this small hydrophobic enzyme was attempted by pre-labelling, co-crystallization, soaking, site-specific mercury binding to genetically engineered single-cysteine mutants and selenomethionine incorporation. Strategies and techniques for special handling are reported, as well as the typical results and the lessons learned for each of these approaches. In addition, an assay to assess the accessibility of cysteine residues in membrane proteins for mercury labelling is introduced. The various techniques and strategies described will provide a valuable reference for future experimental phasing of membrane proteins where crystals are grown by the lipid cubic phase method.
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Affiliation(s)
- Dianfan Li
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Valerie E. Pye
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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132
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Zhao K, Wu H. Structure-dependent water transport across nanopores of carbon nanotubes: toward selective gating upon temperature regulation. Phys Chem Chem Phys 2015; 17:10343-7. [DOI: 10.1039/c4cp06054g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An ultrafast-slow flow transition phenomenon for water transport across nanopores is induced by the change in water structure in nanopores.
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Affiliation(s)
- Kuiwen Zhao
- School of Mechanical Engineering
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Huiying Wu
- School of Mechanical Engineering
- Shanghai Jiao Tong University
- Shanghai
- China
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133
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Liu JL, Eisenberg B. Poisson-Nernst-Planck-Fermi theory for modeling biological ion channels. J Chem Phys 2014; 141:22D532. [DOI: 10.1063/1.4902973] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jinn-Liang Liu
- Department of Applied Mathematics, National Hsinchu University of Education, Hsinchu 300, Taiwan
| | - Bob Eisenberg
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, Illinois 60612, USA
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134
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Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation. Proc Natl Acad Sci U S A 2014; 111:E5354-62. [PMID: 25468964 DOI: 10.1073/pnas.1415751111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Na(+)/Ca(2+) exchangers (NCXs) are ubiquitous membrane transporters with a key role in Ca(2+) homeostasis and signaling. NCXs mediate the bidirectional translocation of either Na(+) or Ca(2+), and thus can catalyze uphill Ca(2+) transport driven by a Na(+) gradient, or vice versa. In a major breakthrough, a prokaryotic NCX homolog (NCX_Mj) was recently isolated and its crystal structure determined at atomic resolution. The structure revealed an intriguing architecture consisting of two inverted-topology repeats, each comprising five transmembrane helices. These repeats adopt asymmetric conformations, yielding an outward-facing occluded state. The crystal structure also revealed four putative ion-binding sites, but the occupancy and specificity thereof could not be conclusively established. Here, we use molecular-dynamics simulations and free-energy calculations to identify the ion configuration that best corresponds to the crystallographic data and that is also thermodynamically optimal. In this most probable configuration, three Na(+) ions occupy the so-called Sext, SCa, and Sint sites, whereas the Smid site is occupied by one water molecule and one H(+), which protonates an adjacent aspartate side chain (D240). Experimental measurements of Na(+)/Ca(2+) and Ca(2+)/Ca(2+) exchange by wild-type and mutagenized NCX_Mj confirm that transport of both Na(+) and Ca(2+) requires protonation of D240, and that this side chain does not coordinate either ion at Smid. These results imply that the ion exchange stoichiometry of NCX_Mj is 3:1 and that translocation of Na(+) across the membrane is electrogenic, whereas transport of Ca(2+) is not. Altogether, these findings provide the basis for further experimental and computational studies of the conformational mechanism of this exchanger.
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135
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Cai X, Wang X, Patel S, Clapham DE. Insights into the early evolution of animal calcium signaling machinery: a unicellular point of view. Cell Calcium 2014; 57:166-73. [PMID: 25498309 PMCID: PMC4355082 DOI: 10.1016/j.ceca.2014.11.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 11/15/2022]
Abstract
The basic principles of Ca(2+) regulation emerged early in prokaryotes. Ca(2+) signaling acquired more extensive and varied functions when life evolved into multicellular eukaryotes with intracellular organelles. Animals, fungi and plants display differences in the mechanisms that control cytosolic Ca(2+) concentrations. The aim of this review is to examine recent findings from comparative genomics of Ca(2+) signaling molecules in close unicellular relatives of animals and in common unicellular ancestors of animals and fungi. Also discussed are the evolution and origins of the sperm-specific CatSper channel complex, cation/Ca(2+) exchangers and four-domain voltage-gated Ca(2+) channels. Newly identified evolutionary evidence suggests that the distinct Ca(2+) signaling machineries in animals, plants and fungi likely originated from an ancient Ca(2+) signaling machinery prior to early eukaryotic radiation.
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Affiliation(s)
- Xinjiang Cai
- Division of Endocrinology, Metabolism and Nutrition, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA.
| | - Xiangbing Wang
- Division of Endocrinology, Metabolism and Nutrition, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - Sandip Patel
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - David E Clapham
- Howard Hughes Medical Institute, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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136
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He C, O'Halloran DM. Analysis of the Na+/Ca2+ exchanger gene family within the phylum Nematoda. PLoS One 2014; 9:e112841. [PMID: 25397810 PMCID: PMC4232491 DOI: 10.1371/journal.pone.0112841] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 10/16/2014] [Indexed: 02/07/2023] Open
Abstract
Na+/Ca2+ exchangers are low affinity, high capacity transporters that rapidly transport calcium at the plasma membrane, mitochondrion, endoplasmic (and sarcoplasmic) reticulum, and the nucleus. Na+/Ca2+ exchangers are widely expressed in diverse cell types where they contribute homeostatic balance to calcium levels. In animals, Na+/Ca2+ exchangers are divided into three groups based upon stoichiometry: Na+/Ca2+ exchangers (NCX), Na+/Ca2+/K+ exchangers (NCKX), and Ca2+/Cation exchangers (CCX). In mammals there are three NCX genes, five NCKX genes and one CCX (NCLX) gene. The genome of the nematode Caenorhabditis elegans contains ten Na+/Ca2+ exchanger genes: three NCX; five CCX; and two NCKX genes. Here we set out to characterize structural and taxonomic specializations within the family of Na+/Ca2+ exchangers across the phylum Nematoda. In this analysis we identify Na+/Ca2+ exchanger genes from twelve species of nematodes and reconstruct their phylogenetic and evolutionary relationships. The most notable feature of the resulting phylogenies was the heterogeneous evolution observed within exchanger subtypes. Specifically, in the case of the CCX exchangers we did not detect members of this class in three Clade III nematodes. Within the Caenorhabditis and Pristionchus lineages we identify between three and five CCX representatives, whereas in other Clade V and also Clade IV nematode taxa we only observed a single CCX gene in each species, and in the Clade III nematode taxa that we sampled we identify NCX and NCKX encoding genes but no evidence of CCX representatives using our mining approach. We also provided re-annotation for predicted CCX gene structures from Heterorhabditis bacteriophora and Caenorhabditis japonica by RT-PCR and sequencing. Together, these findings reveal a complex picture of Na+/Ca2+ transporters in nematodes that suggest an incongruent evolutionary history of proteins that provide central control of calcium dynamics.
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Affiliation(s)
- Chao He
- Department of Biological Sciences, The George Washington University, Washington, D.C., United States of America
- Institute for Neuroscience, The George Washington University, Washington, D.C., United States of America
| | - Damien M. O'Halloran
- Department of Biological Sciences, The George Washington University, Washington, D.C., United States of America
- Institute for Neuroscience, The George Washington University, Washington, D.C., United States of America
- * E-mail:
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137
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Wanichawan P, Hafver TL, Hodne K, Aronsen JM, Lunde IG, Dalhus B, Lunde M, Kvaløy H, Louch WE, Tønnessen T, Sjaastad I, Sejersted OM, Carlson CR. Molecular basis of calpain cleavage and inactivation of the sodium-calcium exchanger 1 in heart failure. J Biol Chem 2014; 289:33984-98. [PMID: 25336645 DOI: 10.1074/jbc.m114.602581] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cardiac sodium (Na(+))-calcium (Ca(2+)) exchanger 1 (NCX1) is central to the maintenance of normal Ca(2+) homeostasis and contraction. Studies indicate that the Ca(2+)-activated protease calpain cleaves NCX1. We hypothesized that calpain is an important regulator of NCX1 in response to pressure overload and aimed to identify molecular mechanisms and functional consequences of calpain binding and cleavage of NCX1 in the heart. NCX1 full-length protein and a 75-kDa NCX1 fragment along with calpain were up-regulated in aortic stenosis patients and rats with heart failure. Patients with coronary artery disease and sham-operated rats were used as controls. Calpain co-localized, co-fractionated, and co-immunoprecipitated with NCX1 in rat cardiomyocytes and left ventricle lysate. Immunoprecipitations, pull-down experiments, and extensive use of peptide arrays indicated that calpain domain III anchored to the first Ca(2+) binding domain in NCX1, whereas the calpain catalytic region bound to the catenin-like domain in NCX1. The use of bioinformatics, mutational analyses, a substrate competitor peptide, and a specific NCX1-Met(369) antibody identified a novel calpain cleavage site at Met(369). Engineering NCX1-Met(369) into a tobacco etch virus protease cleavage site revealed that specific cleavage at Met(369) inhibited NCX1 activity (both forward and reverse mode). Finally, a short peptide fragment containing the NCX1-Met(369) cleavage site was modeled into the narrow active cleft of human calpain. Inhibition of NCX1 activity, such as we have observed here following calpain-induced NCX1 cleavage, might be beneficial in pathophysiological conditions where increased NCX1 activity contributes to cardiac dysfunction.
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Affiliation(s)
- Pimthanya Wanichawan
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, the KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, 0318 Oslo, Norway
| | - Tandekile Lubelwana Hafver
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, the KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, 0318 Oslo, Norway
| | - Kjetil Hodne
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, the KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, 0318 Oslo, Norway
| | - Jan Magnus Aronsen
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, Bjorknes College, 0456 Oslo, Norway
| | - Ida Gjervold Lunde
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, the KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, 0318 Oslo, Norway, the Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Bjørn Dalhus
- the Departments of Microbiology and Medical Biochemistry, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway, and
| | - Marianne Lunde
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, the KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, 0318 Oslo, Norway
| | - Heidi Kvaløy
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, the KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, 0318 Oslo, Norway
| | - William Edward Louch
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, the KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, 0318 Oslo, Norway
| | - Theis Tønnessen
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, the Department of Cardiothoracic Surgery, Oslo University Hospital, Ullevål, 0407 Oslo, Norway
| | - Ivar Sjaastad
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, the KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, 0318 Oslo, Norway
| | - Ole Mathias Sejersted
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, the KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, 0318 Oslo, Norway
| | - Cathrine Rein Carlson
- From the Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway, the KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, 0318 Oslo, Norway,
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138
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de Juan-Sanz J, Núñez E, Zafra F, Berrocal M, Corbacho I, Ibáñez I, Arribas-González E, Marcos D, López-Corcuera B, Mata AM, Aragón C. Presynaptic control of glycine transporter 2 (GlyT2) by physical and functional association with plasma membrane Ca2+-ATPase (PMCA) and Na+-Ca2+ exchanger (NCX). J Biol Chem 2014; 289:34308-24. [PMID: 25315779 DOI: 10.1074/jbc.m114.586966] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fast inhibitory glycinergic transmission occurs in spinal cord, brainstem, and retina to modulate the processing of motor and sensory information. After synaptic vesicle fusion, glycine is recovered back to the presynaptic terminal by the neuronal glycine transporter 2 (GlyT2) to maintain quantal glycine content in synaptic vesicles. The loss of presynaptic GlyT2 drastically impairs the refilling of glycinergic synaptic vesicles and severely disrupts neurotransmission. Indeed, mutations in the gene encoding GlyT2 are the main presynaptic cause of hyperekplexia in humans. Here, we show a novel endogenous regulatory mechanism that can modulate GlyT2 activity based on a compartmentalized interaction between GlyT2, neuronal plasma membrane Ca(2+)-ATPase (PMCA) isoforms 2 and 3, and Na(+)/Ca(2+)-exchanger 1 (NCX1). This GlyT2·PMCA2,3·NCX1 complex is found in lipid raft subdomains where GlyT2 has been previously found to be fully active. We show that endogenous PMCA and NCX activities are necessary for GlyT2 activity and that this modulation depends on lipid raft integrity. Besides, we propose a model in which GlyT2·PMCA2-3·NCX complex would help Na(+)/K(+)-ATPase in controlling local Na(+) increases derived from GlyT2 activity after neurotransmitter release.
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Affiliation(s)
- Jaime de Juan-Sanz
- From the Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065
| | - Enrique Núñez
- the Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049-Madrid, Spain, the Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 46009-Valencia, Spain, the IdiPAZ-Hospital, Universitario La Paz, 28046-Madrid, Spain, and
| | - Francisco Zafra
- the Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049-Madrid, Spain, the Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 46009-Valencia, Spain, the IdiPAZ-Hospital, Universitario La Paz, 28046-Madrid, Spain, and
| | - María Berrocal
- the Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06006-Badajoz, Spain
| | - Isaac Corbacho
- the Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06006-Badajoz, Spain
| | - Ignacio Ibáñez
- the Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049-Madrid, Spain, the Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 46009-Valencia, Spain, the IdiPAZ-Hospital, Universitario La Paz, 28046-Madrid, Spain, and
| | - Esther Arribas-González
- the Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049-Madrid, Spain, the Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 46009-Valencia, Spain, the IdiPAZ-Hospital, Universitario La Paz, 28046-Madrid, Spain, and
| | - Daniel Marcos
- the Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06006-Badajoz, Spain
| | - Beatriz López-Corcuera
- the Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049-Madrid, Spain, the Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 46009-Valencia, Spain, the IdiPAZ-Hospital, Universitario La Paz, 28046-Madrid, Spain, and
| | - Ana M Mata
- the Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06006-Badajoz, Spain
| | - Carmen Aragón
- the Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049-Madrid, Spain, the Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 46009-Valencia, Spain, the IdiPAZ-Hospital, Universitario La Paz, 28046-Madrid, Spain, and
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139
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Almagor L, Giladi M, van Dijk L, Buki T, Hiller R, Khananshvili D. Functional asymmetry of bidirectional Ca2+-movements in an archaeal sodium-calcium exchanger (NCX_Mj). Cell Calcium 2014; 56:276-84. [PMID: 25218934 DOI: 10.1016/j.ceca.2014.08.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/11/2014] [Accepted: 08/20/2014] [Indexed: 11/25/2022]
Abstract
Dynamic features of Ca(2+) interactions with transport and regulatory sites control the Ca(2+)-fluxes in mammalian Na(+)/Ca(2+)(NCX) exchangers bearing the Ca(2+)-binding regulatory domains on the cytosolic 5L6 loop. The crystal structure of Methanococcus jannaschii NCX (NCX_Mj) may serve as a template for studying ion-transport mechanisms since NCX_Mj does not contain the regulatory domains. The turnover rate of Na(+)/Ca(2+) exchange (kcat=0.5±0.2 s(-1)) in WT-NCX_Mj is 10(3)-10(4) times slower than in mammalian NCX. In NCX_Mj, the intrinsic equilibrium (Kint) for bidirectional Ca(2+) movements (defined as the ratio between the cytosolic and extracellular Km of Ca(2+)/Ca(2+) exchange) is asymmetric, Kint=0.15±0.5. Therefore, the Ca(2+) movement from the cytosol to the extracellular side is ∼7-times faster than in the opposite direction, thereby representing a stabilization of outward-facing (extracellular) access. This intrinsic asymmetry accounts for observed differences in the cytosolic and extracellulr Km values having a physiological relevance. Bidirectional Ca(2+) movements are also asymmetric in mammalian NCX. Thus, the stabilization of the outward-facing access along the transport cycle is a common feature among NCX orthologs despite huge differences in the ion-transport kinetics. Elongation of the cytosolic 5L6 loop in NCX_Mj by 8 or 14 residues accelerates the ion transport rates (kcat) ∼10 fold, while increasing the Kint values 100-250-fold (Kint=15-35). Therefore, 5L6 controls both the intrinsic equilibrium and rates of bidirectional Ca(2+) movements in NCX proteins. Some additional structural elements may shape the kinetic variances among phylogenetically distant NCX variants, although the intrinsic asymmetry (Kint) of bidirectional Ca(2+) movements seems to be comparable among evolutionary diverged NCX variants.
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Affiliation(s)
- Lior Almagor
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Moshe Giladi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Liat van Dijk
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Tal Buki
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel.
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140
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Liu JL, Eisenberg B. Analytical models of calcium binding in a calcium channel. J Chem Phys 2014; 141:075102. [DOI: 10.1063/1.4892839] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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141
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Chang Y, Bruni R, Kloss B, Assur Z, Kloppmann E, Rost B, Hendrickson WA, Liu Q. Structural basis for a pH-sensitive calcium leak across membranes. Science 2014; 344:1131-5. [PMID: 24904158 DOI: 10.1126/science.1252043] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Calcium homeostasis balances passive calcium leak and active calcium uptake. Human Bax inhibitor-1 (hBI-1) is an antiapoptotic protein that mediates a calcium leak and is representative of a highly conserved and widely distributed family, the transmembrane Bax inhibitor motif (TMBIM) proteins. Here, we present crystal structures of a bacterial homolog and characterize its calcium leak activity. The structure has a seven-transmembrane-helix fold that features two triple-helix sandwiches wrapped around a central C-terminal helix. Structures obtained in closed and open conformations are reversibly interconvertible by change of pH. A hydrogen-bonded, pKa (where Ka is the acid dissociation constant)-perturbed pair of conserved aspartate residues explains the pH dependence of this transition, and biochemical studies show that pH regulates calcium influx in proteoliposomes. Homology models for hBI-1 provide insights into TMBIM-mediated calcium leak and cytoprotective activity.
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Affiliation(s)
- Yanqi Chang
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA
| | - Renato Bruni
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA
| | - Zahra Assur
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Edda Kloppmann
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. Department of Bioinformatics and Computational Biology, Fakultät für Informatik, Technische Universität München, Garching, Germany
| | - Burkhard Rost
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. Department of Bioinformatics and Computational Biology, Fakultät für Informatik, Technische Universität München, Garching, Germany
| | - Wayne A Hendrickson
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. New York Structural Biology Center, National Synchrotron Light Source (NSLS) X4, Brookhaven National Laboratory, Upton, NY 11973, USA. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Qun Liu
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. New York Structural Biology Center, National Synchrotron Light Source (NSLS) X4, Brookhaven National Laboratory, Upton, NY 11973, USA.
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142
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Koshy C, Ziegler C. Structural insights into functional lipid-protein interactions in secondary transporters. Biochim Biophys Acta Gen Subj 2014; 1850:476-87. [PMID: 24859688 DOI: 10.1016/j.bbagen.2014.05.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Structural evidences with functional corroborations have revealed distinct features of lipid-protein interactions especially in channels and receptors. Many membrane embedded transporters are also known to require specific lipids for their functions and for some of them cellular and biochemical data suggest tight regulation by the lipid bilayer. However, molecular details on lipid-protein interactions in transporters are sparse since lipids are either depleted from the detergent solubilized transporters in three-dimensional crystals or not readily resolved in crystal structures. Nevertheless the steady increase in the progress of transporter structure determination contributed more examples of structures with resolved lipids. SCOPE OF REVIEW This review gives an overview on transporter structures in complex with lipids reported to date and discusses commonly encountered difficulties in the identification of functionally significant lipid-protein interactions based on those structures and functional in vitro data. Recent structures provided molecular details into regulation mechanism of transporters by specific lipids. The review highlights common findings and conserved patterns for distantly related transporter families to draw a more general picture on the regulatory role of lipid-protein interactions. MAJOR CONCLUSIONS Several common themes of the manner in which lipids directly influence membrane-mediated folding, oligomerization and structure stability can be found. Especially for LeuT-like fold transporters similarities in structurally resolved lipid-protein interactions suggest a common way in which transporter conformations are affected by lipids even in evolutionarily distinct transporters. Lipids appear to play an additional role as joints mechanically reinforcing the inverted repeat topology, which is a major determinant in the alternating access mechanism of secondary transporters. GENERAL SIGNIFICANCE This review brings together and adds to the repertoire of knowledge on lipid-protein interactions of functional significance presented in structures of membrane transporters. Knowledge of specific lipid-binding sites and modes of lipid influence on these proteins not only accomplishes the molecular description of transport cycle further, but also sheds light into localization dependent differences of transporter function. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Caroline Koshy
- Max Planck Institute of Biophysics, Structural Biology Department, Frankfurt am Main, Germany; Max-Planck Institute of Biophysics, Computational Structural Biology Group, Frankfurt am Main, Germany
| | - Christine Ziegler
- Max Planck Institute of Biophysics, Structural Biology Department, Frankfurt am Main, Germany; Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany.
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143
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Coupling between inter-helical hydrogen bonding and water dynamics in a proton transporter. J Struct Biol 2014; 186:95-111. [DOI: 10.1016/j.jsb.2014.02.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 02/13/2014] [Accepted: 02/15/2014] [Indexed: 12/20/2022]
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144
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Michel LYM, Verkaart S, Koopman WJH, Willems PHGM, Hoenderop JGJ, Bindels RJM. Function and regulation of the Na+-Ca2+ exchanger NCX3 splice variants in brain and skeletal muscle. J Biol Chem 2014; 289:11293-11303. [PMID: 24616101 DOI: 10.1074/jbc.m113.529388] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Isoform 3 of the Na(+)-Ca(2+) exchanger (NCX3) is crucial for maintaining intracellular calcium ([Ca(2+)]i) homeostasis in excitable tissues. In this sense NCX3 plays a key role in neuronal excitotoxicity and Ca(2+) extrusion during skeletal muscle relaxation. Alternative splicing generates two variants (NCX3-AC and NCX3-B). Here, we demonstrated that NCX3 variants display a tissue-specific distribution in mice, with NCX3-B as mostly expressed in brain and NCX-AC as predominant in skeletal muscle. Using Fura-2-based Ca(2+) imaging, we measured the capacity and regulation of the two variants during Ca(2+) extrusion and uptake in different conditions. Functional studies revealed that, although both variants are activated by intracellular sodium ([Na(+)]i), NCX3-AC has a higher [Na(+)]i sensitivity, as Ca(2+) influx is observed in the presence of extracellular Na(+). This effect could be partially mimicked for NCX3-B by mutating several glutamate residues in its cytoplasmic loop. In addition, NCX3-AC displayed a higher capacity of both Ca(2+) extrusion and uptake compared with NCX3-B, together with an increased sensitivity to intracellular Ca(2+). Strikingly, substitution of Glu(580) in NCX3-B with its NCX3-AC equivalent Lys(580) recapitulated the functional properties of NCX3-AC regarding Ca(2+) sensitivity, Lys(580) presumably acting through a structure stabilization of the Ca(2+) binding site. The higher Ca(2+) uptake capacity of NCX3-AC compared with NCX3-B is in line with the necessity to restore Ca(2+) levels in the sarcoplasmic reticulum during prolonged exercise. The latter result, consistent with the high expression in the slow-twitch muscle, suggests that this variant may contribute to the Ca(2+) handling beyond that of extruding Ca(2+).
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Affiliation(s)
- Lauriane Y M Michel
- From the Departments of Physiology and Radboud University Medical Centre, 6500HB Nijmegen, The Netherlands; Centre for System Biology and Bioenergetics, Radboud University Medical Centre, 6500HB Nijmegen, The Netherlands
| | - Sjoerd Verkaart
- From the Departments of Physiology and Radboud University Medical Centre, 6500HB Nijmegen, The Netherlands
| | - Werner J H Koopman
- Centre for System Biology and Bioenergetics, Radboud University Medical Centre, 6500HB Nijmegen, The Netherlands; Departments of Biochemistry, Radboud University Medical Centre, 6500HB Nijmegen, The Netherlands
| | - Peter H G M Willems
- Centre for System Biology and Bioenergetics, Radboud University Medical Centre, 6500HB Nijmegen, The Netherlands; Departments of Biochemistry, Radboud University Medical Centre, 6500HB Nijmegen, The Netherlands
| | - Joost G J Hoenderop
- From the Departments of Physiology and Radboud University Medical Centre, 6500HB Nijmegen, The Netherlands
| | - René J M Bindels
- From the Departments of Physiology and Radboud University Medical Centre, 6500HB Nijmegen, The Netherlands; Centre for System Biology and Bioenergetics, Radboud University Medical Centre, 6500HB Nijmegen, The Netherlands.
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145
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Batista-García RA, Sánchez-Reyes A, Millán-Pacheco C, González-Zuñiga VM, Juárez S, Folch-Mallol JL, Pastor N. A novel TctA citrate transporter from an activated sludge metagenome: structural and mechanistic predictions for the TTT family. Proteins 2014; 82:1756-64. [PMID: 24493659 DOI: 10.1002/prot.24529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 01/14/2014] [Accepted: 01/28/2014] [Indexed: 11/10/2022]
Abstract
We isolated a putative citrate transporter of the tripartite tricarboxylate transporter (TTT) class from a metagenomic library of activated sludge from a sewage treatment plant. The transporter, dubbed TctA_ar, shares ∼50% sequence identity with TctA of Comamonas testosteroni (TctA_ct) and other β-Proteobacteria, and contains two 20-amino acid repeat signature sequences, considered a hallmark of this particular transporter class. The structures for both TctA_ar and TctA_ct were modeled with I-TASSER and two possible structures for this transporter family were proposed. Docking assays with citrate resulted in the corresponding sets of proposed critical residues for function. These models suggest functions for the 20-amino acid repeats in the context of the two different architectures. This constitutes the first attempt at structure modeling of the TTT family, to the best of our knowledge, and could aid functional understanding of this little-studied family.
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146
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Götz AW, Clark MA, Walker RC. An extensible interface for QM/MM molecular dynamics simulations with AMBER. J Comput Chem 2014; 35:95-108. [PMID: 24122798 PMCID: PMC4063945 DOI: 10.1002/jcc.23444] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 08/05/2013] [Accepted: 08/31/2013] [Indexed: 11/09/2022]
Abstract
We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface.
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Affiliation(s)
- Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
| | - Matthew A. Clark
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
- Department of Chemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
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147
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Mi L, Chen Y, Zheng Z, Hou H, Chen W, Cui S. Beneficial metal ion insertion into dandelion-like MnS with enhanced catalytic performance and genetic morphology. RSC Adv 2014. [DOI: 10.1039/c4ra00961d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Large-scale novel hierarchical dandelion-like MnS was successfully synthesized with manganese complex as a template under mild reaction conditions.
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Affiliation(s)
- Liwei Mi
- Center For Advanced Functional Materials Research
- Zhongyuan University of Technology
- , P. R. China
- Key Laboratory for Micro-Nano Energy Storage and Conversion Materials of Henan Province
- Institute of Surface Micro and Nano Materials
| | - Yuanfang Chen
- Department of Chemistry
- Zhengzhou University
- , P. R. China
| | - Zhi Zheng
- Key Laboratory for Micro-Nano Energy Storage and Conversion Materials of Henan Province
- Institute of Surface Micro and Nano Materials
- Xuchang University
- , P. R. China
| | - Hongwei Hou
- Department of Chemistry
- Zhengzhou University
- , P. R. China
| | - Weihua Chen
- Department of Chemistry
- Zhengzhou University
- , P. R. China
| | - Shizhong Cui
- Center For Advanced Functional Materials Research
- Zhongyuan University of Technology
- , P. R. China
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148
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149
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Abstract
Members of the urea transporter (UT) family mediate rapid, selective transport of urea down its concentration gradient. To date, crystal structures of two evolutionarily distant UTs have been solved. These structures reveal a common UT fold involving two structurally homologous domains that encircle a continuous membrane-spanning pore and indicate that UTs transport urea via a channel-like mechanism. Examination of the conserved architecture of the pore, combined with crystal structures of ligand-bound proteins, molecular dynamics simulations, and functional data on permeation and inhibition by a broad range of urea analogs and other small molecules, provides insight into the structural basis of urea permeation and selectivity.
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Affiliation(s)
- Elena J. Levin
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine 1 Baylor Plaza, Houston, TX 77030 USA
| | - Ming Zhou
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine 1 Baylor Plaza, Houston, TX 77030 USA
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150
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Sharma V, O'Halloran DM. Recent structural and functional insights into the family of sodium calcium exchangers. Genesis 2013; 52:93-109. [PMID: 24376088 DOI: 10.1002/dvg.22735] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 12/04/2013] [Accepted: 12/08/2013] [Indexed: 01/08/2023]
Abstract
Maintenance of calcium homeostasis is necessary for the development and survival of all animals. Calcium ions modulate excitability and bind effectors capable of initiating many processes such as muscular contraction and neurotransmission. However, excessive amounts of calcium in the cytosol or within intracellular calcium stores can trigger apoptotic pathways in cells that have been implicated in cardiac and neuronal pathologies. Accordingly, it is critical for cells to rapidly and effectively regulate calcium levels. The Na(+) /Ca(2+) exchangers (NCX), Na(+) /Ca(2+) /K(+) exchangers (NCKX), and Ca(2+) /Cation exchangers (CCX) are the three classes of sodium calcium antiporters found in animals. These exchanger proteins utilize an electrochemical gradient to extrude calcium. Although they have been studied for decades, much is still unknown about these proteins. In this review, we examine current knowledge about the structure, function, and physiology and also discuss their implication in various developmental disorders. Finally, we highlight recent data characterizing the family of sodium calcium exchangers in the model system, Caenorhabditis elegans, and propose that C. elegans may be an ideal model to complement other systems and help fill gaps in our knowledge of sodium calcium exchange biology.
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Affiliation(s)
- Vishal Sharma
- Department of Biological Sciences, The George Washington University, Washington, DC; Institute for Neuroscience, The George Washington University, Washington, DC
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