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Gamboa-Tuz SD, Pereira-Santana A, Zhao T, Schranz ME, Castano E, Rodriguez-Zapata LC. New insights into the phylogeny of the TMBIM superfamily across the tree of life: Comparative genomics and synteny networks reveal independent evolution of the BI and LFG families in plants. Mol Phylogenet Evol 2018; 126:266-278. [PMID: 29702215 DOI: 10.1016/j.ympev.2018.04.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022]
Abstract
The Transmembrane BAX Inhibitor Motif containing (TMBIM) superfamily, divided into BAX Inhibitor (BI) and Lifeguard (LFG) families, comprises a group of cytoprotective cell death regulators conserved in prokaryotes and eukaryotes. However, no research has focused on the evolution of this superfamily in plants. We identified 685 TMBIM proteins in 171 organisms from Archaea, Bacteria, and Eukarya, and provided a phylogenetic overview of the whole TMBIM superfamily. Then, we used orthology and synteny network analyses to further investigate the evolution and expansion of the BI and LFG families in 48 plants from diverse taxa. Plant BI family forms a single monophyletic group; however, monocot BI sequences transposed to another genomic context during evolution. Plant LFG family, which expanded trough whole genome and tandem duplications, is subdivided in LFG I, LFG IIA, and LFG IIB major phylogenetic groups, and retains synteny in angiosperms. Moreover, two orthologous groups (OGs) are shared between bryophytes and seed plants. Other several lineage-specific OGs are present in plants. This work clarifies the phylogenetic classification of the TMBIM superfamily across the three domains of life. Furthermore, it sheds new light on the evolution of the BI and LFG families in plants providing a benchmark for future research.
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Affiliation(s)
- Samuel D Gamboa-Tuz
- Biotechnology Unit, Centro de Investigacion Cientifica de Yucatan, 97205 Yucatan, Mexico
| | | | - Tao Zhao
- Biosystematics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Enrique Castano
- Biochemistry and Molecular Biology Unit, Centro de Investigacion Cientifica de Yucatan, 97205 Yucatan, Mexico
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52
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Carrara G, Parsons M, Saraiva N, Smith GL. Golgi anti-apoptotic protein: a tale of camels, calcium, channels and cancer. Open Biol 2018; 7:rsob.170045. [PMID: 28469007 PMCID: PMC5451544 DOI: 10.1098/rsob.170045] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022] Open
Abstract
Golgi anti-apoptotic protein (GAAP), also known as transmembrane Bax inhibitor-1 motif-containing 4 (TMBIM4) or Lifeguard 4 (Lfg4), shares remarkable amino acid conservation with orthologues throughout eukaryotes, prokaryotes and some orthopoxviruses, suggesting a highly conserved function. GAAPs regulate Ca2+ levels and fluxes from the Golgi and endoplasmic reticulum, confer resistance to a broad range of apoptotic stimuli, promote cell adhesion and migration via the activation of store-operated Ca2+ entry, are essential for the viability of human cells, and affect orthopoxvirus virulence. GAAPs are oligomeric, multi-transmembrane proteins that are resident in Golgi membranes and form cation-selective ion channels that may explain the multiple functions of these proteins. Residues contributing to the ion-conducting pore have been defined and provide the first clues about the mechanistic link between these very different functions of GAAP. Although GAAPs are naturally oligomeric, they can also function as monomers, a feature that distinguishes them from other virus-encoded ion channels that must oligomerize for function. This review summarizes the known functions of GAAPs and discusses their potential importance in disease.
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Affiliation(s)
- Guia Carrara
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Maddy Parsons
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Nuno Saraiva
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK .,CBIOS, Universidade Lusófona Research Centre for Biosciences and Health Technologies, Campo Grande 376, Lisbon 1749-024, Portugal
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
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53
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Li Z, Tang Y, Wu Y, Zhao S, Bao J, Luo Y, Li D. Structural insights into the committed step of bacterial phospholipid biosynthesis. Nat Commun 2017; 8:1691. [PMID: 29167463 PMCID: PMC5700162 DOI: 10.1038/s41467-017-01821-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/18/2017] [Indexed: 11/09/2022] Open
Abstract
The membrane-integral glycerol 3-phosphate (G3P) acyltransferase PlsY catalyses the committed and essential step in bacterial phospholipid biosynthesis by acylation of G3P, forming lysophosphatidic acid. It contains no known acyltransferase motifs, lacks eukaryotic homologs, and uses the unusual acyl-phosphate as acyl donor, as opposed to acyl-CoA or acyl-carrier protein for other acyltransferases. Previous studies have identified several PlsY inhibitors as potential antimicrobials. Here we determine the crystal structure of PlsY at 1.48 Å resolution, revealing a seven-transmembrane helix fold. Four additional substrate- and product-bound structures uncover the atomic details of its relatively inflexible active site. Structure and mutagenesis suggest a different acylation mechanism of ‘substrate-assisted catalysis’ that, unlike other acyltransferases, does not require a proteinaceous catalytic base to complete. The structure data and a high-throughput enzymatic assay developed in this work should prove useful for virtual and experimental screening of inhibitors against this vital bacterial enzyme. The first step in bacterial phospholipid biosynthesis is the acylation of glycerol 3-phosphate to form lysophosphatidic acid. Here, the authors present the high resolution crystal structure of the glycerol 3-phosphate acyltransferase PlsY, a membrane protein and give insights into its catalytical mechanism.
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Affiliation(s)
- Zhenjian Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China
| | - Yannan Tang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China
| | - Yitian Luo
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.
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Transcriptome Sequencing Reveals Novel Candidate Genes for Cardinium hertigii-Caused Cytoplasmic Incompatibility and Host-Cell Interaction. mSystems 2017; 2:mSystems00141-17. [PMID: 29181449 PMCID: PMC5698495 DOI: 10.1128/msystems.00141-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 11/29/2022] Open
Abstract
The majority of insects carry maternally inherited intracellular bacteria that are important in their hosts’ biology, ecology, and evolution. Some of these bacterial symbionts cause a reproductive failure known as cytoplasmic incompatibility (CI). In CI, the mating of symbiont-infected males and uninfected females produces few or no daughters. The CI symbiont then spreads and can have a significant impact on the insect host population. Cardinium, a bacterial endosymbiont of the parasitoid wasp Encarsia in the Bacteroidetes, is the only bacterial lineage known to cause CI outside the Alphaproteobacteria, where Wolbachia and another recently discovered CI symbiont reside. Here, we sought insight into the gene expression of a CI-inducing Cardinium strain in its natural host, Encarsia suzannae. Our study provides the first insights into the Cardinium transcriptome and provides support for the hypothesis that Wolbachia and Cardinium target similar host pathways with distinct and largely unrelated sets of genes. Cytoplasmic incompatibility (CI) is an intriguing, widespread, symbiont-induced reproductive failure that decreases offspring production of arthropods through crossing incompatibility of infected males with uninfected females or with females infected with a distinct symbiont genotype. For years, the molecular mechanism of CI remained unknown. Recent genomic, proteomic, biochemical, and cell biological studies have contributed to understanding of CI in the alphaproteobacterium Wolbachia and implicate genes associated with the WO prophage. Besides a recently discovered additional lineage of alphaproteobacterial symbionts only moderately related to Wolbachia, Cardinium (Bacteroidetes) is the only other symbiont known to cause CI, and genomic evidence suggests that it has very little homology with Wolbachia and evolved this phenotype independently. Here, we present the first transcriptomic study of the CI Cardinium strain cEper1, in its natural host, Encarsia suzannae, to detect important CI candidates and genes involved in the insect-Cardinium symbiosis. Highly expressed transcripts included genes involved in manipulating ubiquitination, apoptosis, and host DNA. Female-biased genes encoding ribosomal proteins suggest an increase in general translational activity of Cardinium in female wasps. The results confirm previous genomic analyses that indicated that Wolbachia and Cardinium utilize different genes to induce CI, and transcriptome patterns further highlight expression of some common pathways that these bacteria use to interact with the host and potentially cause this enigmatic and fundamental manipulation of host reproduction. IMPORTANCE The majority of insects carry maternally inherited intracellular bacteria that are important in their hosts’ biology, ecology, and evolution. Some of these bacterial symbionts cause a reproductive failure known as cytoplasmic incompatibility (CI). In CI, the mating of symbiont-infected males and uninfected females produces few or no daughters. The CI symbiont then spreads and can have a significant impact on the insect host population. Cardinium, a bacterial endosymbiont of the parasitoid wasp Encarsia in the Bacteroidetes, is the only bacterial lineage known to cause CI outside the Alphaproteobacteria, where Wolbachia and another recently discovered CI symbiont reside. Here, we sought insight into the gene expression of a CI-inducing Cardinium strain in its natural host, Encarsia suzannae. Our study provides the first insights into the Cardinium transcriptome and provides support for the hypothesis that Wolbachia and Cardinium target similar host pathways with distinct and largely unrelated sets of genes.
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Somavarapu AK, Kepp KP. Membrane Dynamics of γ-Secretase Provides a Molecular Basis for β-Amyloid Binding and Processing. ACS Chem Neurosci 2017; 8:2424-2436. [PMID: 28841371 DOI: 10.1021/acschemneuro.7b00208] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
γ-Secretase produces β-amyloid (Aβ) within its presenilin (PS1) subunit, mutations in which cause Alzheimer's disease, and current therapies thus seek to modulate its activity. While the general structure is known from recent electron microscopy studies, direct loop and membrane interactions and explicit dynamics relevant to substrate processing remain unknown. We report a modeled structure utilizing the optimal multitemplate information available, including loops and missing side chains, account of maturation cleavage, and explicit all-atom molecular dynamics in the membrane. We observe three distinct conformations of γ-secretase (open, semiopen, and closed) that remarkably differ by tilting of helices 2 and 3 of PS1, directly controlling active site availability. The large hydrophilic loop of PS1 where maturation occurs reveals a new helix segment that parallels the likely helix character of other substrates. The semiopen conformation consistently shows the best fit of Aβ peptides, that is, longer residence before release and by inference more trimming. In contrast, the closed, hydrophobic conformation is largely inactive and the open conformation is active but provides fewer optimal interactions and induces shorter residence time and by inference releases Aβ peptides of longer lengths. Our simulations thus provide a molecular basis for substrate processing and changes in the Aβ42/Aβ40 ratio. Accordingly, selective binding to protect the semiopen "innocent" conformation provides a molecular recipe for effective γ-secretase modulators; we provide the full atomic structures for these states that may play a key role in developing selective γ-secretase modulators for treatment of Alzheimer's disease.
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Affiliation(s)
| | - Kasper P. Kepp
- Technical University of Denmark, DTU Chemistry, DK-2800 Kongens Lyngby, Denmark
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56
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A Novel Calcium Uptake Transporter of Uncharacterized P-Type ATPase Family Supplies Calcium for Cell Surface Integrity in Mycobacterium smegmatis. mBio 2017; 8:mBio.01388-17. [PMID: 28951477 PMCID: PMC5615198 DOI: 10.1128/mbio.01388-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ca2+ plays an important role in the physiology of bacteria. Intracellular Ca2+ concentrations are tightly maintained in the nanomolar range. Molecular mechanisms of Ca2+ uptake in bacteria remain elusive. Here we show that CtpE is responsible for Ca2+ uptake in Mycobacterium smegmatis. It represents a previously uncharacterized P-type ATPase family in bacteria. Disruption of ctpE in M. smegmatis resulted in a mutant with impaired growth under Ca2+-deficient conditions. The growth defect of the mutant could be rescued by Ca2+ or by ectopic expression of ctpE from M. smegmatis or the orthologous gene (Rv0908) from Mycobacterium tuberculosis H37Rv. Radioactive transport assays revealed that CtpE is a Ca2+-specific transporter. Ca2+ deficiency increased expression of ctpE, resulting in increased 45Ca2+ accumulation in cells. ctpE is a gene that is part of an operon, which is negatively regulated by Ca2+. The ctpE mutant also showed hypersensitivity to polymyxin B, increased biofilm formation, and higher cell aggregation, indicating cell envelope defects. Our work establishes, for the first time, the presence of Ca2+ uptake pumps of the energy-dependent P-type ATPase superfamily in bacteria and also implicates that intracellular Ca2+ is essential for growth and cell envelope integrity in M. smegmatis. Ca2+ is essential for gene regulation, enzymatic activity, and maintenance of structural integrity of cell walls in bacteria. Bacteria maintain intracellular calcium concentrations in a narrow range, creating a gradient with low cytoplasmic calcium concentration and high extracellular calcium concentration. Due to this steep gradient, active pumps belonging to family 2 of P-type ATPases and antiporters are used for Ca2+ efflux, whereas Ca2+ uptake is usually carried out by channels. Molecular mechanisms of Ca2+ uptake in bacteria are still elusive and are mainly limited to a nonproteinaceous channel in Escherichia coli and a pH-dependent channel protein from Bacillus subtilis. Energy-dependent active transporters are not reported for Ca2+ uptake from any organism. Here we show that CtpE belonging to a family of previously uncharacterized bacterial P-type ATPases is involved in specific uptake of Ca2+ into Mycobacterium smegmatis. We also demonstrate that intracellular Ca2+ obtained through CtpE is essential for growth and maintenance of cell surface properties under Ca2+-deficient conditions.
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57
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Carreras-Sureda A, Pihán P, Hetz C. Calcium signaling at the endoplasmic reticulum: fine-tuning stress responses. Cell Calcium 2017; 70:24-31. [PMID: 29054537 DOI: 10.1016/j.ceca.2017.08.004] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/11/2017] [Accepted: 08/11/2017] [Indexed: 01/21/2023]
Abstract
Endoplasmic reticulum (ER) calcium signaling is implicated in a myriad of coordinated cellular processes. The ER calcium content is tightly regulated as it allows a favorable environment for protein folding, in addition to operate as a major reservoir for fast and specific release of calcium. Altered ER homeostasis impacts protein folding, activating the unfolded protein response (UPR) as a rescue mechanism to restore proteostasis. ER calcium release impacts mitochondrial metabolism and also fine-tunes the threshold to undergo apoptosis under chronic stress. The global coordination between UPR signaling and energetic demands takes place at mitochondrial associated membranes (MAMs), specialized subdomains mediating interorganelle communication. Here we discuss current models explaining the functional relationship between ER homeostasis and various cellular responses to coordinate proteostasis and metabolic maintenance.
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Affiliation(s)
- Amado Carreras-Sureda
- Center for Geroscience, Brain Health and Metabolism, Faculty of Medicine, University of Chile, Chile; Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Philippe Pihán
- Center for Geroscience, Brain Health and Metabolism, Faculty of Medicine, University of Chile, Chile; Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Claudio Hetz
- Center for Geroscience, Brain Health and Metabolism, Faculty of Medicine, University of Chile, Chile; Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile; Buck Institute for Research on Aging, Novato, CA, 94945, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA.
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58
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Pihán P, Carreras-Sureda A, Hetz C. BCL-2 family: integrating stress responses at the ER to control cell demise. Cell Death Differ 2017. [PMID: 28622296 DOI: 10.1038/cdd.2017.82] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In the last decade, the endoplasmic reticulum (ER) has emerged as a central organelle regulating the core mitochondrial apoptosis pathway. At the ER membrane, a variety of stress signals are integrated toward determining cell fate, involving a complex cross talk between key homeostatic pathways including the unfolded protein response, autophagy, calcium signaling and mitochondrial bioenergetics. In this context, key regulators of cell death of the BCL-2 and TMBIM/BI-1 family of proteins have relevant functions as stress rheostats mediated by the formation of distinct protein complexes that regulate the switch between adaptive and proapoptotic phases under stress. Here, we overview recent advances on our molecular understanding of how the apoptotic machinery integrates stress signals toward cell fate decisions upstream of the mitochondrial gateway of death.
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Affiliation(s)
- Philippe Pihán
- Faculty of Medicine, Biomedical Neuroscience Institute, University of Chile, Santiago, Chile.,Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile.,Faculty of Medicine, Center for Geroscience, Brain Health and Metabolism, University of Chile, Santiago, Chile
| | - Amado Carreras-Sureda
- Faculty of Medicine, Biomedical Neuroscience Institute, University of Chile, Santiago, Chile.,Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile.,Faculty of Medicine, Center for Geroscience, Brain Health and Metabolism, University of Chile, Santiago, Chile
| | - Claudio Hetz
- Faculty of Medicine, Biomedical Neuroscience Institute, University of Chile, Santiago, Chile.,Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile.,Faculty of Medicine, Center for Geroscience, Brain Health and Metabolism, University of Chile, Santiago, Chile.,Buck Institute for Research on Aging, Novato, CA 94945, USA.,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston MA 02115, USA
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59
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Liu Q. TMBIM-mediated Ca 2+ homeostasis and cell death. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:850-857. [PMID: 28064000 DOI: 10.1016/j.bbamcr.2016.12.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/22/2016] [Accepted: 12/22/2016] [Indexed: 11/25/2022]
Abstract
Ca2+ is a ubiquitous intracellular messenger that regulates numerous physiological activities in humans, animals, plants, and bacteria. Cytosolic Ca2+ is kept at a low level, but subcellular organelles such as the endoplasmic reticulum (ER) and Golgi apparatus maintain high-concentration Ca2+ stores. Under resting conditions, store Ca2+ homeostasis is dynamically regulated to equilibrate between active Ca2+ uptake and passive Ca2+ leak processes. The evolutionarily conserved Transmembrane BAX Inhibitor-1 Motif-containing (TMBIM) proteins mediate Ca2+ homeostasis and cell death. This review focuses on recent advances in functional and structural analysis of TMBIM proteins in regulation of the two related functions. The roles of TMBIM proteins in pathogen infection and cancer are also discussed with prospects for treatment. 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)
- Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
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60
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ER-luminal thiol/selenol-mediated regulation of Ca2+ signalling. Biochem Soc Trans 2016; 44:452-9. [PMID: 27068954 DOI: 10.1042/bst20150233] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Indexed: 01/05/2023]
Abstract
The endoplasmic reticulum (ER) is the main cellular Ca(2+)storage unit. Among other signalling outputs, the ER can release Ca(2+)ions, which can, for instance, communicate the status of ER protein folding to the cytosol and to other organelles, in particular the mitochondria. As a consequence, ER Ca(2+)flux can alter the apposition of the ER with mitochondria, influence mitochondrial ATP production or trigger apoptosis. All aspects of ER Ca(2+)flux have emerged as processes that are intimately controlled by intracellular redox conditions. In this review, we focus on ER-luminal redox-driven regulation of Ca(2+)flux. This involves the direct reduction of disulfides within ER Ca(2+)handling proteins themselves, but also the regulated interaction of ER chaperones and oxidoreductases such as calnexin or ERp57 with them. Well-characterized examples are the activating interactions of Ero1α with inositol 1,4,5-trisphosphate receptors (IP3Rs) or of selenoprotein N (SEPN1) with sarco/endoplasmic reticulum Ca(2+)transport ATPase 2 (SERCA2). The future discovery of novel ER-luminal modulators of Ca(2+)handling proteins is likely. Based on the currently available information, we describe how the variable ER redox conditions govern Ca(2+)flux from the ER.
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Planells-Ferrer L, Urresti J, Coccia E, Galenkamp KMO, Calleja-Yagüe I, López-Soriano J, Carriba P, Barneda-Zahonero B, Segura MF, Comella JX. Fas apoptosis inhibitory molecules: more than death-receptor antagonists in the nervous system. J Neurochem 2016; 139:11-21. [DOI: 10.1111/jnc.13729] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/14/2016] [Accepted: 07/02/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Laura Planells-Ferrer
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Jorge Urresti
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Elena Coccia
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Koen M. O. Galenkamp
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Isabel Calleja-Yagüe
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Joaquín López-Soriano
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Paulina Carriba
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Bruna Barneda-Zahonero
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Miguel F. Segura
- Group of Translational Research in Childhood and Adolescent Cancer; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
| | - Joan X. Comella
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
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Zhang CY, Chen Q, Wu WS, Guo XD, Cai CZ, Zhang LJ. Synthesis and evaluation of cholesterol-grafted PEGylated peptides with pH-triggered property as novel drug carriers for cancer chemotherapy. Colloids Surf B Biointerfaces 2016; 142:55-64. [DOI: 10.1016/j.colsurfb.2016.02.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/22/2016] [Accepted: 02/09/2016] [Indexed: 12/17/2022]
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63
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Renault TT, Dejean LM, Manon S. A brewing understanding of the regulation of Bax function by Bcl-xL and Bcl-2. Mech Ageing Dev 2016; 161:201-210. [PMID: 27112371 DOI: 10.1016/j.mad.2016.04.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/19/2016] [Accepted: 04/22/2016] [Indexed: 12/17/2022]
Abstract
Bcl-2 family members form a network of protein-protein interactions that regulate apoptosis through permeabilization of the mitochondrial outer membrane. Deciphering this intricate network requires streamlined experimental models, including the heterologous expression in yeast. This approach had previously enabled researchers to identify domains and residues that underlie the conformational changes driving the translocation, the insertion and the oligomerization of the pro-apoptotic protein Bax at the level of the mitochondrial outer membrane. Recent studies that combine experiments in yeast and in mammalian cells have shown the unexpected effect of the anti-apoptotic protein Bcl-xL on the priming of Bax. As demonstrated with the BH3-mimetic molecule ABT-737, this property of Bcl-xL, and of Bcl-2, is crucial to elaborate about how apoptosis could be reactivated in tumoral cells.
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Affiliation(s)
- Thibaud T Renault
- Helmholtz Center for Infection Research, Junior Research Group Infection Biology of Salmonella, Inhoffenstraße 7, 38124 Braunschweig, Germany; Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
| | - Laurent M Dejean
- California State University of Fresno, Department of Chemistry, 2555 E. San Ramon Ave M/S SB70, Fresno, CA 93740-8034, USA
| | - Stéphen Manon
- CNRS, UMR5095, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France.
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64
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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: 4.4] [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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65
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Structural analysis of the dodecameric proteasome activator PafE in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2016; 113:E1983-92. [PMID: 27001842 DOI: 10.1073/pnas.1512094113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The human pathogen Mycobacterium tuberculosis (Mtb) requires a proteasome system to cause lethal infections in mice. We recently found that proteasome accessory factor E (PafE, Rv3780) activates proteolysis by the Mtb proteasome independently of adenosine triphosphate (ATP). Moreover, PafE contributes to the heat-shock response and virulence of Mtb Here, we show that PafE subunits formed four-helix bundles similar to those of the eukaryotic ATP-independent proteasome activator subunits of PA26 and PA28. However, unlike any other known proteasome activator, PafE formed dodecamers with 12-fold symmetry, which required a glycine-XXX-glycine-XXX-glycine motif that is not found in previously described activators. Intriguingly, the truncation of the PafE carboxyl-terminus resulted in the robust binding of PafE rings to native proteasome core particles and substantially increased proteasomal activity, suggesting that the extended carboxyl-terminus of this cofactor confers suboptimal binding to the proteasome core particle. Collectively, our data show that proteasomal activation is not limited to hexameric ATPases in bacteria.
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66
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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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67
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Chen SG, Zhao ZX, Jiang XN, Wang L, Zhou TY, Lu CL, Zhao X, Jiang XK, Ma Y, Wang RX, Li ZT. Temperature-Responsive Chiral (A)6
B Supramolecular Cages Based on Conformational Preferences. Chem Asian J 2015; 11:465-9. [DOI: 10.1002/asia.201501090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/11/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Shi-Gui Chen
- Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
| | - Zhi-Xiong Zhao
- Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
| | - Xiao-Nan Jiang
- Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
| | - Lu Wang
- Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
| | - Tian-You Zhou
- Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
| | - Cheng-Lu Lu
- Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
| | - Xin Zhao
- Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
| | - Xi-Kui Jiang
- Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
| | - Yuguo Ma
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Polymer Chemistry and Physics of Ministry of Education; College of Chemistry; Peking University; Beijing 100871 China
| | - Ren-Xiao Wang
- Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
| | - Zhan-Ting Li
- Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
- Department of Chemistry; Fudan University; 220 Handan Road Shanghai 200433 China
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68
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Lisak D, Schacht T, Gawlitza A, Albrecht P, Aktas O, Koop B, Gliem M, Hofstetter HH, Zanger K, Bultynck G, Parys JB, De Smedt H, Kindler T, Adams-Quack P, Hahn M, Waisman A, Reed JC, Hövelmeyer N, Methner A. BAX inhibitor-1 is a Ca(2+) channel critically important for immune cell function and survival. Cell Death Differ 2015; 23:358-68. [PMID: 26470731 DOI: 10.1038/cdd.2015.115] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 07/20/2015] [Accepted: 07/21/2015] [Indexed: 01/03/2023] Open
Abstract
The endoplasmic reticulum (ER) serves as the major intracellular Ca(2+) store and has a role in the synthesis and folding of proteins. BAX (BCL2-associated X protein) inhibitor-1 (BI-1) is a Ca(2+) leak channel also implicated in the response against protein misfolding, thereby connecting the Ca(2+) store and protein-folding functions of the ER. We found that BI-1-deficient mice suffer from leukopenia and erythrocytosis, have an increased number of splenic marginal zone B cells and higher abundance and nuclear translocation of NF-κB (nuclear factor-κ light-chain enhancer of activated B cells) proteins, correlating with increased cytosolic and ER Ca(2+) levels. When put into culture, purified knockout T cells and even more so B cells die spontaneously. This is preceded by increased activity of the mitochondrial initiator caspase-9 and correlated with a significant surge in mitochondrial Ca(2+) levels, suggesting an exhausted mitochondrial Ca(2+) buffer capacity as the underlying cause for cell death in vitro. In vivo, T-cell-dependent experimental autoimmune encephalomyelitis and B-cell-dependent antibody production are attenuated, corroborating the ex vivo results. These results suggest that BI-1 has a major role in the functioning of the adaptive immune system by regulating intracellular Ca(2+) homeostasis in lymphocytes.
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Affiliation(s)
- D Lisak
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn) and Department of Neurology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - T Schacht
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn) and Department of Neurology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - A Gawlitza
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn) and Department of Neurology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - P Albrecht
- Heinrich Heine Universität Düsseldorf, Department of Neurology, Düsseldorf, Germany
| | - O Aktas
- Heinrich Heine Universität Düsseldorf, Department of Neurology, Düsseldorf, Germany
| | - B Koop
- Heinrich Heine Universität Düsseldorf, Department of Neurology, Düsseldorf, Germany
| | - M Gliem
- Heinrich Heine Universität Düsseldorf, Department of Neurology, Düsseldorf, Germany
| | - H H Hofstetter
- Heinrich Heine Universität Düsseldorf, Department of Neurology, Düsseldorf, Germany
| | - K Zanger
- Center for Anatomy and Brain Research, Düsseldorf, Germany
| | - G Bultynck
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, Belgium
| | - J B Parys
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, Belgium
| | - H De Smedt
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, Belgium
| | - T Kindler
- III Medical Clinic, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - P Adams-Quack
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - M Hahn
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - A Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - J C Reed
- Sanford Burnham Institute, La Jolla, CA, USA
| | - N Hövelmeyer
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - A Methner
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn) and Department of Neurology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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69
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Crystallographic phasing from weak anomalous signals. Curr Opin Struct Biol 2015; 34:99-107. [PMID: 26432413 DOI: 10.1016/j.sbi.2015.08.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/03/2015] [Accepted: 08/06/2015] [Indexed: 11/22/2022]
Abstract
The exploitation of anomalous signals for biological structural solution is maturing. Single-wavelength anomalous diffraction (SAD) is dominant in de novo structure analysis. Nevertheless, for challenging structures where the resolution is low (dmin≥3.5Å) or where only lighter atoms (Z≤20) are present, as for native macromolecules, solved SAD structures are still scarce. With the recent rapid development in crystal handling, beamline instrumentation, optimization of data collection strategies, use of multiple crystals and structure determination technologies, the weak anomalous diffraction signals are now robustly measured and should be used for routine SAD structure determination. The review covers these recent advances on weak anomalous signals measurement, analysis and utilization.
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70
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Hidaka T, Shimada A, Nakata Y, Kodama H, Kurihara H, Tokihiro T, Ihara S. Simple model of pH-induced protein denaturation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:012709. [PMID: 26274205 DOI: 10.1103/physreve.92.012709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Indexed: 06/04/2023]
Abstract
The pH-induced conformational changes of proteins are systematically studied in the framework of a hydrophobic-polar (HP) model, in which proteins are dramatically simplified as chains of hydrophobic (H) and polar (P) beads on a lattice. We express the electrostatic interaction, the principal driving force of pH-induced unfolding that is not included in the conventional HP model, as the repulsive energy term between P monomers. As a result of the exact enumeration of all of the 14- to 18-mers, it is found that lowest-energy states in many sequences change from single "native" conformations to multiple sets of "denatured" conformations with an increase in the electrostatic repulsion. The switching of the lowest-energy states occurs in quite a similar way to real proteins: it is almost always between two states, while in a small fraction of ≥16-mers it is between three states. We also calculate the structural fluctuations for all of the denatured states and find that the denatured states contain a broad range of incompletely unfolded conformations, similar to "molten globule" states referred to in acid or alkaline denatured real proteins. These results show that the proposed model provides a simple physical picture of pH-induced protein denaturation.
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Affiliation(s)
- T Hidaka
- Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - A Shimada
- Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Y Nakata
- Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan
- Graduate School of Mathematical Sciences, The University of Tokyo, Komaba, Tokyo 153-8902, Japan
| | - H Kodama
- Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan
- Graduate School of Mathematical Sciences, The University of Tokyo, Komaba, Tokyo 153-8902, Japan
| | - H Kurihara
- Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
- Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0076, Japan
| | - T Tokihiro
- Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan
- Graduate School of Mathematical Sciences, The University of Tokyo, Komaba, Tokyo 153-8902, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0076, Japan
| | - S Ihara
- Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan
- Graduate School of Mathematical Sciences, The University of Tokyo, Komaba, Tokyo 153-8902, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Komaba, Tokyo 153-8904, Japan
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71
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Buried ionizable networks are an ancient hallmark of G protein-coupled receptor activation. Proc Natl Acad Sci U S A 2015; 112:5702-7. [PMID: 25902551 DOI: 10.1073/pnas.1417888112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Seven-transmembrane receptors (7TMRs) have evolved in prokaryotes and eukaryotes over hundreds of millions of years. Comparative structural analysis suggests that these receptors may share a remote evolutionary origin, despite their lack of sequence similarity. Here we used structure-based computations to compare 221 7TMRs from all domains of life. Unexpectedly, we discovered that these receptors contain spatially conserved networks of buried ionizable groups. In microbial 7TMRs these networks are used to pump ions across the cell membrane in response to light. In animal 7TMRs, which include light- and ligand-activated G protein-coupled receptors (GPCRs), homologous networks were found to be characteristic of activated receptor conformations. These networks are likely relevant to receptor function because they connect the ligand-binding pocket of the receptor to the nucleotide-binding pocket of the G protein. We propose that agonist and G protein binding facilitate the formation of these electrostatic networks and promote important structural rearrangements such as the displacement of transmembrane helix-6. We anticipate that robust classification of activated GPCR structures will aid the identification of ligands that target activated GPCR structural states.
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72
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Lisak DA, Schacht T, Enders V, Habicht J, Kiviluoto S, Schneider J, Henke N, Bultynck G, Methner A. The transmembrane Bax inhibitor motif (TMBIM) containing protein family: Tissue expression, intracellular localization and effects on the ER CA²⁺-filling state. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2104-14. [PMID: 25764978 DOI: 10.1016/j.bbamcr.2015.03.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 01/19/2015] [Accepted: 03/01/2015] [Indexed: 10/23/2022]
Abstract
Bax inhibitor-1 (BI-1) is an evolutionarily conserved pH-dependent Ca²⁺ leak channel in the endoplasmic reticulum and the founding member of a family of six highly hydrophobic mammalian proteins named transmembrane BAX inhibitor motif containing (TMBIM) 1-6 with BI-1 being TMBIM6. Here we compared the structure, subcellular localization, tissue expression and the effect on the cellular Ca²⁺ homeostasis of all family members side by side. We found that all TMBIM proteins possess the di-aspartyl pH sensor responsible for pH sensing identified in TMBIM6 and its bacterial homologue BsYetJ. TMBIM1-3 and TMBIM4-6 represent two phylogenetically distinct groups that are localized in the Golgi apparatus (TMBIM1-3), endoplasmic reticulum (TMBIM4-6) or mitochondria (TMBIM5) but share a common structure of at least seven transmembrane domains with the last domain being semi-hydrophobic. TMBIM1 is mainly expressed in muscle, TMBIM2 and 3 in the nervous system, TMBIM4 and 5 are ubiquitously expressed and TMBIM6 in skeletal muscle, kidney, liver and spleen. All TMBIM proteins reduce the Ca²⁺ content of the endoplasmic reticulum, and all but TMBIM5 also reduce the cytosolic resting Ca²⁺ concentration. These results suggest that the TMBIM family has comparable functions in the maintenance of intracellular Ca²⁺ homeostasis in a wide variety of tissues. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.
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Affiliation(s)
- Dmitrij A Lisak
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn(2)), Department of Neurology, Johannes Gutenberg University Medical Center Mainz, Langenbeckstr. 1, Mainz D-55131, Germany
| | - Teresa Schacht
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn(2)), Department of Neurology, Johannes Gutenberg University Medical Center Mainz, Langenbeckstr. 1, Mainz D-55131, Germany
| | - Vitalij Enders
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn(2)), Department of Neurology, Johannes Gutenberg University Medical Center Mainz, Langenbeckstr. 1, Mainz D-55131, Germany
| | - Jörn Habicht
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn(2)), Department of Neurology, Johannes Gutenberg University Medical Center Mainz, Langenbeckstr. 1, Mainz D-55131, Germany
| | - Santeri Kiviluoto
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, Leuven BE-3000, Belgium
| | - Julia Schneider
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn(2)), Department of Neurology, Johannes Gutenberg University Medical Center Mainz, Langenbeckstr. 1, Mainz D-55131, Germany
| | - Nadine Henke
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn(2)), Department of Neurology, Johannes Gutenberg University Medical Center Mainz, Langenbeckstr. 1, Mainz D-55131, Germany
| | - Geert Bultynck
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, Leuven BE-3000, Belgium
| | - Axel Methner
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn(2)), Department of Neurology, Johannes Gutenberg University Medical Center Mainz, Langenbeckstr. 1, Mainz D-55131, Germany.
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73
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Abstract
Permeabilization of the outer mitochondrial membrane that leads to the release of cytochrome c and several other apoptogenic proteins from mitochondria into cytosol represents a commitment point of apoptotic pathway in mammalian cells. This crucial event is governed by proteins of the Bcl-2 family. Molecular mechanisms, by which Bcl-2 family proteins permeabilize mitochondrial membrane, remain under dispute. Although yeast does not have apparent homologues of these proteins, when mammalian members of Bcl-2 family are expressed in yeast, they retain their activity, making yeast an attractive model system, in which to study their action. This review focuses on using yeast expressing mammalian proteins of the Bcl-2 family as a tool to investigate mechanisms, by which these proteins permeabilize mitochondrial membranes, mechanisms, by which pro- and antiapoptotic members of this family interact, and involvement of other cellular components in the regulation of programmed cell death by Bcl-2 family proteins.
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Affiliation(s)
- Peter Polčic
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Petra Jaká
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
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74
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Yuan H, Myers SJ, Wells G, Nicholson KL, Swanger SA, Lyuboslavsky P, Tahirovic YA, Menaldino DS, Ganesh T, Wilson LJ, Liotta DC, Snyder JP, Traynelis SF. Context-dependent GluN2B-selective inhibitors of NMDA receptor function are neuroprotective with minimal side effects. Neuron 2015; 85:1305-1318. [PMID: 25728572 DOI: 10.1016/j.neuron.2015.02.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 01/12/2015] [Accepted: 01/29/2015] [Indexed: 01/09/2023]
Abstract
Stroke remains a significant problem despite decades of work on neuroprotective strategies. NMDA receptor (NMDAR) antagonists are neuroprotective in preclinical models, but have been clinically unsuccessful, in part due to side effects. Here we describe a prototypical GluN2B-selective antagonist with an IC50 value that is 10-fold more potent at acidic pH 6.9 associated with ischemic tissue compared to pH 7.6, a value close to the pH in healthy brain tissue. This should maximize neuroprotection in ischemic tissue while minimizing on-target side effects associated with NMDAR blockade in noninjured brain regions. We have determined the mechanism underlying pH-dependent inhibition and demonstrate the utility of this approach in vivo. We also identify dicarboxylate dimers as a novel proton sensor in proteins. These results provide insight into the molecular basis of pH-dependent neuroprotective NMDAR block, which could be beneficial in a wide range of neurological insults associated with tissue acidification.
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Affiliation(s)
- Hongjie Yuan
- Department of Pharmacology, Emory University, Atlanta, GA 30322 USA
| | - Scott J Myers
- Department of Pharmacology, Emory University, Atlanta, GA 30322 USA
| | - Gordon Wells
- Department of Chemistry, Emory University, Atlanta, GA 30322 USA
| | - Katherine L Nicholson
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298 USA.,Institute for Drug and Alcohol Studies, Virginia Commonwealth University, Richmond, VA 23298 USA
| | - Sharon A Swanger
- Department of Pharmacology, Emory University, Atlanta, GA 30322 USA
| | | | | | | | - Thota Ganesh
- Department of Pharmacology, Emory University, Atlanta, GA 30322 USA
| | | | - Dennis C Liotta
- Department of Chemistry, Emory University, Atlanta, GA 30322 USA
| | - James P Snyder
- Department of Chemistry, Emory University, Atlanta, GA 30322 USA
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75
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Carrara G, Saraiva N, Parsons M, Byrne B, Prole DL, Taylor CW, Smith GL. Golgi anti-apoptotic proteins are highly conserved ion channels that affect apoptosis and cell migration. J Biol Chem 2015; 290:11785-801. [PMID: 25713081 PMCID: PMC4416878 DOI: 10.1074/jbc.m115.637306] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Indexed: 12/03/2022] Open
Abstract
Golgi anti-apoptotic proteins (GAAPs) are multitransmembrane proteins that are expressed in the Golgi apparatus and are able to homo-oligomerize. They are highly conserved throughout eukaryotes and are present in some prokaryotes and orthopoxviruses. Within eukaryotes, GAAPs regulate the Ca2+ content of intracellular stores, inhibit apoptosis, and promote cell adhesion and migration. Data presented here demonstrate that purified viral GAAPs (vGAAPs) and human Bax inhibitor 1 form ion channels and that vGAAP from camelpox virus is selective for cations. Mutagenesis of vGAAP, including some residues conserved in the recently solved structure of a related bacterial protein, BsYetJ, altered the conductance (E207Q and D219N) and ion selectivity (E207Q) of the channel. Mutation of residue Glu-207 or -178 reduced the effects of GAAP on cell migration and adhesion without affecting protection from apoptosis. In contrast, mutation of Asp-219 abrogated the anti-apoptotic activity of GAAP but not its effects on cell migration and adhesion. These results demonstrate that GAAPs are ion channels and define residues that contribute to the ion-conducting pore and affect apoptosis, cell adhesion, and migration independently.
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Affiliation(s)
- Guia Carrara
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Nuno Saraiva
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Maddy Parsons
- the Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom
| | - Bernadette Byrne
- the Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom, and
| | - David L Prole
- the Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom,
| | - Colin W Taylor
- the Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom,
| | - Geoffrey L Smith
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom,
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76
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Affiliation(s)
- Lonny R. Levin
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065; ,
| | - Jochen Buck
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065; ,
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77
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Schultz JE, Kanchan K, Ziegler M. Intraprotein signal transduction by HAMP domains: a balancing act. Int J Med Microbiol 2014; 305:243-51. [PMID: 25595022 DOI: 10.1016/j.ijmm.2014.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
HAMP domains are small protein modules that predominantly operate as signal transducers in bacterial sensor proteins most of which are membrane delimited. The domain organization of such sensors has the HAMPs localized at the intersection between the membrane-anchored input sensor and the cytosolic output machinery. The data summarized here indicate that HAMP modules use a universal signaling language in balancing the communication between diverse membrane-bound input domains and cytosolic output domains that are completely foreign to each other.
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Affiliation(s)
- Joachim E Schultz
- Pharmazeutische Biochemie, Pharmazeutisches Institut, Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Kajal Kanchan
- Department of Biochemistry and Molecular Biology, Medical and Health Science Center, University of Debrecen, Debrecen H 4032, Hungary
| | - Miriam Ziegler
- Pharmazeutische Biochemie, Pharmazeutisches Institut, Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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78
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Calcium binding proteins and calcium signaling in prokaryotes. Cell Calcium 2014; 57:151-65. [PMID: 25555683 DOI: 10.1016/j.ceca.2014.12.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022]
Abstract
With the continued increase of genomic information and computational analyses during the recent years, the number of newly discovered calcium binding proteins (CaBPs) in prokaryotic organisms has increased dramatically. These proteins contain sequences that closely resemble a variety of eukaryotic calcium (Ca(2+)) binding motifs including the canonical and pseudo EF-hand motifs, Ca(2+)-binding β-roll, Greek key motif and a novel putative Ca(2+)-binding domain, called the Big domain. Prokaryotic CaBPs have been implicated in diverse cellular activities such as division, development, motility, homeostasis, stress response, secretion, transport, signaling and host-pathogen interactions. However, the majority of these proteins are hypothetical, and only few of them have been studied functionally. The finding of many diverse CaBPs in prokaryotic genomes opens an exciting area of research to explore and define the role of Ca(2+) in organisms other than eukaryotes. This review presents the most recent developments in the field of CaBPs and novel advancements in the role of Ca(2+) in prokaryotes.
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79
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Liu Q, Guo Y, Chang Y, Cai Z, Assur Z, Mancia F, Greene MI, Hendrickson WA. Multi-crystal native SAD analysis at 6 keV. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2544-57. [PMID: 25286840 PMCID: PMC4188002 DOI: 10.1107/s1399004714013376] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/08/2014] [Indexed: 11/10/2022]
Abstract
Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy.
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Affiliation(s)
- Qun Liu
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
- New York Structural Biology Center, NSLS X4, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Youzhong Guo
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Yanqi Chang
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
| | - Zheng Cai
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zahra Assur
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Mark I. Greene
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wayne A. Hendrickson
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
- New York Structural Biology Center, NSLS X4, Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
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80
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Bultynck G, Kiviluoto S, Methner A. Bax Inhibitor-1 Is Likely a pH-Sensitive Calcium Leak Channel, Not a H+/Ca2+ Exchanger. Sci Signal 2014; 7:pe22. [DOI: 10.1126/scisignal.2005764] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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