1
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Yeste M, Ahmad A, Viñolas E, Recuero S, Bonet S, Pinart E. Inhibition of forward and reverse transport of Ca 2+ via Na +/Ca 2+ exchangers (NCX) prevents sperm capacitation. Biol Res 2024; 57:57. [PMID: 39175101 PMCID: PMC11342557 DOI: 10.1186/s40659-024-00535-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 08/06/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND While calcium is known to play a crucial role in mammalian sperm physiology, how it flows in and out of the male gamete is not completely understood. Herein, we investigated the involvement of Na+/Ca2+ exchangers (NCX) in mammalian sperm capacitation. Using the pig as an animal model, we first confirmed the presence of NCX1 and NCX2 isoforms in the sperm midpiece. Next, we partially or totally blocked Ca2+ outflux (forward transport) via NCX1/NCX2 with different concentrations of SEA0400 (2-[4-[(2,5-difluorophenyl)methoxy]phenoxy]-5-ethoxyaniline; 0, 0.5, 5 and 50 µM) and Ca2+ influx (reverse transport) with SN6 (ethyl 2-[[4-[(4-nitrophenyl)methoxy]phenyl]methyl]-1,3-thiazolidine-4-carboxylate; 0, 0.3, 3 or 30 µM). Sperm were incubated under capacitating conditions for 180 min; after 120 min, progesterone was added to induce the acrosome reaction. At 0, 60, 120, 130, and 180 min, sperm motility, membrane lipid disorder, acrosome integrity, mitochondrial membrane potential (MMP), tyrosine phosphorylation of sperm proteins, and intracellular levels of Ca2+, reactive oxygen species (ROS) and superoxides were evaluated. RESULTS Partial and complete blockage of Ca2+ outflux and influx via NCX induced a significant reduction of sperm motility after progesterone addition. Early alterations on sperm kinematics were also observed, the effects being more obvious in totally blocked than in partially blocked samples. Decreased sperm motility and kinematics were related to both defective tyrosine phosphorylation and mitochondrial activity, the latter being associated to diminished MMP and ROS levels. As NCX blockage did not affect the lipid disorder of plasma membrane, the impaired acrosome integrity could result from reduced tyrosine phosphorylation. CONCLUSIONS Inhibition of outflux and influx of Ca2+ triggered similar effects, thus indicating that both forward and reverse Ca2+ transport through NCX exchangers are essential for sperm capacitation.
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Affiliation(s)
- Marc Yeste
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, ES-17003, Spain
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, ES-17003, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, ES-08010, Spain
| | - Adeel Ahmad
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, ES-17003, Spain
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, ES-17003, Spain
| | - Estel Viñolas
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, ES-17003, Spain
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, ES-17003, Spain
| | - Sandra Recuero
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, ES-17003, Spain
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, ES-17003, Spain
| | - Sergi Bonet
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, ES-17003, Spain
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, ES-17003, Spain
| | - Elisabeth Pinart
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, ES-17003, Spain.
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, ES-17003, Spain.
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2
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Nguyen K, Strauss T, Refaeli B, Hiller R, Vinogradova O, Khananshvili D. 19F-NMR Probing of Ion-Induced Conformational Changes in Detergent-Solubilized and Nanodisc-Reconstituted NCX_Mj. Int J Mol Sci 2024; 25:6909. [PMID: 39000018 PMCID: PMC11241019 DOI: 10.3390/ijms25136909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
Consecutive interactions of 3Na+ or 1Ca2+ with the Na+/Ca2+ exchanger (NCX) result in an alternative exposure (access) of the cytosolic and extracellular vestibules to opposite sides of the membrane, where ion-induced transitions between the outward-facing (OF) and inward-facing (IF) conformational states drive a transport cycle. Here, we investigate sub-state populations of apo and ion-bound species in the OF and IF states by analyzing detergent-solubilized and nanodisc-reconstituted preparations of NCX_Mj with 19F-NMR. The 19F probe was covalently attached to the cysteine residues at entry locations of the cytosolic and extracellular vestibules. Multiple sub-states of apo and ion-bound species were observed in nanodisc-reconstituted (but not in detergent-solubilized) NCX_Mj, meaning that the lipid-membrane environment preconditions multiple sub-state populations toward the OF/IF swapping. Most importantly, ion-induced sub-state redistributions occur within each major (OF or IF) state, where sub-state interconversions may precondition the OF/IF swapping. In contrast with large changes in population redistributions, the sum of sub-state populations within each inherent state (OF or IF) remains nearly unchanged upon ion addition. The present findings allow the further elucidation of structure-dynamic modules underlying ion-induced conformational changes that determine a functional asymmetry of ion access/translocation at opposite sides of the membrane and ion transport rates concurring physiological demands.
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Affiliation(s)
- Khiem Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
| | - Tali Strauss
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Bosmat Refaeli
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
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3
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Giladi M, Fojtík L, Strauss T, Da'adoosh B, Hiller R, Man P, Khananshvili D. Structural dynamics of Na + and Ca 2+ interactions with full-size mammalian NCX. Commun Biol 2024; 7:463. [PMID: 38627576 PMCID: PMC11021524 DOI: 10.1038/s42003-024-06159-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
Cytosolic Ca2+ and Na+ allosterically regulate Na+/Ca2+ exchanger (NCX) proteins to vary the NCX-mediated Ca2+ entry/exit rates in diverse cell types. To resolve the structure-based dynamic mechanisms underlying the ion-dependent allosteric regulation in mammalian NCXs, we analyze the apo, Ca2+, and Na+-bound species of the brain NCX1.4 variant using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations. Ca2+ binding to the cytosolic regulatory domains (CBD1 and CBD2) rigidifies the intracellular regulatory loop (5L6) and promotes its interaction with the membrane domains. Either Na+ or Ca2+ stabilizes the intracellular portions of transmembrane helices TM3, TM4, TM9, TM10, and their connecting loops (3L4 and 9L10), thereby exposing previously unappreciated regulatory sites. Ca2+ or Na+ also rigidifies the palmitoylation domain (TMH2), and neighboring TM1/TM6 bundle, thereby uncovering a structural entity for modulating the ion transport rates. The present analysis provides new structure-dynamic clues underlying the regulatory diversity among tissue-specific NCX variants.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel.
- Tel-Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel.
| | - Lukáš Fojtík
- Division BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Prumyslova, 595, 252 50 Vestec, Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, 128 00, Prague, Czech Republic
| | - Tali Strauss
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel
| | - Benny Da'adoosh
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel
| | - Petr Man
- Division BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Prumyslova, 595, 252 50 Vestec, Prague, Czech Republic.
- Department of Biochemistry, Faculty of Science, Charles University, 128 00, Prague, Czech Republic.
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel.
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4
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Marinelli F, Faraldo-Gómez JD. Conformational free-energy landscapes of a Na +/Ca 2+ exchanger explain its alternating-access mechanism and functional specificity. Proc Natl Acad Sci U S A 2024; 121:e2318009121. [PMID: 38588414 PMCID: PMC11032461 DOI: 10.1073/pnas.2318009121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/20/2024] [Indexed: 04/10/2024] Open
Abstract
Secondary-active transporters catalyze the movement of myriad substances across all cellular membranes, typically against opposing concentration gradients, and without consuming any ATP. To do so, these proteins employ an intriguing structural mechanism evolved to be activated only upon recognition or release of the transported species. We examine this self-regulated mechanism using a homolog of the cardiac Na+/Ca2+ exchanger as a model system. Using advanced computer simulations, we map out the complete functional cycle of this transporter, including unknown conformations that we validate against existing experimental data. Calculated free-energy landscapes reveal why this transporter functions as an antiporter rather than a symporter, why it specifically exchanges Na+ and Ca2+, and why the stoichiometry of this exchange is exactly 3:1. We also rationalize why the protein does not exchange H+ for either Ca2+ or Na+, despite being able to bind H+ and its high similarity with H+/Ca2+ exchangers. Interestingly, the nature of this transporter is not explained by its primary structural states, known as inward- and outward-open conformations; instead, the defining factor is the feasibility of conformational intermediates between those states, wherein access pathways leading to the substrate binding sites become simultaneously occluded from both sides of the membrane. This analysis offers a physically coherent, broadly transferable route to understand the emergence of function from structure among secondary-active membrane transporters.
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Affiliation(s)
- Fabrizio Marinelli
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20814
| | - José D. Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20814
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5
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Souza Bomfim GH, Mitaishvili E, Schnetkamp PP, Lacruz RS. Na+/Ca2+ exchange in enamel cells is dominated by the K+-dependent NCKX exchanger. J Gen Physiol 2024; 156:e202313372. [PMID: 37947795 PMCID: PMC10637953 DOI: 10.1085/jgp.202313372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/15/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Calcium (Ca2+) extrusion is an essential function of the enamel-forming ameloblasts, providing Ca2+ for extracellular mineralization. The plasma membrane Ca2+ ATPases (PMCAs) remove cytosolic Ca2+ (cCa2+) and were recently shown to be efficient when ameloblasts experienced low cCa2+ elevation. Sodium-calcium (Na+/Ca2+) exchange has higher capacity to extrude cCa2+, but there is limited evidence on the function of the two main families of Na+/Ca2+ exchangers in enamel formation. The purpose of this study was to analyze the function of the NCX (coded by SLC8) and the K+-dependent NCKX (coded by SLC24) exchangers in rat ameloblasts and to compare their efficacy in the two main stages of enamel formation: the enamel forming secretory stage and the mineralizing or maturation stage. mRNA expression profiling confirmed the expression of Slc8 and Slc24 genes in enamel cells, Slc24a4 being the most highly upregulated transcript during the maturation stage, when Ca2+ transport increases. Na+/Ca2+ exchange was analyzed in the Ca2+ influx mode in Fura-2 AM-loaded ameloblasts. We show that maturation-stage ameloblasts have a higher Na+/Ca2+ exchange capacity than secretory-stage cells. We also show that Na+/Ca2+ exchange in both stages is dominated by NCKX over NCX. The importance of NCKX function in ameloblasts may partly explain why mutations in the SLC24A4 gene, but not in SLC8 genes, result in enamel disease. Our results demonstrate that Na+/Ca2+ exchangers are fully operational in ameloblasts and that their contribution to Ca2+ homeostasis increases in the maturation stage, when Ca2+ transport need is higher.
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Affiliation(s)
| | - Erna Mitaishvili
- Department of Chemistry, Herbert H. Lehman College, City University of New York. PhD Program in Biology, The Graduate Center of The City University of New York, New York, NY, USA
| | - Paul P.M. Schnetkamp
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Rodrigo S. Lacruz
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, USA
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Khananshvili D. Neuronal and astrocyte NCX isoform/splice variants: How do they participate in Na + and Ca 2+ signalling? Cell Calcium 2023; 116:102818. [PMID: 37918135 DOI: 10.1016/j.ceca.2023.102818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023]
Abstract
NCX1, NCX2, and NCX3 gene isoforms and their splice variants are characteristically expressed in different regions of the brain. The tissue-specific splice variants of NCX1-3 isoforms show specific expression profiles in neurons and astrocytes, whereas the relevant NCX isoform/splice variants exhibit diverse allosteric modes of Na+- and Ca2+-dependent regulation. In general, overexpression of NCX1-3 genes leads to neuroprotective effects, whereas their ablation gains the opposite results. At this end, the partial contributions of NCX isoform/splice variants to neuroprotective effects remain unresolved. The glutamate-dependent Na+ entry generates Na+ transients (in response to neuronal cell activities), whereas the Na+-driven Ca2+ entry (through the reverse NCX mode) raises Ca2+ transients. This special mode of signal coupling translates Na+ transients into the Ca2+ signals while being a part of synaptic neurotransmission. This mechanism is of general interest since disease-related conditions (ischemia, metabolic stress, and stroke among many others) trigger Na+ and Ca2+ overload with deadly outcomes of downstream apoptosis and excitotoxicity. The recently discovered mechanisms of NCX allosteric regulation indicate that some NCX variants might play a critical role in the dynamic coupling of Na+-driven Ca2+ entry. In contrast, the others are less important or even could be dangerous under altered conditions (e.g., metabolic stress). This working hypothesis can be tested by applying advanced experimental approaches and highly focused computational simulations. This may allow the development of structure-based blockers/activators that can selectively modulate predefined NCX variants to lessen the life-threatening outcomes of excitotoxicity, ischemia, apoptosis, metabolic deprivation, brain injury, and stroke.
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Affiliation(s)
- Daniel Khananshvili
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel.
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7
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Structure-Based Function and Regulation of NCX Variants: Updates and Challenges. Int J Mol Sci 2022; 24:ijms24010061. [PMID: 36613523 PMCID: PMC9820601 DOI: 10.3390/ijms24010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
The plasma-membrane homeostasis Na+/Ca2+ exchangers (NCXs) mediate Ca2+ extrusion/entry to dynamically shape Ca2+ signaling/in biological systems ranging from bacteria to humans. The NCX gene orthologs, isoforms, and their splice variants are expressed in a tissue-specific manner and exhibit nearly 104-fold differences in the transport rates and regulatory specificities to match the cell-specific requirements. Selective pharmacological targeting of NCX variants could benefit many clinical applications, although this intervention remains challenging, mainly because a full-size structure of eukaryotic NCX is unavailable. The crystal structure of the archaeal NCX_Mj, in conjunction with biophysical, computational, and functional analyses, provided a breakthrough in resolving the ion transport mechanisms. However, NCX_Mj (whose size is nearly three times smaller than that of mammalian NCXs) cannot serve as a structure-dynamic model for imitating high transport rates and regulatory modules possessed by eukaryotic NCXs. The crystal structures of isolated regulatory domains (obtained from eukaryotic NCXs) and their biophysical analyses by SAXS, NMR, FRET, and HDX-MS approaches revealed structure-based variances of regulatory modules. Despite these achievements, it remains unclear how multi-domain interactions can decode and integrate diverse allosteric signals, thereby yielding distinct regulatory outcomes in a given ortholog/isoform/splice variant. This article summarizes the relevant issues from the perspective of future developments.
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8
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Giladi M, Mitra S, Simhaev L, Hiller R, Refaeli B, Strauss T, Baiz CR, Khananshvili D. Exploring the Li + transporting mutant of NCX_Mj for assigning ion binding sites of mitochondrial NCLX. Cell Calcium 2022; 107:102651. [PMID: 36116246 PMCID: PMC10124574 DOI: 10.1016/j.ceca.2022.102651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/14/2022] [Accepted: 09/01/2022] [Indexed: 11/02/2022]
Abstract
The plasma membrane (NCX) and mitochondrial (NCLX) Na+/Ca2+ exchangers are structurally related proteins, although they operate under strictly different ionic conditions and membrane potentials. In contrast with NCX, NCLX can transport either Li+ or Na+ in exchange for Ca2+. Whereas the crystal structure of the archaeal NCX (NCX_Mj) describes the binding sites for alternative binding of 3Na+ or 1Ca2+, these features remain elusive for NCLX due to the lack of structural information. To elucidate the ion-binding features of mitochondrial NCLX, we analyzed here the Li+-transporting NCLX_Mj mutant, produced by replacing the ion-coordinating residues in the archaeal NCX (NCX_Mj) to match the ion-coordinating residues of human NCLX. The NCLX_Mj-mediated Na+/Ca2+ or Li+/Ca2+ exchange rates are insensitive to varying voltage, consistent with an electroneutral ion exchange. Molecular dynamics (MD) simulations revealed that NCLX_Mj contains two novel Li+ binding sites with four ion-coordinating residues, derived from the three Na+ binding sites of NCX_Mj. The ion-coordination modes, observed in the MD simulations, were further supported by two-dimensional infrared (2D IR) spectroscopy and by testing the mutational effects on the ion fluxes. Collectively, our results revealed a structural basis for Li+ binding and electroneutral transport (2Na+/Li+:1Ca2+) by NCLX_Mj, meaning that the NCLX-mediated electroneutral transport may predefine mitochondrial Ca2+ and Na+ signaling to modulate cellular functions.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel; Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Sunayana Mitra
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA
| | - Luba Simhaev
- Computer-Assisted Drug Design Unit, Blavatnik Center for Drug Discovery, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Bosmat Refaeli
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Tali Strauss
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA.
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel.
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9
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Fagnen C, Bannwarth L, Oubella I, Zuniga D, Haouz A, Forest E, Scala R, Bendahhou S, De Zorzi R, Perahia D, Vénien-Bryan C. Integrative Study of the Structural and Dynamical Properties of a KirBac3.1 Mutant: Functional Implication of a Highly Conserved Tryptophan in the Transmembrane Domain. Int J Mol Sci 2021; 23:335. [PMID: 35008764 PMCID: PMC8745282 DOI: 10.3390/ijms23010335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 12/02/2022] Open
Abstract
ATP-sensitive potassium (K-ATP) channels are ubiquitously expressed on the plasma membrane of cells in several organs, including the heart, pancreas, and brain, and they govern a wide range of physiological processes. In pancreatic β-cells, K-ATP channels composed of Kir6.2 and SUR1 play a key role in coupling blood glucose and insulin secretion. A tryptophan residue located at the cytosolic end of the transmembrane helix is highly conserved in eukaryote and prokaryote Kir channels. Any mutation on this amino acid causes a gain of function and neonatal diabetes mellitus. In this study, we have investigated the effect of mutation on this highly conserved residue on a KirBac channel (prokaryotic homolog of mammalian Kir6.2). We provide the crystal structure of the mutant KirBac3.1 W46R (equivalent to W68R in Kir6.2) and its conformational flexibility properties using HDX-MS. In addition, the detailed dynamical view of the mutant during the gating was investigated using the in silico method. Finally, functional assays have been performed. A comparison of important structural determinants for the gating mechanism between the wild type KirBac and the mutant W46R suggests interesting structural and dynamical clues and a mechanism of action of the mutation that leads to the gain of function.
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Affiliation(s)
- Charline Fagnen
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, 4 Ave. des Sciences, 91190 Gif-sur-Yvette, France;
| | - Ludovic Bannwarth
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Iman Oubella
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Dania Zuniga
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Ahmed Haouz
- Institut Pasteur, C2RT-Plate-Forme de Cristallographie CNRS-UMR3528, 75724 Paris, France;
| | - Eric Forest
- CNRS, IBS, CEA, University Grenoble Alpes, 38044 Grenoble, France;
| | - Rosa Scala
- CNRS UMR7370, LP2M, Labex ICST, Faculté de Médecine, University Côte d’Azur, 06560 Nice, France; (R.S.); (S.B.)
| | - Saïd Bendahhou
- CNRS UMR7370, LP2M, Labex ICST, Faculté de Médecine, University Côte d’Azur, 06560 Nice, France; (R.S.); (S.B.)
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgeri 1, 34127 Trieste, Italy;
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, 4 Ave. des Sciences, 91190 Gif-sur-Yvette, France;
| | - Catherine Vénien-Bryan
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
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10
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Magli E, Fattorusso C, Persico M, Corvino A, Esposito G, Fiorino F, Luciano P, Perissutti E, Santagada V, Severino B, Tedeschi V, Pannaccione A, Pignataro G, Caliendo G, Annunziato L, Secondo A, Frecentese F. New Insights into the Structure-Activity Relationship and Neuroprotective Profile of Benzodiazepinone Derivatives of Neurounina-1 as Modulators of the Na +/Ca 2+ Exchanger Isoforms. J Med Chem 2021; 64:17901-17919. [PMID: 34845907 PMCID: PMC8713167 DOI: 10.1021/acs.jmedchem.1c01212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Due to the neuroprotective role of the Na+/Ca2+ exchanger (NCX) isoforms NCX1 and NCX3, we synthesized novel benzodiazepinone derivatives of the unique NCX activator Neurounina-1, named compounds 1-19. The derivatives are characterized by a benzodiazepinonic nucleus linked to five- or six-membered cyclic amines via a methylene, ethylene, or acetyl spacer. The compounds have been screened on NCX1/NCX3 isoform activities by a high-throughput screening approach, and the most promising were characterized by patch-clamp electrophysiology and Fura-2AM video imaging. We identified two novel modulators of NCX: compound 4, inhibiting NCX1 reverse mode, and compound 14, enhancing NCX1 and NCX3 activity. Compound 1 displayed neuroprotection in two preclinical models of brain ischemia. The analysis of the conformational and steric features led to the identification of the molecular volume required for selective NCX1 activation for mixed NCX1/NCX3 activation or for NCX1 inhibition, providing the first prototypal model for the design of optimized isoform modulators.
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Affiliation(s)
- Elisa Magli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Caterina Fattorusso
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Marco Persico
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Angela Corvino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Gianluca Esposito
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Ferdinando Fiorino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Paolo Luciano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Elisa Perissutti
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Vincenzo Santagada
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Beatrice Severino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Valentina Tedeschi
- Department of Neuroscience, Division of Pharmacology, University of Naples "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Anna Pannaccione
- Department of Neuroscience, Division of Pharmacology, University of Naples "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Giuseppe Pignataro
- Department of Neuroscience, Division of Pharmacology, University of Naples "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Giuseppe Caliendo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | | | - Agnese Secondo
- Department of Neuroscience, Division of Pharmacology, University of Naples "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Francesco Frecentese
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
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11
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Proton-modulated interactions of ions with transport sites of prokaryotic and eukaryotic NCX prototypes. Cell Calcium 2021; 99:102476. [PMID: 34564055 DOI: 10.1016/j.ceca.2021.102476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/23/2022]
Abstract
The cytosolic pH decline from 7.2 to 6.9 results in 90% inactivation of mammalian Na+/Ca2+ exchangers (NCXs) due to protons interactions with regulatory and transport domains ("proton block"). Remarkably, the pH titration curves of mammalian and prokaryotic NCXs significantly differ, even after excluding the allosteric effects through regulatory domains. This is fascinating since "only" three (out of twelve) ion-coordinating residues (T50S, E213D, and D240N) differ between the archaeal NCX_Mj and mammalian NCXs although they contain either three or two carboxylates, respectively. To resolve the underlying mechanisms of pH-dependent regulation, the ion-coordinating residues of NCX_Mj were mutated to imitate the ion ligation arrays of mammalian NCXs; the mutational effects were tested on the ion binding/transport by using ion-flux assays and two-dimensional infrared (2D IR) spectroscopy. Our analyses revealed that two deprotonated carboxylates ligate 3Na+ or 1Ca2+ in NCX prototypes with three or two carboxylates. The Na+/Ca2+ exchange rates of NCX_Mj reach saturation at pH 5.0, whereas the Na+/Ca2+ exchange rates of the cardiac NCX1.1 gradually increase even at alkaline pHs. The T50S replacement in NCX_Mj "recapitulates" the pH titration curves of mammalian NCX by instigating an alkaline shift. Proteolytic shaving of regulatory CBD domains activates NCX1.1, although the normalized pH-titration curves are comparable in trypsin treated and untreated NCX1.1. Thus, the T50S-dependent alkaline shift sets a dynamic range for "proton block" function at physiological pH, whereas the CBDs (and other regulatory modes) modulate incremental changes in the transport rates rather than affect the shape of pH dependent curves.
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12
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Khananshvili D. The Archaeal Na +/Ca 2+ Exchanger (NCX_Mj) as a Model of Ion Transport for the Superfamily of Ca 2+/CA Antiporters. Front Chem 2021; 9:722336. [PMID: 34409017 PMCID: PMC8366772 DOI: 10.3389/fchem.2021.722336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
The superfamily of Calcium/Cation (Ca2+/CA) antiporters extrude Ca2+ from the cytosol or subcellular compartments in exchange with Na+, K+, H+, Li+, or Mg2+ and thereby provide a key mechanism for Ca2+ signaling and ion homeostasis in biological systems ranging from bacteria to humans. The structure-dynamic determinants of ion selectivity and transport rates remain unclear, although this is of primary physiological significance. Despite wide variances in the ion selectivity and transport rates, the Ca2+/CA proteins share structural motifs, although it remains unclear how the ion recognition/binding is coupled to the ion translocation events. Here, the archaeal Na+/Ca2+ exchanger (NCX_Mj) is considered as a structure-based model that can help to resolve the ion transport mechanisms by using X-ray, HDX-MS, ATR-FTIR, and computational approaches in conjunction with functional analyses of mutants. Accumulating data reveal that the local backbone dynamics at ion-coordinating residues is characteristically constrained in apo NCX_Mj, which may predefine the affinity and stability of ion-bound species in the ground and transition states. The 3Na+ or 1Ca2+ binding to respective sites of NCX_Mj rigidify the backbone dynamics at specific segments, where the ion-dependent compression of the ion-permeating four-helix bundle (TM2, TM3, TM7, and TM8) induces the sliding of the two-helix cluster (TM1/TM6) on the protein surface to switch the OF (outward-facing) and IF (inward-facing) conformations. Taking into account the common structural elements shared by Ca2+/CAs, NCX_Mj may serve as a model for studying the structure-dynamic and functional determinants of ion-coupled alternating access, transport catalysis, and ion selectivity in Ca2+/CA proteins.
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Affiliation(s)
- Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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13
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Lin QT, Lee R, Feng AL, Kim MS, Stathopulos PB. The leucine zipper EF-hand containing transmembrane protein-1 EF-hand is a tripartite calcium, temperature, and pH sensor. Protein Sci 2021; 30:855-872. [PMID: 33576522 DOI: 10.1002/pro.4042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/15/2022]
Abstract
Leucine Zipper EF-hand containing transmembrane protein-1 (LETM1) is an inner mitochondrial membrane protein that mediates mitochondrial calcium (Ca2+ )/proton exchange. The matrix residing carboxyl (C)-terminal domain contains a sequence identifiable EF-hand motif (EF1) that is highly conserved among orthologues. Deletion of EF1 abrogates LETM1 mediated mitochondrial Ca2+ flux, highlighting the requirement of EF1 for LETM1 function. To understand the mechanistic role of this EF-hand in LETM1 function, we characterized the biophysical properties of EF1 in isolation. Our data show that EF1 exhibits α-helical secondary structure that is augmented in the presence of Ca2+ . Unexpectedly, EF1 features a weak (~mM), but specific, apparent Ca2+ -binding affinity, consistent with the canonical Ca2+ coordination geometry, suggested by our solution NMR. The low affinity is, at least in part, due to an Asp at position 12 of the binding loop, where mutation to Glu increases the affinity by ~4-fold. Further, the binding affinity is sensitive to pH changes within the physiological range experienced by mitochondria. Remarkably, EF1 unfolds at high and low temperatures. Despite these unique EF-hand properties, Ca2+ binding increases the exposure of hydrophobic regions, typical of EF-hands; however, this Ca2+ -induced conformational change shifts EF1 from a monomer to higher order oligomers. Finally, we showed that a second, putative EF-hand within LETM1 is unreactive to Ca2+ either in isolation or tandem with EF1. Collectively, our data reveal that EF1 is structurally and biophysically responsive to pH, Ca2+ and temperature, suggesting a role as a multipartite environmental sensor within LETM1.
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Affiliation(s)
- Qi-Tong Lin
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Rachel Lee
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.,Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Allen L Feng
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.,Faculty of Dentistry, University of Toronto, Toronto, Canada
| | - Michael S Kim
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.,Department of Radiation Oncology, Dalhousie University, Halifax, Canada
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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14
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New Structural insights into Kir channel gating from molecular simulations, HDX-MS and functional studies. Sci Rep 2020; 10:8392. [PMID: 32439887 PMCID: PMC7242327 DOI: 10.1038/s41598-020-65246-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
Inward rectifier potassium (Kir) channels play diverse and important roles in shaping action potentials in biological membranes. An increasing number of diseases are now known to be directly associated with abnormal Kir function. However, the gating of Kir still remains unknown. To increase our understanding of its gating mechanism, a dynamical view of the entire channel is essential. Here the gating activation was studied using a recent developped in silico method, MDeNM, which combines normal mode analysis and molecular dynamics simulations that showed for the very first time the importance of interrelated collective and localized conformational movements. In particular, we highlighted the role played by concerted movements of the different regions throughout the entire protein, such as the cytoplasmic and transmembrane domains and the slide helices. In addition, the HDX-MS analysis achieved in these studies provided a comprehensive and detailed view of the dynamics associated with open/closed transition of the Kir channel in coherence with the theoretical results. MDeNM gives access to the probability of the different opening states that are in agreement with our electrophysiological experiments. The investigations presented in this article are important to remedy dysfunctional channels and are of interest for designing new pharmacological compounds.
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15
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Giladi M, Khananshvili D. Hydrogen-Deuterium Exchange Mass-Spectrometry of Secondary Active Transporters: From Structural Dynamics to Molecular Mechanisms. Front Pharmacol 2020; 11:70. [PMID: 32140107 PMCID: PMC7042309 DOI: 10.3389/fphar.2020.00070] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane transporters allow the selective transport of otherwise poorly permeable solutes across the cell membrane and thus, play a key role in maintaining cellular homeostasis in all kingdoms of life. Importantly, these proteins also serve as important drug targets. Over the last decades, major progress in structural biology methods has elucidated important structure-function relationships in membrane transporters. However, structures obtained using methods such as X-ray crystallography and high-resolution cryogenic electron microscopy merely provide static snapshots of an intrinsically dynamic, multi-step transport process. Therefore, there is a growing need for developing new experimental approaches capable of exploiting the data obtained from the high-resolution snapshots in order to investigate the dynamic features of membrane proteins. Here, we present the basic principles of hydrogen-deuterium exchange mass-spectrometry (HDX-MS) and recent advancements in its use to study membrane transporters. In HDX-MS experiments, minute amounts of a protein sample can be used to investigate its structural dynamics under native conditions, without the need for chemical labelling and with practically no limit on the protein size. Thus, HDX-MS is instrumental for resolving the structure-dynamic landscapes of membrane proteins in their apo (ligand-free) and ligand-bound forms, shedding light on the molecular mechanism underlying the transport process and drug binding.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Tel Aviv Sourasky Medical Center, 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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16
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Bradshaw RT, Marinelli F, Faraldo-Gómez JD, Forrest LR. Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles. Biophys J 2020; 118:1649-1664. [PMID: 32105651 PMCID: PMC7136279 DOI: 10.1016/j.bpj.2020.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 01/12/2023] Open
Abstract
Hydrogen-deuterium exchange combined with mass spectrometry (HDX-MS) is a widely applied biophysical technique that probes the structure and dynamics of biomolecules without the need for site-directed modifications or bio-orthogonal labels. The mechanistic interpretation of HDX data, however, is often qualitative and subjective, owing to a lack of quantitative methods to rigorously translate observed deuteration levels into atomistic structural information. To help address this problem, we have developed a methodology to generate structural ensembles that faithfully reproduce HDX-MS measurements. In this approach, an ensemble of protein conformations is first generated, typically using molecular dynamics simulations. A maximum-entropy bias is then applied post hoc to the resulting ensemble such that averaged peptide-deuteration levels, as predicted by an empirical model, agree with target values within a given level of uncertainty. We evaluate this approach, referred to as HDX ensemble reweighting (HDXer), for artificial target data reflecting the two major conformational states of a binding protein. We demonstrate that the information provided by HDX-MS experiments and by the model of exchange are sufficient to recover correctly weighted structural ensembles from simulations, even when the relevant conformations are rarely observed. Degrading the information content of the target data—e.g., by reducing sequence coverage, by averaging exchange levels over longer peptide segments, or by incorporating different sources of uncertainty—reduces the structural accuracy of the reweighted ensemble but still allows for useful insights into the distinctive structural features reflected by the target data. Finally, we describe a quantitative metric to rank candidate structural ensembles according to their correspondence with target data and illustrate the use of HDXer to describe changes in the conformational ensemble of the membrane protein LeuT. In summary, HDXer is designed to facilitate objective structural interpretations of HDX-MS data and to inform experimental approaches and further developments of theoretical exchange models.
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Affiliation(s)
- Richard T Bradshaw
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland.
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17
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O'Brien DP, Hourdel V, Chenal A, Brier S. Hydrogen/Deuterium Exchange Mass Spectrometry for the Structural Analysis of Detergent-Solubilized Membrane Proteins. Methods Mol Biol 2020; 2127:339-358. [PMID: 32112332 DOI: 10.1007/978-1-0716-0373-4_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Integral membrane proteins are involved in numerous biological functions and represent important drug targets. Despite their abundance in the human proteome, the number of integral membrane protein structures is largely underrepresented in the Protein Data Bank. The challenges associated with the biophysical characterization of such biological systems are well known. Most structural approaches, including X-ray crystallography, SAXS, or mass spectrometry (MS), require the complete solubilization of membrane proteins in aqueous solutions. Detergents are frequently used for this task, but may interfere with the analysis, as is the case with MS. The use of "MS-friendly" detergents, such as non-ionic alkyl glycoside detergents, has greatly facilitated the analysis of detergent-solubilized membrane proteins. Here, we describe a protocol, which we have successfully implemented in our laboratory to study the structure and dynamics of detergent-solubilized integral membrane proteins by Hydrogen/Deuterium eXchange and Mass Spectrometry (HDX-MS). The procedure does not require detergent removal prior to MS analysis, instead taking advantage of the ultra-high pressure chromatographic system to separate deuterated peptides from "MS-friendly" detergents.
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Affiliation(s)
- Darragh P O'Brien
- Biochemistry of Macromolecular Interaction Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Véronique Hourdel
- Environment and Infectious Risks Unit, Department of Infection and Epidemiology, Institut Pasteur, Paris, France
| | - Alexandre Chenal
- Biochemistry of Macromolecular Interaction Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Sébastien Brier
- Biological NMR Technological Platform, Center for Technological Resources and Research, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.
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18
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Structure-function relationships of K +-dependent Na +/Ca 2+ exchangers (NCKX). Cell Calcium 2019; 86:102153. [PMID: 31927187 DOI: 10.1016/j.ceca.2019.102153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 01/13/2023]
Abstract
K+-dependent Na+/Ca2+ exchanger proteins (NCKX1-5) of the SLC24 gene family play important roles in a wide range of biological processes including but not limited to rod and cone photoreceptor vision, olfaction, enamel formation and skin pigmentation. NCKX proteins are also widely expressed throughout the brain and NCKX2 and NCKX4 knockouts in mice have specific phenotypes. Here we review our work on structure-function relationships of NCKX proteins. We discuss membrane topology, domains critical to transport function, and residues critical to cation binding and transport function, all in the context of crystal structures that were obtained for the archaeal Na+/Ca2+ exchanger NCX_Mj.
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19
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Giladi M, Lee SY, Refaeli B, Hiller R, Chung KY, Khananshvili D. Structure-dynamic and functional relationships in a Li+-transporting sodium‑calcium exchanger mutant. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:189-200. [DOI: 10.1016/j.bbabio.2018.11.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/27/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022]
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20
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van Dijk L, Giladi M, Refaeli B, Hiller R, Cheng MH, Bahar I, Khananshvili D. Key residues controlling bidirectional ion movements in Na +/Ca 2+ exchanger. Cell Calcium 2018; 76:10-22. [PMID: 30248574 PMCID: PMC6688843 DOI: 10.1016/j.ceca.2018.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/13/2018] [Accepted: 09/13/2018] [Indexed: 01/06/2023]
Abstract
Prokaryotic and eukaryotic Na+/Ca2+ exchangers (NCX) control Ca2+ homeostasis. NCX orthologs exhibit up to 104-fold differences in their turnover rates (kcat), whereas the ratios between the cytosolic (cyt) and extracellular (ext) Km values (Kint = KmCyt/KmExt) are highly asymmetric and alike (Kint ≤ 0.1) among NCXs. The structural determinants controlling a huge divergence in kcat at comparable Kint remain unclear, although 11 (out of 12) ion-coordinating residues are highly conserved among NCXs. The crystal structure of the archaeal NCX (NCX_Mj) was explored for testing the mutational effects of pore-allied and loop residues on kcat and Kint. Among 55 tested residues, 26 mutations affect either kcat or Kint, where two major groups can be distinguished. The first group of mutations (14 residues) affect kcat rather than Kint. The majority of these residues (10 out of 14) are located within the extracellular vestibule near the pore center. The second group of mutations (12 residues) affect Kint rather than kcat, whereas the majority of residues (9 out 12) are randomly dispersed within the extracellular vestibule. In conjunction with computational modeling-simulations and hydrogen-deuterium exchange mass-spectrometry (HDX-MS), the present mutational analysis highlights structural elements that differentially govern the intrinsic asymmetry and transport rates. The key residues, located at specific segments, can affect the characteristic features of local backbone dynamics and thus, the conformational flexibility of ion-transporting helices contributing to critical conformational transitions. The underlying mechanisms might have a physiological relevance for matching the response modes of NCX variants to cell-specific Ca2+ and Na+ signaling.
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Affiliation(s)
- Liat van Dijk
- 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
| | - Bosmat Refaeli
- 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
| | - Mary Hongying Cheng
- Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Ivet Bahar
- Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv, 69978, Israel.
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21
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Jalloul AH, Cai S, Szerencsei RT, Schnetkamp PP. Residues important for K+ ion transport in the K+-dependent Na+-Ca2+ exchanger (NCKX2). Cell Calcium 2018; 74:61-72. [DOI: 10.1016/j.ceca.2018.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 06/14/2018] [Accepted: 06/18/2018] [Indexed: 10/28/2022]
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22
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Jalloul AH, Liu G, Szerencsei RT, Schnetkamp PP. Residues important for Ca2+ ion transport in the neuronal K+-dependent Na+-Ca2+ exchanger (NCKX2). Cell Calcium 2018; 74:187-197. [DOI: 10.1016/j.ceca.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 06/07/2018] [Accepted: 06/14/2018] [Indexed: 12/18/2022]
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23
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Gupta K, Watson AA, Baptista T, Scheer E, Chambers AL, Koehler C, Zou J, Obong-Ebong I, Kandiah E, Temblador A, Round A, Forest E, Man P, Bieniossek C, Laue ED, Lemke EA, Rappsilber J, Robinson CV, Devys D, Tora L, Berger I. Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID. eLife 2017; 6:e30395. [PMID: 29111974 PMCID: PMC5690282 DOI: 10.7554/elife.30395] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/03/2017] [Indexed: 11/13/2022] Open
Abstract
General transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds to core promoter DNA, recognizing the TATA-box. We identified a ternary complex formed by TBP and the histone fold (HF) domain-containing TFIID subunits TAF11 and TAF13. We demonstrate that TAF11/TAF13 competes for TBP binding with TATA-box DNA, and also with the N-terminal domain of TAF1 previously implicated in TATA-box mimicry. In an integrative approach combining crystal coordinates, biochemical analyses and data from cross-linking mass-spectrometry (CLMS), we determine the architecture of the TAF11/TAF13/TBP complex, revealing TAF11/TAF13 interaction with the DNA binding surface of TBP. We identify a highly conserved C-terminal TBP-interaction domain (CTID) in TAF13, which is essential for supporting cell growth. Our results thus have implications for cellular TFIID assembly and suggest a novel regulatory state for TFIID function.
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Affiliation(s)
- Kapil Gupta
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
- European Molecular Biology LaboratoryGrenobleFrance
| | | | - Tiago Baptista
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Anna L Chambers
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
| | | | - Juan Zou
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
- Chair of BioanalyticsInstitute of Biotechnology, Technische Universität BerlinBerlinGermany
| | - Ima Obong-Ebong
- Physical and Theoretical Chemistry LaboratoryOxfordUnited Kingdom
| | - Eaazhisai Kandiah
- European Molecular Biology LaboratoryGrenobleFrance
- Institut de Biologie Structurale IBSGrenobleFrance
| | | | - Adam Round
- European Molecular Biology LaboratoryGrenobleFrance
| | - Eric Forest
- Institut de Biologie Structurale IBSGrenobleFrance
| | - Petr Man
- Institute of MicrobiologyThe Czech Academy of SciencesVestecCzech Republic
- BioCeV - Faculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Ernest D Laue
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Juri Rappsilber
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
- Chair of BioanalyticsInstitute of Biotechnology, Technische Universität BerlinBerlinGermany
| | - Carol V Robinson
- Physical and Theoretical Chemistry LaboratoryOxfordUnited Kingdom
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Làszlò Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Imre Berger
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
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24
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Huang Y, Cui G, Zhao Y, Wang H, Li Z, Dai S, Wang J. Preorganization and Cooperation for Highly Efficient and Reversible Capture of Low-Concentration CO 2 by Ionic Liquids. Angew Chem Int Ed Engl 2017; 56:13293-13297. [PMID: 28857376 DOI: 10.1002/anie.201706280] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/20/2017] [Indexed: 12/12/2022]
Abstract
A novel strategy based on the concept of preorganization and cooperation has been designed for a superior capacity to capture low-concentration CO2 by imide-based ionic liquids. By using this strategy, for the first time, an extremely high gravimetric CO2 capacity of up to 22 wt % (1.65 mol mol-1 ) and excellent reversibility (16 cycles) have been achieved from 10 vol. % of CO2 in N2 when using an ionic liquid having a preorganized anion. Through a combination of quantum-chemical calculations and spectroscopic investigations, it is suggested that cooperative interactions between CO2 and multiple active sites in the preorganized anion are the driving force for the superior CO2 capacity and excellent reversibility.
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Affiliation(s)
- Yanjie Huang
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Guokai Cui
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yuling Zhao
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Huiyong Wang
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Zhiyong Li
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Sheng Dai
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Department of Chemistry, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jianji Wang
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
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Huang Y, Cui G, Zhao Y, Wang H, Li Z, Dai S, Wang J. Preorganization and Cooperation for Highly Efficient and Reversible Capture of Low-Concentration CO2
by Ionic Liquids. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706280] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Yanjie Huang
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
| | - Guokai Cui
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Yuling Zhao
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
| | - Huiyong Wang
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
| | - Zhiyong Li
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
| | - Sheng Dai
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
- Department of Chemistry; University of Tennessee; Knoxville TN 37996 USA
| | - Jianji Wang
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
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Giladi M, van Dijk L, Refaeli B, Almagor L, Hiller R, Man P, Forest E, Khananshvili D. Dynamic distinctions in the Na +/Ca 2+ exchanger adopting the inward- and outward-facing conformational states. J Biol Chem 2017; 292:12311-12323. [PMID: 28572509 DOI: 10.1074/jbc.m117.787168] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/18/2017] [Indexed: 12/16/2022] Open
Abstract
Na+/Ca2+ exchanger (NCX) proteins operate through the alternating access mechanism, where the ion-binding pocket is exposed in succession either to the extracellular or the intracellular face of the membrane. The archaeal NCX_Mj (Methanococcus jannaschii NCX) system was used to resolve the backbone dynamics in the inward-facing (IF) and outward-facing (OF) states by analyzing purified preparations of apo- and ion-bound forms of NCX_Mj-WT and its mutant, NCX_Mj-5L6-8. First, the exposure of extracellular and cytosolic vestibules to the bulk phase was evaluated as the reactivity of single cysteine mutants to a fluorescent probe, verifying that NCX_Mj-WT and NCX_Mj-5L6-8 preferentially adopt the OF and IF states, respectively. Next, hydrogen-deuterium exchange-mass spectrometry (HDX-MS) was employed to analyze the backbone dynamics profiles in proteins, preferentially adopting the OF (WT) and IF (5L6-8) states either in the presence or absence of ions. Characteristic differences in the backbone dynamics were identified between apo NCX_Mj-WT and NCX_Mj-5L6-8, thereby underscoring specific conformational patterns owned by the OF and IF states. Saturating concentrations of Na+ or Ca2+ specifically modify HDX patterns, revealing that the ion-bound/occluded states are much more stable (rigid) in the OF than in the IF state. Conformational differences observed in the ion-occluded OF and IF states can account for diversifying the ion-release dynamics and apparent affinity (Km ) at opposite sides of the membrane, where specific structure-dynamic elements can effectively match the rates of bidirectional ion movements at physiological ion concentrations.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel; Tel-Aviv Sourasky Medical Center, Tel-Aviv 39040, Israel
| | - Liat van Dijk
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Bosmat Refaeli
- 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
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv 69978, Israel
| | - Petr Man
- BioCeV-Institute of Microbiology, Academy of Sciences of the Czech Republic, CZ-14220 Prague, Czech Republic; Faculty of Science, Charles University, CZ-14220 Prague, Czech Republic
| | - Eric Forest
- University of Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; Commissariat à l'Energie Atomique, 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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Yee AW, Blakeley MP, Moulin M, Haertlein M, Mitchell E, Forsyth VT. Back-exchange of deuterium in neutron crystallography: characterization by IR spectroscopy. J Appl Crystallogr 2017; 50:660-664. [PMID: 28381984 PMCID: PMC5377354 DOI: 10.1107/s1600576717003624] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/07/2017] [Indexed: 01/02/2023] Open
Abstract
The application of IR spectroscopy to the characterization and quality control of samples used in neutron crystallography is described. While neutron crystallography is a growing field, the limited availability of neutron beamtime means that there may be a delay between crystallogenesis and data collection. Since essentially all neutron crystallographic work is carried out using D2O-based solvent buffers, a particular concern for these experiments is the possibility of H2O back-exchange across reservoir or capillary sealants. This may limit the quality of neutron scattering length density maps and of the associated analysis. Given the expense of central facility beamtime and the effort that goes into the production of suitably sized (usually perdeuterated) crystals, a systematic method of exploiting IR spectroscopy for the analysis of back-exchange phenomena in the reservoirs used for crystal growth is valuable. Examples are given in which the characterization of D2O/H2O back-exchange in transthyretin crystals is described.
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Affiliation(s)
- Ai Woon Yee
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
| | - Martine Moulin
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
| | - Michael Haertlein
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
| | - Edward Mitchell
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
- European Synchrotron Research Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
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Conformational dynamics of a neurotransmitter:sodium symporter in a lipid bilayer. Proc Natl Acad Sci U S A 2017; 114:E1786-E1795. [PMID: 28223522 DOI: 10.1073/pnas.1613293114] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Neurotransmitter:sodium symporters (NSSs) are integral membrane proteins responsible for the sodium-dependent reuptake of small-molecule neurotransmitters from the synaptic cleft. The symporters for the biogenic amines serotonin (SERT), dopamine (DAT), and norepinephrine (NET) are targets of multiple psychoactive agents, and their dysfunction has been implicated in numerous neuropsychiatric ailments. LeuT, a thermostable eubacterial NSS homolog, has been exploited as a model protein for NSS members to canvass the conformational mechanism of transport with a combination of X-ray crystallography, cysteine accessibility, and solution spectroscopy. Despite yielding remarkable insights, these studies have primarily been conducted with protein in the detergent-solubilized state rather than embedded in a membrane mimic. In addition, solution spectroscopy has required site-specific labeling of nonnative cysteines, a labor-intensive process occasionally resulting in diminished transport and/or binding activity. Here, we overcome these limitations by reconstituting unlabeled LeuT in phospholipid bilayer nanodiscs, subjecting them to hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS), and facilitating interpretation of the data with molecular dynamics simulations. The data point to changes of accessibility and dynamics of structural elements previously implicated in the transport mechanism, in particular transmembrane helices (TMs) 1a and 7 as well as extracellular loops (ELs) 2 and 4. The results therefore illuminate the value of this strategy for interrogating the conformational mechanism of the more clinically significant mammalian membrane proteins including SERT and DAT, neither of which tolerates complete removal of endogenous cysteines, and whose activity is heavily influenced by neighboring lipids.
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Roy S, Dey K, Hershfinkel M, Ohana E, Sekler I. Identification of residues that control Li + versus Na + dependent Ca 2+ exchange at the transport site of the mitochondrial NCLX. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:997-1008. [PMID: 28130126 DOI: 10.1016/j.bbamcr.2017.01.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/07/2017] [Accepted: 01/10/2017] [Indexed: 11/25/2022]
Abstract
BACKGROUND The Na+/Ca2+/Li+ exchanger (NCLX) is a member of the Na+/Ca2+ exchanger family. NCLX is unique in its capacity to transport both Na+ and Li+, unlike other members, which are Na+ selective. The major aim of this study was twofold, i.e., to identify NCLX residues that confer Li+ or Na+ selective Ca2+ transport and map their putative location on NCLX cation transport site. METHOD We combined molecular modeling to map transport site of NCLX with euryarchaeal H+/Ca2+ exchanger, CAX_Af, and fluorescence analysis to monitor Li+ versus Na+ dependent mitochondrial Ca2+ efflux of transport site mutants of NCLX in permeabilized cells. RESULT Mutation of Asn149, Pro152, Asp153, Gly176, Asn467, Ser468, Gly494 and Asn498 partially or strongly abolished mitochondrial Ca2+ exchange activity in intact cells. In permeabilized cells, N149A, P152A, D153A, N467Q, S468T and G494S demonstrated normal Li+/Ca2+ exchange activity but a reduced Na+/Ca2+ exchange activity. On the other hand, D471A showed dramatically reduced Li+/Ca2+ exchange, but Na+/Ca2+ exchange activity was unaffected. Finally, simultaneous mutation of four putative Ca2+ binding residues was required to completely abolish both Na+/Ca2+ and Li+/Ca2+ exchange activities. CONCLUSIONS We identified distinct Na+ and Li+ selective residues in the NCLX transport site. We propose that functional segregation in Li+ and Na+ sites reflects the functional properties of NCLX required for Ca2+ exchange under the unique membrane potential and ion gradient across the inner mitochondrial membrane. GENERAL SIGNIFICANCE The results of this study provide functional insights into the unique Li+ and Na+ selectivity of the mitochondrial exchanger. This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech.
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Affiliation(s)
- Soumitra Roy
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
| | - Kuntal Dey
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
| | - Michal Hershfinkel
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
| | - Ehud Ohana
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben Gurion University of the Negev, 84105 Beer Sheva, Israel.
| | - Israel Sekler
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel.
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Structure-Dynamic Coupling Through Ca2+-Binding Regulatory Domains of Mammalian NCX Isoform/Splice Variants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 981:41-58. [DOI: 10.1007/978-3-319-55858-5_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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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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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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