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Schuster CD, Salvatore F, Moens L, Martí MA. Globin phylogeny, evolution and function, the newest update. Proteins 2024; 92:720-734. [PMID: 38192262 DOI: 10.1002/prot.26659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/22/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024]
Abstract
Our globin census update allows us to refine our vision of globin origin, evolution, and structure to function relationship in the context of the currently accepted tree of life. The modern globin domain originates as a single domain, three-over-three α-helical folded structure before the diversification of the kingdoms of life (Bacteria, Archaea, Eukarya). Together with the diversification of prokaryotes, three monophyletic globin families (M, S, and T) emerged, most likely in Proteobacteria and Actinobacteria, displaying specific sequence and structural features, and spread by vertical and horizontal gene transfer, most probably already present in the last universal common ancestor (LUCA). Non-globin domains were added, and eventually lost again, creating multi-domain structures in key branches of M- (FHb and Adgb) and the vast majority of S globins, which with their coevolved multi-domain architectures, have predominantly "sensor" functions. Single domain T-family globins diverged into four major groups and most likely display functions related to reactive nitrogen and oxygen species (RNOS) chemistry, as well as oxygen storage/transport which drives the evolution of its major branches with their characteristic key distal residues (B10, E11, E7, and G8). M-family evolution also lead to distinctive major types (FHb and Fgb, Ngb, Adgb, GbX vertebrate Gbs), and shows the shift from high oxygen affinity controlled by TyrB10-Gln/AsnE11 likely related to RNOS chemistry in microorganisms, to a moderate oxygen affinity storage/transport function controlled by hydrophobic B10/E11-HisE7 in multicellular animals.
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Affiliation(s)
- Claudio David Schuster
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Franco Salvatore
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Marcelo Adrián Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Autónoma de Buenos Aires, Argentina
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2
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Schuelke-Sanchez A, Yennawar NH, Weinert EE. Oxygen-selective regulation of cyclic di-GMP synthesis by a globin coupled sensor with a shortened linking domain modulates Shewanella sp. ANA-3 biofilm. J Inorg Biochem 2024; 252:112482. [PMID: 38218138 DOI: 10.1016/j.jinorgbio.2024.112482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/15/2024]
Abstract
Bacteria utilize heme proteins, such as globin coupled sensors (GCSs), to sense and respond to oxygen levels. GCSs are predicted in almost 2000 bacterial species and consist of a globin domain linked by a central domain to a variety of output domains, including diguanylate cyclase domains that synthesize c-di-GMP, a major regulator of biofilm formation. To investigate the effects of middle domain length and heme edge residues on GCS diguanylate cyclase activity and cellular function, a putative diguanylate cyclase-containing GCS from Shewanella sp. ANA-3 (SA3GCS) was characterized. Binding of O2 to the heme resulted in activation of diguanylate cyclase activity, while NO and CO binding had minimal effects on catalysis, demonstrating that SA3GCS exhibits greater ligand selectivity for cyclase activation than many other diguanylate cyclase-containing GCSs. Small angle X-ray scattering analysis of dimeric SA3GCS identified movement of the cyclase domains away from each other, while maintaining the globin dimer interface, as a potential mechanism for regulating cyclase activity. Comparison of the Shewanella ANA-3 wild type and SA3GCS deletion (ΔSA3GCS) strains identified changes in biofilm formation, demonstrating that SA3GCS diguanylate cyclase activity modulates Shewanella phenotypes.
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Affiliation(s)
- Ariel Schuelke-Sanchez
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Emily E Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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3
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De Simone G, di Masi A, Pasquadibisceglie A, Coletta A, Sebastiani F, Smulevich G, Coletta M, Ascenzi P. Nitrobindin versus myoglobin: A comparative structural and functional study. J Inorg Biochem 2024; 250:112387. [PMID: 37914583 DOI: 10.1016/j.jinorgbio.2023.112387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/20/2023] [Accepted: 09/24/2023] [Indexed: 11/03/2023]
Abstract
Most hemoproteins display an all-α-helical fold, showing the classical three on three (3/3) globin structural arrangement characterized by seven or eight α-helical segments that form a sandwich around the heme. Over the last decade, a completely distinct class of heme-proteins called nitrobindins (Nbs), which display an all-β-barrel fold, has been identified and characterized from both structural and functional perspectives. Nbs are ten-stranded anti-parallel all-β-barrel heme-proteins found across the evolutionary ladder, from bacteria to Homo sapiens. Myoglobin (Mb), commonly regarded as the prototype of monomeric all-α-helical globins, is involved along with the oligomeric hemoglobin (Hb) in diatomic gas transport, storage, and sensing, as well as in the detoxification of reactive nitrogen and oxygen species. On the other hand, the function(s) of Nbs is still obscure, even though it has been postulated that they might participate to O2/NO signaling and metabolism. This function might be of the utmost importance in poorly oxygenated tissues, such as the eye's retina, where a delicate balance between oxygenation and blood flow (regulated by NO) is crucial. Dysfunction in this balance is associated with several pathological conditions, such as glaucoma and diabetic retinopathy. Here a detailed comparison of the structural, spectroscopic, and functional properties of Mb and Nbs is reported to shed light on the similarities and differences between all-α-helical and all-β-barrel heme-proteins.
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Affiliation(s)
| | | | | | | | - Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | | | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, 00146 Roma, Italy.
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Martinez Grundman JE, Johnson EA, Lecomte JTJ. Architectural digest: Thermodynamic stability and domain structure of a consensus monomeric globin. Biophys J 2023; 122:3117-3132. [PMID: 37353934 PMCID: PMC10432219 DOI: 10.1016/j.bpj.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023] Open
Abstract
Artificial proteins representing the consensus of a set of homologous sequences have attracted attention for their increased thermodynamic stability and conserved activity. Here, we applied the consensus approach to a b-type heme-binding protein to inspect the contribution of a dissociable cofactor to enhanced stability and the chemical consequences of creating a generic heme environment. We targeted the group 1 truncated hemoglobin (TrHb1) subfamily of proteins for their small size (∼120 residues) and ease of characterization. The primary structure, derived from a curated set of ∼300 representative sequences, yielded a highly soluble consensus globin (cGlbN) enriched in acidic residues. Optical and NMR spectroscopies revealed high-affinity heme binding in the expected site and in two orientations. At neutral pH, proximal and distal iron coordination was achieved with a pair of histidine residues, as observed in some natural TrHb1s, and with labile ligation on the distal side. As opposed to studied TrHb1s, which undergo additional folding upon heme binding, cGlbN displayed the same extent of secondary structure whether the heme was associated with the protein or not. Denaturation required guanidine hydrochloride and showed that apo- and holoprotein unfolded in two transitions-the first (occurring with a midpoint of ∼2 M) was shifted to higher denaturant concentration in the holoprotein (∼3.7 M) and reflected stabilization due to heme binding, while the second transition (∼6.2 M) was common to both forms. Thus, the consensus sequence stabilized the protein but exposed the existence of two separately cooperative subdomains within the globin architecture, masked as one single domain in TrHb1s with typical stabilities. The results suggested ways in which specific chemical or thermodynamic features may be controlled in artificial heme proteins.
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Affiliation(s)
| | - Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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Linhart I, Hanzlíková I, Mráz J, Dušková Š. New Aminobiphenylcysteine Derivatives in Globin and Urine of Rats Dosed with 4-Aminobiphenyl, a Tobacco Smoke Carcinogen. Chem Res Toxicol 2023; 36:430-437. [PMID: 36861465 DOI: 10.1021/acs.chemrestox.2c00366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The 4-biphenylnitrenium ion (BPN), a reactive metabolic intermediate of the tobacco smoke carcinogen 4-aminobiphenyl (4-ABP), can react with nucleophilic sulfanyl groups in glutathione (GSH) as well as in proteins. The main site of attack of these S-nucleophiles was predicted using simple orientational rules of aromatic nucleophilic substitution. Thereafter, a series of presumptive 4-ABP metabolites and adducts with cysteine were synthesized, namely, S-(4-amino-3-biphenyl)cysteine (ABPC), N-acetyl-S-(4-amino-3-biphenyl)cysteine (4-amino-3-biphenylmercapturic acid, ABPMA), S-(4-acetamido-3-biphenyl)cysteine (AcABPC), and N-acetyl-S-(4-acetamido-3-biphenyl)cysteine (4-acetamido-3-biphenylmercapturic acid, AcABPMA). Then, globin and urine of rats dosed with a single ip dose of 4-ABP (27 mg/kg b.w.) was analyzed by HPLC-ESI-MS2. ABPC was identified in acid-hydrolyzed globin at levels of 3.52 ± 0.50, 2.74 ± 0.51, and 1.25 ± 0.12 nmol/g globin (mean ± S.D.; n = 6) on days 1, 3, and 8 after dosing, respectively. In the urine collected on day 1 (0-24 h) after dosing, excretion of ABPMA, AcABPMA, and AcABPC amounted to 1.97 ± 0.88, 3.09 ± 0.75, and 3.69 ± 1.49 nmol/kg b.w. (mean ± S.D.; n = 6), respectively. On day 2, excretion of the metabolites decreased by one order of magnitude followed by a slower decrease on day 8. Regarding the possible formation of AcABPC from ABPC, N-acetylation of the amino group at the biphenyl moiety prior to that at cysteine appears to be very unlikely. Thus, the structure of AcABPC indicates the involvement of N-acetyl-4-biphenylnitrenium ion (AcBPN) and/or its reactive ester precursors in in vivo reactions with GSH and protein-bound cysteine. ABPC in globin might become an alternative biomarker of the dose of toxicologically relevant metabolic intermediates of 4-ABP.
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Affiliation(s)
- Igor Linhart
- Department of Organic Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Iveta Hanzlíková
- National Institute of Public Health, Prague, Šrobárova 49/48, 100 00 Prague, Czech Republic
| | - Jaroslav Mráz
- National Institute of Public Health, Prague, Šrobárova 49/48, 100 00 Prague, Czech Republic
| | - Šárka Dušková
- National Institute of Public Health, Prague, Šrobárova 49/48, 100 00 Prague, Czech Republic
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Kim DS, Baek HJ, Kim BR, Yoon BA, Lee JH, Kook H. The First Korean Family with Hemoglobin-M Milwaukee-2 Leading to Hereditary Methemoglobinemia. Yonsei Med J 2020; 61:1064-1067. [PMID: 33251782 PMCID: PMC7700874 DOI: 10.3349/ymj.2020.61.12.1064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/08/2020] [Indexed: 11/27/2022] Open
Abstract
Hemoglobin M (HbM) is a group of abnormal hemoglobin variants that form methemoglobin, which leads to cyanosis and hemolytic anemia. HbM-Milwaukee-2 is a rare variant caused by the point mutation CAC>TAC on codon 93 of the hemoglobin subunit beta (HBB) gene, resulting in the replacement of histidine by tyrosine. We here report the first Korean family with HbM-Milwaukee-2, whose diagnosis was confirmed by gene sequencing. A high index of suspicion for this rare Hb variant is necessary in a patient presenting with cyanosis since childhood, along with methemoglobinemia and a family history of cyanosis.
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Affiliation(s)
- Dae Sung Kim
- Department of Pediatrics, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Hee Jo Baek
- Department of Pediatrics, Chonnam National University Hwasun Hospital, Hwasun, Korea
- Department of Pediatrics, Chonnam National University Medical School, Gwangju, Korea.
| | - Bo Ram Kim
- Department of Pediatrics, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Bo Ae Yoon
- Department of Pediatrics, Chonnam National University Hwasun Hospital, Hwasun, Korea
- Department of Pediatrics, Chonnam National University Medical School, Gwangju, Korea
| | - Jun Hyung Lee
- Department of Laboratory Medicine, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Gwangju, Korea
| | - Hoon Kook
- Department of Pediatrics, Chonnam National University Hwasun Hospital, Hwasun, Korea
- Department of Pediatrics, Chonnam National University Medical School, Gwangju, Korea
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7
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Abstract
Animals depend on the sequential oxidation of organic molecules to survive; thus, oxygen-carrying/transporting proteins play a fundamental role in aerobic metabolism. Globins are the most common and widespread group of respiratory proteins. They can be divided into three types: circulating intracellular, noncirculating intracellular, and extracellular, all of which have been reported in annelids. The diversity of oxygen transport proteins has been underestimated across metazoans. We probed 250 annelid transcriptomes in search of globin diversity in order to elucidate the evolutionary history of this gene family within this phylum. We report two new globin types in annelids, namely androglobins and cytoglobins. Although cytoglobins and myoglobins from vertebrates and from invertebrates are referred to by the same name, our data show they are not genuine orthologs. Our phylogenetic analyses show that extracellular globins from annelids are more closely related to extracellular globins from other metazoans than to the intracellular globins of annelids. Broadly, our findings indicate that multiple gene duplication and neo-functionalization events shaped the evolutionary history of the globin family.
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Affiliation(s)
- Flávia A Belato
- Department of Zoology, Institute of Biosciences, University of Sao Paulo, Brazil
| | - Christopher J Coates
- Department of Biosciences, College of Science, Swansea University, United Kingdom
| | - Kenneth M Halanych
- Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
| | - Roy E Weber
- Zoophysiology, Department of Biology, Aarhus University, Denmark
| | - Elisa M Costa-Paiva
- Department of Zoology, Institute of Biosciences, University of Sao Paulo, Brazil
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Skalova T, Lengalova A, Dohnalek J, Harlos K, Mihalcin P, Kolenko P, Stranava M, Blaha J, Shimizu T, Martínková M. Disruption of the dimerization interface of the sensing domain in the dimeric heme-based oxygen sensor AfGcHK abolishes bacterial signal transduction. J Biol Chem 2020; 295:1587-1597. [PMID: 31914416 PMCID: PMC7008379 DOI: 10.1074/jbc.ra119.011574] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/30/2019] [Indexed: 12/17/2022] Open
Abstract
The heme-based oxygen sensor protein AfGcHK is a globin-coupled histidine kinase in the soil bacterium Anaeromyxobacter sp. Fw109-5. Its C-terminal functional domain exhibits autophosphorylation activity induced by oxygen binding to the heme-Fe(II) complex located in the oxygen-sensing N-terminal globin domain. A detailed understanding of the signal transduction mechanisms in heme-containing sensor proteins remains elusive. Here, we investigated the role of the globin domain's dimerization interface in signal transduction in AfGcHK. We present a crystal structure of a monomeric imidazole-bound AfGcHK globin domain at 1.8 Å resolution, revealing that the helices of the WT globin dimer are under tension and suggesting that Tyr-15 plays a role in both this tension and the globin domain's dimerization. Biophysical experiments revealed that whereas the isolated WT globin domain is dimeric in solution, the Y15A and Y15G variants in which Tyr-15 is replaced with Ala or Gly, respectively, are monomeric. Additionally, we found that although the dimerization of the full-length protein is preserved via the kinase domain dimerization interface in all variants, full-length AfGcHK variants bearing the Y15A or Y15G substitutions lack enzymatic activity. The combined structural and biophysical results presented here indicate that Tyr-15 plays a key role in the dimerization of the globin domain of AfGcHK and that globin domain dimerization is essential for internal signal transduction and autophosphorylation in this protein. These findings provide critical insights into the signal transduction mechanism of the histidine kinase AfGcHK from Anaeromyxobacter.
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Affiliation(s)
- Tereza Skalova
- Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, 252 50 Czech Republic
| | - Alzbeta Lengalova
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Jan Dohnalek
- Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, 252 50 Czech Republic
| | - Karl Harlos
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - Peter Mihalcin
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Petr Kolenko
- Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, 252 50 Czech Republic; FNSPE, Czech Technical University in Prague, Brehova 7, Prague 1, 115 19 Czech Republic
| | - Martin Stranava
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Jan Blaha
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Markéta Martínková
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic.
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Abstract
A methodology to cluster proteins based on their dynamics’ similarity is presented. For each pair of proteins from a dataset, the structures are superimposed, and the Anisotropic Network Model modes of motions are calculated. The twelve slowest modes from each protein are matched using a local mode alignment algorithm based on the local sequence alignment algorithm of Smith–Waterman. The dynamical similarity distance matrix is calculated based on the top scoring matches of each pair and the proteins are clustered using a hierarchical clustering algorithm. The utility of this method is exemplified on a dataset of protein chains from the globin family and a dataset of tetrameric hemoglobins. The results demonstrate the effect of the quaternary structure of globin members on their intrinsic dynamics and show good ability to distinguish between different states of hemoglobin, revealing the dynamical relations between them.
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Affiliation(s)
- Dror Tobi
- Department of Molecular Biology, Ariel University, Ariel, Israel
- Department of Computer Sciences, Ariel University, Ariel, Israel
- * E-mail:
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10
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Kumar MR, Farmer PJ. Chemical trapping and characterization of small oxoacids of sulfur (SOS) generated in aqueous oxidations of H 2S. Redox Biol 2018; 14:485-491. [PMID: 29096321 PMCID: PMC5680521 DOI: 10.1016/j.redox.2017.10.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/08/2017] [Accepted: 10/15/2017] [Indexed: 12/29/2022] Open
Abstract
Small oxoacids of sulfur (SOS) are elusive molecules like sulfenic acid, HSOH, and sulfinic acid, HS(O)OH, generated during the oxidation of hydrogen sulfide, H2S, in aqueous solution. Unlike their alkyl homologs, there is a little data on their generation and speciation during H2S oxidation. These SOS may exhibit both nucleophilic and electrophilic reactivity, which we attribute to interconversion between S(II) and S(IV) tautomers. We find that SOS may be trapped in situ by derivatization with nucleophilic and electrophilic trapping agents and then characterized by high resolution LC MS. In this report, we compare SOS formation from H2S oxidation by a variety of biologically relevant oxidants. These SOS appear relatively long lived in aqueous solution, and thus may be involved in the observed physiological effects of H2S.
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Affiliation(s)
- Murugaeson R Kumar
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, United States
| | - Patrick J Farmer
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, United States.
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Wu M, Chen N, Huang CX, He Y, Zhao YZ, Chen XH, Chen XL, Wang HL. Effect of Low Temperature on Globin Expression, Respiratory Metabolic Enzyme Activities, and Gill Structure of Litopenaeus vannamei. Biochemistry (Mosc) 2017; 82:844-851. [PMID: 28918749 DOI: 10.1134/s0006297917070100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Low temperature frequently influences growth, development, and even survival of aquatic animals. In the present study, physiological and molecular responses to low temperature in Litopenaeus vannamei were investigated. The cDNA sequences of two oxygen-carrying proteins, cytoglobin (Cygb) and neuroglobin (Ngb), were isolated. Protein structure analysis revealed that both proteins share a globin superfamily domain. Real-time PCR analysis indicated that Cygb and Ngb mRNA levels gradually increased during decrease in temperatures from 25 to 15°C and then decreased at 10°C in muscle, brain, stomach, and heart, except for a continuing increase in gills, whereas they showed a different expression trend in the hepatopancreas. Hemocyanin concentration gradually reduced as the temperature decreased. Moreover, the activities of respiratory metabolic enzymes including lactate dehydrogenase (LDH) and succinate dehydrogenase (SDH) were measured, and it was found that LDH activity gradually increased while SDH activity decreased after low-temperature treatment. Finally, damage to gill structure at low temperature was also observed, and this intensified with further decrease in temperature. Taken together, these results show that low temperature has an adverse influence in L. vannamei, which contributes to systematic understanding of the adaptation mechanisms of shrimp at low temperature.
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Affiliation(s)
- Meng Wu
- Ministry of Education, Huazhong Agricultural University, College of Fishery, Key Lab of Freshwater Animal Breeding, Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction, Wuhan, 430070, PR China.
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Linhart I, Hanzlíková I, Mráz J, Dušková Š. S-(3-Aminobenzanthron-2-yl)cysteine in the globin of rats as a novel type of adduct and possible biomarker of exposure to 3-nitrobenzanthrone, a potent environmental carcinogen. Arch Toxicol 2017; 91:3317-3325. [PMID: 28283705 DOI: 10.1007/s00204-017-1943-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/23/2017] [Indexed: 12/21/2022]
Abstract
3-Nitrobenzanthrone (3-NBA), a potent environmental mutagen and carcinogen, is known to be activated in vivo to 3-benzanthronylnitrenium ion which forms both NH and C2-bound adducts with DNA and also reacts with glutathione giving rise to urinary 3-aminobenzanthron-2-ylmercapturic acid. In this study, acid hydrolysate of globin from rats dosed intraperitoneally with 3-NBA was analysed by HPLC/MS to identify a novel type of cysteine adduct, 3-aminobenzanthron-2-ylcysteine (3-ABA-Cys), confirmed using a synthesised standard. The 3-ABA-Cys levels in globin peaked after single 3-NBA doses of 1 and 2 mg/kg on day 2 to attain 0.25 and 0.49 nmol/g globin, respectively, thereafter declining slowly to 70-80% of their maximum values during 15 days. After dosing rats for three consecutive days with 1 mg 3-NBA/kg a significant cumulation of 3-ABA-Cys in globin was observed. 3-ABA-Cys was also found in the plasma hydrolysate. Herein, after dosing with 1 and 2 mg 3-NBA/kg the adduct levels peaked on day 1 at 0.15 and 0.51 nmol/ml plasma, respectively, thereafter declining rapidly to undetectable levels on day 15. In addition, sulphinamide adducts were also found in the exposed rats, measured indirectly as 3-aminobenzanthrone (3-ABA) split off from globin by mild acid hydrolysis. Levels of both types of adducts in the globin samples parallelled very well with 3-ABA/3-ABA-Cys ratio being around 1:8. In conclusion, 3-ABA-Cys is the first example of arylnitrenium-cysteine adduct in globin representing a new promising class of biomarkers to assess cumulative exposures to aromatic amines, nitroaromatics and heteroaromatic amines.
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Affiliation(s)
- Igor Linhart
- Department of Organic Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic.
| | - Iveta Hanzlíková
- National Institute of Public Health, Prague, Šrobárova 48, 10042, Prague, Czech Republic
| | - Jaroslav Mráz
- National Institute of Public Health, Prague, Šrobárova 48, 10042, Prague, Czech Republic
| | - Šárka Dušková
- National Institute of Public Health, Prague, Šrobárova 48, 10042, Prague, Czech Republic
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14
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Affiliation(s)
- Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
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15
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Guidolin D, Tortorella C, Marcoli M, Maura G, Agnati LF. Neuroglobin, a Factor Playing for Nerve Cell Survival. Int J Mol Sci 2016; 17:ijms17111817. [PMID: 27809238 PMCID: PMC5133818 DOI: 10.3390/ijms17111817] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/14/2016] [Accepted: 10/26/2016] [Indexed: 12/17/2022] Open
Abstract
Cell death represents the final outcome of several pathological conditions of the central nervous system and available evidence suggests that in both acute injuries and neurodegenerative diseases it is often associated with mitochondrial dysfunction. Thus, the possibility to prevent mitochondrial events involved in cell death might represent efficient tools to limit neuronal damage. In recent years, increased attention has been paid to the endogenous protein neuroglobin, since accumulating evidence showed that its high expression was associated with preserved mitochondrial function and to an increased survival of nerve cells in vitro and in vivo in a variety of experimental models of cell insult. The biological and structural features of neuroglobin and the mitochondria-related mechanisms of neuroglobin-induced neuroprotection will be here briefly discussed. In this respect, the inhibition of the intrinsic pathway of apoptosis emerges as a key neuroprotective effect induced by the protein. These findings could open the possibility to develop efficient neuroglobin-mediated therapeutic strategies aimed at minimizing the neuronal cell death occurring in impacting neurological pathologies like stroke and neurodegenerative diseases.
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Affiliation(s)
- Diego Guidolin
- Department of Neuroscience, University of Padova, Padova 35122, Italy.
| | - Cinzia Tortorella
- Department of Neuroscience, University of Padova, Padova 35122, Italy.
| | - Manuela Marcoli
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, Genova 16126, Italy.
| | - Guido Maura
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, Genova 16126, Italy.
| | - Luigi F Agnati
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy.
- Department of Neuroscience, Karolinska Institutet, Stockholm 17177, Sweden.
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16
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Minai-Tehrani D, Toofani S, Yazdi F, Minai-Tehrani A, Mollasalehi H, Bakhtiari Ziabari K. Inhibition of pseudoperoxiadse activity of human red blood cell hemoglobin by methocarbamol. Int J Biol Macromol 2016; 94:788-792. [PMID: 27645932 DOI: 10.1016/j.ijbiomac.2016.09.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 06/08/2016] [Accepted: 09/15/2016] [Indexed: 11/17/2022]
Abstract
After red blood cells lysis, hemoglobin is released to blood circulation. Hemoglobin is carried in blood by binding to haptoglobin. In normal individuals, no free hemoglobin is observed in the blood, because most of the hemoglobin is in the form of haptoglobin complex. In some diseases that are accompanied by hemolysis, the amount of released hemoglobin is higher than its complementary haptoglobin. As a result, free hemoglobin appears in the blood, which is a toxic compound for these patients and may cause renal failure, hypertensive response and risk of atherogenesis. Free hemoglobin has been determined to have peroxidase activity and considered a pseudoenzyme. In this study, the effect of methocarbamol on the peroxidase activity of human hemoglobin was investigated. Our results showed that the drug inhibited the pseudoenzyme by un-competitive inhibition. Both Km and Vmax decreased by increasing the drug concentration. Ki and IC50 values were determined as 6 and 10mM, respectively. Docking results demonstrated that methocarbamol did not attach to heme group directly. A hydrogen bond linked NH2 of carbamate group of methocarbamol to the carboxyl group of Asp126 side chain. Two other hydrogen bonds could be also observed between hydroxyl group of the drug and Ser102 and Ser133 residues of the pseudoenzyme.
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Affiliation(s)
- Dariush Minai-Tehrani
- BioResearch Lab, Faculty of Biological Sciences, Shahid Beheshti University, G.C., Iran.
| | - Sara Toofani
- Department of Pharmacology & Toxicology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Fatemeh Yazdi
- Department of Pharmacology & Toxicology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Arash Minai-Tehrani
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
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17
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Motion C, Lovett JE, Bell S, Cassidy SL, Cruickshank PAS, Bolton DR, Hunter RI, El Mkami H, Van Doorslaer S, Smith GM. DEER Sensitivity between Iron Centers and Nitroxides in Heme-Containing Proteins Improves Dramatically Using Broadband, High-Field EPR. J Phys Chem Lett 2016; 7:1411-5. [PMID: 27035368 PMCID: PMC4863198 DOI: 10.1021/acs.jpclett.6b00456] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/30/2016] [Indexed: 05/22/2023]
Abstract
This work demonstrates the feasibility of making sensitive nanometer distance measurements between Fe(III) heme centers and nitroxide spin labels in proteins using the double electron-electron resonance (DEER) pulsed EPR technique at 94 GHz. Techniques to measure accurately long distances in many classes of heme proteins using DEER are currently strongly limited by sensitivity. In this paper we demonstrate sensitivity gains of more than 30 times compared with previous lower frequency (X-band) DEER measurements on both human neuroglobin and sperm whale myoglobin. This is achieved by taking advantage of recent instrumental advances, employing wideband excitation techniques based on composite pulses and exploiting more favorable relaxation properties of low-spin Fe(III) in high magnetic fields. This gain in sensitivity potentially allows the DEER technique to be routinely used as a sensitive probe of structure and conformation in the large number of heme and many other metalloproteins.
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Affiliation(s)
- Claire
L. Motion
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Janet E. Lovett
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Stacey Bell
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Scott L. Cassidy
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Paul A. S. Cruickshank
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - David R. Bolton
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Robert I. Hunter
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Hassane El Mkami
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | | | - Graham M. Smith
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
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18
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De Henau S, Tilleman L, Vangheel M, Luyckx E, Trashin S, Pauwels M, Germani F, Vlaeminck C, Vanfleteren JR, Bert W, Pesce A, Nardini M, Bolognesi M, De Wael K, Moens L, Dewilde S, Braeckman BP. A redox signalling globin is essential for reproduction in Caenorhabditis elegans. Nat Commun 2015; 6:8782. [PMID: 26621324 PMCID: PMC4686822 DOI: 10.1038/ncomms9782] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 10/02/2015] [Indexed: 12/17/2022] Open
Abstract
Moderate levels of reactive oxygen species (ROS) are now recognized as redox signalling molecules. However, thus far, only mitochondria and NADPH oxidases have been identified as cellular sources of ROS in signalling. Here we identify a globin (GLB-12) that produces superoxide, a type of ROS, which serves as an essential signal for reproduction in C. elegans. We find that GLB-12 has an important role in the regulation of multiple aspects in germline development, including germ cell apoptosis. We further describe how GLB-12 displays specific molecular, biochemical and structural properties that allow this globin to act as a superoxide generator. In addition, both an intra- and extracellular superoxide dismutase act as key partners of GLB-12 to create a transmembrane redox signal. Our results show that a globin can function as a driving factor in redox signalling, and how this signal is regulated at the subcellular level by multiple control layers.
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Affiliation(s)
- Sasha De Henau
- Department of Biology, Ghent University, Ghent B-9000, Belgium
| | - Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | | | - Evi Luyckx
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | - Stanislav Trashin
- Department of Chemistry, University of Antwerp, Antwerp B-2000, Belgium
| | - Martje Pauwels
- Department of Chemistry, University of Antwerp, Antwerp B-2000, Belgium
| | - Francesca Germani
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | | | | | - Wim Bert
- Department of Biology, Ghent University, Ghent B-9000, Belgium
| | - Alessandra Pesce
- Department of Physics, University of Genova, Genova I-16146, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano I-20133, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Milano I-20133, Italy
- CNR-IBF and CIMAINA, University of Milano, Milano I-20133, Italy
| | - Karolien De Wael
- Department of Chemistry, University of Antwerp, Antwerp B-2000, Belgium
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
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19
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Ferreira JC, Marcondes MF, Icimoto MY, Cardoso THS, Tofanello A, Pessoto FS, Miranda EGA, Prieto T, Nascimento OR, Oliveira V, Nantes IL. Intermediate Tyrosyl Radical and Amyloid Structure in Peroxide-Activated Cytoglobin. PLoS One 2015; 10:e0136554. [PMID: 26312997 PMCID: PMC4552303 DOI: 10.1371/journal.pone.0136554] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 08/04/2015] [Indexed: 11/22/2022] Open
Abstract
We characterized the peroxidase mechanism of recombinant rat brain cytoglobin (Cygb) challenged by hydrogen peroxide, tert-butylhydroperoxide and by cumene hydroperoxide. The peroxidase mechanism of Cygb is similar to that of myoglobin. Cygb challenged by hydrogen peroxide is converted to a Fe4+ oxoferryl π cation, which is converted to Fe4+ oxoferryl and tyrosyl radical detected by direct continuous wave-electron paramagnetic resonance and by 3,5-dibromo-4-nitrosobenzene sulfonate spin trapping. When organic peroxides are used as substrates at initial reaction times, and given an excess of peroxide present, the EPR signals of the corresponding peroxyl radicals precede those of the direct tyrosyl radical. This result is consistent with the use of peroxide as a reducing agent for the recycling of Cygb high-valence species. Furthermore, we found that the Cygb oxidation by peroxides leads to the formation of amyloid fibrils. This result suggests that Cygb possibly participates in the development of degenerative diseases; our findings also support the possible biological role of Cygb related to peroxidase activity.
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Affiliation(s)
- Juliana C. Ferreira
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Marcelo F. Marcondes
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Marcelo Y. Icimoto
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Thyago H. S. Cardoso
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Aryane Tofanello
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Felipe S. Pessoto
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Erica G. A. Miranda
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Tatiana Prieto
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
- Grupo de Biofísica Molecular “Sérgio Mascarenhas,” Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Otaciro R. Nascimento
- Grupo de Biofísica Molecular “Sérgio Mascarenhas,” Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Vitor Oliveira
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Iseli L. Nantes
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
- * E-mail:
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20
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Christensen AB, Herman JL, Elphick MR, Kober KM, Janies D, Linchangco G, Semmens DC, Bailly X, Vinogradov SN, Hoogewijs D. Phylogeny of Echinoderm Hemoglobins. PLoS One 2015; 10:e0129668. [PMID: 26247465 PMCID: PMC4527676 DOI: 10.1371/journal.pone.0129668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/12/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Recent genomic information has revealed that neuroglobin and cytoglobin are the two principal lineages of vertebrate hemoglobins, with the latter encompassing the familiar myoglobin and α-globin/β-globin tetramer hemoglobin, and several minor groups. In contrast, very little is known about hemoglobins in echinoderms, a phylum of exclusively marine organisms closely related to vertebrates, beyond the presence of coelomic hemoglobins in sea cucumbers and brittle stars. We identified about 50 hemoglobins in sea urchin, starfish and sea cucumber genomes and transcriptomes, and used Bayesian inference to carry out a molecular phylogenetic analysis of their relationship to vertebrate sequences, specifically, to assess the hypothesis that the neuroglobin and cytoglobin lineages are also present in echinoderms. RESULTS The genome of the sea urchin Strongylocentrotus purpuratus encodes several hemoglobins, including a unique chimeric 14-domain globin, 2 androglobin isoforms and a unique single androglobin domain protein. Other strongylocentrotid genomes appear to have similar repertoires of globin genes. We carried out molecular phylogenetic analyses of 52 hemoglobins identified in sea urchin, brittle star and sea cucumber genomes and transcriptomes, using different multiple sequence alignment methods coupled with Bayesian and maximum likelihood approaches. The results demonstrate that there are two major globin lineages in echinoderms, which are related to the vertebrate neuroglobin and cytoglobin lineages. Furthermore, the brittle star and sea cucumber coelomic hemoglobins appear to have evolved independently from the cytoglobin lineage, similar to the evolution of erythroid oxygen binding globins in cyclostomes and vertebrates. CONCLUSION The presence of echinoderm globins related to the vertebrate neuroglobin and cytoglobin lineages suggests that the split between neuroglobins and cytoglobins occurred in the deuterostome ancestor shared by echinoderms and vertebrates.
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Affiliation(s)
- Ana B. Christensen
- Biology Department, Lamar University, Beaumont, Texas, United States of America
| | - Joseph L. Herman
- Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom
- Division of Mathematical Biology, National Institute of Medical Research, London, NW7 1AA, United Kingdom
| | - Maurice R. Elphick
- School of Biological & Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Kord M. Kober
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Daniel Janies
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States of America
| | - Gregorio Linchangco
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States of America
| | - Dean C. Semmens
- School of Biological & Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Xavier Bailly
- Marine Plants and Biomolecules, Station Biologique de Roscoff, 2968 Roscoff, France
| | - Serge N. Vinogradov
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201, United States of America
| | - David Hoogewijs
- Institute of Physiology, University of Duisburg-Essen, Essen, Germany
- * E-mail:
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21
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Yang Y, Allemand F, Guca E, Vallone B, Delbecq S, Roumestand C. (1)H, (15)N and (13)C backbone resonance assignments of murine met-neuroglobin, free and in complex with cyanide. Biomol NMR Assign 2015; 9:153-156. [PMID: 24830543 DOI: 10.1007/s12104-014-9563-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/06/2014] [Indexed: 06/03/2023]
Abstract
Neuroglobin is a globin present in the brain and retina of mammals. This hexacoordinated hemoprotein binds small diatomic molecules, albeit with lower affinity compared with other globins. We report here the resonance assignment of murine met-Neuroglobine, free and in complex with cyanide.
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Affiliation(s)
- Yinshan Yang
- CNRS UMR 5048, Centre de Biochimie Structurale, Université de Montpellier I and II, 29 rue de Navacelles, 34090, Montpellier Cedex, France
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22
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Meng Z, Yang X, Hu D, Wang K, Zhi F, Chen X, Gong G, Wu J, Hu Y. Replacing heme with paclitaxel to prepare drug-loaded globin nanoassembles for CD163 targeting. J Pharm Sci 2015; 104:1045-55. [PMID: 25640195 DOI: 10.1002/jps.24290] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 01/22/2023]
Abstract
Protein-based nanoparticles hold great promises in both preclinical and clinical practices, such as oncology diagnosis and treatment, because of their high biocompatibility and biodegradability. However, the complicated preparation and lack of targeting specific cells or tissues may limit their further uses. To overcome these limitations, we developed a novel replacing method for preparing dual-functional protein nanocarrier, such that one function is capable of encapsulating small molecule into protein, whereas the other function is cable of recognizing CD163 receptor [hemoglobin (Hb) scavenger receptor]. In this study, Hb was chosen as the targeting drug carrier. First, the heme group in the Hb was removed and replaced by paclitaxel (PTX) to form nanoparticles (Gb-NPs-PTX). The resulted Gb-NPs-PTX showed spherical shape and their diameter could be controlled in the range of 120-160 nm by altering the ratio of PTX to Hb. The binding activity of Gb-NPs-PTX to CD163 was confirmed by cell uptake in CD163(+) Chinese hamster ovary cells. Results in vivo also showed a CD163-dependent tissue accumulation of Gb-NPs-PTX in mice. In summary, by using the novel replacing method, PTX could be easily encapsulated into Hb nanoparticles and the targeting effects of Hb could also be kept.
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MESH Headings
- Animals
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antigens, Differentiation, Myelomonocytic/genetics
- Antigens, Differentiation, Myelomonocytic/metabolism
- Antineoplastic Agents, Phytogenic/administration & dosage
- Antineoplastic Agents, Phytogenic/chemistry
- Antineoplastic Agents, Phytogenic/pharmacokinetics
- Biological Transport
- CHO Cells
- Chemistry, Pharmaceutical
- Cricetulus
- Drug Carriers
- Globins/chemistry
- Globins/metabolism
- Heme/chemistry
- Heme/metabolism
- Mice, Inbred BALB C
- Nanoparticles
- Nanotechnology
- Paclitaxel/administration & dosage
- Paclitaxel/chemistry
- Paclitaxel/pharmacokinetics
- Particle Size
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Technology, Pharmaceutical/methods
- Tissue Distribution
- Transfection
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Affiliation(s)
- Zhengjie Meng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, People's Republic of China; College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
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23
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Ioannidis NE, Kotzabasis K. Could structural similarity of specific domains between animal globins and plant antenna proteins provide hints important for the photoprotection mechanism? J Theor Biol 2015; 364:71-9. [PMID: 25218499 DOI: 10.1016/j.jtbi.2014.08.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/30/2014] [Accepted: 08/28/2014] [Indexed: 11/26/2022]
Abstract
Non photochemical quenching is a fundamental mechanism in photosynthesis, which protects plants against excess excitation energy and is of crucial importance for their survival and fitness. In the last decades hundreds of papers have appeared that describe the role of antenna regulation in protection or the so called qE response. However, the exact quenching site is still obscure. Previously overlooked features of the antenna may provide hints towards the elucidation of its functionality and of the quenching mechanism. Recently it was demonstrated that the catalytic domain of human myoglobin that binds the pigment (i.e. heme) is similar in structure to the domain of the light harvesting complex II of pea that binds Chl a 614 (former known as b3). In addition, it is well accepted that conformational changes of the chlorophyll macrocycle result in reversible changes of fluorescence (the lowest fluorescence corresponds to non planar macrocycle). Here we put forward a hypothesis regarding the molecular mechanism that leads to the formation of a quenching center inside the antenna proteins. Our main suggestion is that a conformational change of helix H5 (known also as helix D) forces conformational changes in the macrocycle of Chl a 614 is implicated in the ΔA535 absorbance change and quenching during photoprotective qE. The specific features (some of them similar to those of heme domain of globins) of the b3 domain account for these traits. The model predicts that antenna proteins having b3 pigments (i.e. LHCII, CP29, CP26) can act as potential quenchers.
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Affiliation(s)
- Nikolaos E Ioannidis
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece.
| | - Kiriakos Kotzabasis
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece
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24
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Kuleva NV, Krasovskaya IE. [THE ROLE OF HEME-CONTAINING GLOBINS IN HYPOXIC NO-SIGNALING OF VERTEBRATE CELLS]. Tsitologiia 2015; 57:563-571. [PMID: 26591567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nitric oxide is one of the most important signaling molecule of living organisms. It may be produced by two ways: from arginine by means of NO-syntases and from nitrite by means of nitrite reductases. The last way is realized mostly at hypoxic state of organisms and heme-containing globins of vertebrates (hemoglobin, myoglobin, cytoglobin, neuroglobin) mediate the transformation of NO2 into NO by means of their nitrite reductase activities. Hypoxic NO-signaling depends on oxygen concentration and is important for exercise, vascular hypoxic vasodilation, myocardial preconditioning and angiogenesis. Data of scientific literature of last 15 years show that the nitrite-reductase activity of heme-containing globins was used for oxygen sensing and ROS/RNS defence at early stages of life evolution.
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25
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Herman JL, Challis CJ, Novák Á, Hein J, Schmidler SC. Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure. Mol Biol Evol 2014; 31:2251-66. [PMID: 24899668 PMCID: PMC4137710 DOI: 10.1093/molbev/msu184] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
For sequences that are highly divergent, there is often insufficient information to infer accurate alignments, and phylogenetic uncertainty may be high. One way to address this issue is to make use of protein structural information, since structures generally diverge more slowly than sequences. In this work, we extend a recently developed stochastic model of pairwise structural evolution to multiple structures on a tree, analytically integrating over ancestral structures to permit efficient likelihood computations under the resulting joint sequence-structure model. We observe that the inclusion of structural information significantly reduces alignment and topology uncertainty, and reduces the number of topology and alignment errors in cases where the true trees and alignments are known. In some cases, the inclusion of structure results in changes to the consensus topology, indicating that structure may contain additional information beyond that which can be obtained from sequences. We use the model to investigate the order of divergence of cytoglobins, myoglobins, and hemoglobins and observe a stabilization of phylogenetic inference: although a sequence-based inference assigns significant posterior probability to several different topologies, the structural model strongly favors one of these over the others and is more robust to the choice of data set.
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Affiliation(s)
- Joseph L Herman
- Department of Statistics, University of Oxford, Oxford, United KingdomDivision of Mathematical Biology, National Institute of Medical Research, London, United Kingdom
| | | | - Ádám Novák
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Jotun Hein
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Scott C Schmidler
- Department of Statistical Science, Duke UniversityDepartment of Computer Science, Duke University
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26
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Ascenzi P, Leboffe L, Pesce A, Ciaccio C, Sbardella D, Bolognesi M, Coletta M. Nitrite-reductase and peroxynitrite isomerization activities of Methanosarcina acetivorans protoglobin. PLoS One 2014; 9:e95391. [PMID: 24827820 PMCID: PMC4020757 DOI: 10.1371/journal.pone.0095391] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/25/2014] [Indexed: 12/04/2022] Open
Abstract
Within the globin superfamily, protoglobins (Pgb) belong phylogenetically to the same cluster of two-domain globin-coupled sensors and single-domain sensor globins. Multiple functional roles have been postulated for Methanosarcina acetivorans Pgb (Ma-Pgb), since the detoxification of reactive nitrogen and oxygen species might co-exist with enzymatic activity(ies) to facilitate the conversion of CO to methane. Here, the nitrite-reductase and peroxynitrite isomerization activities of the CysE20Ser mutant of Ma-Pgb (Ma-Pgb*) are reported and analyzed in parallel with those of related heme-proteins. Kinetics of nitrite-reductase activity of ferrous Ma-Pgb* (Ma-Pgb*-Fe(II)) is biphasic and values of the second-order rate constant for the reduction of NO2– to NO and the concomitant formation of nitrosylated Ma-Pgb*-Fe(II) (Ma-Pgb*-Fe(II)-NO) are kapp1 = 9.6±0.2 M–1 s–1 and kapp2 = 1.2±0.1 M–1 s–1 (at pH 7.4 and 20°C). The kapp1 and kapp2 values increase by about one order of magnitude for each pH unit decrease, between pH 8.3 and 6.2, indicating that the reaction requires one proton. On the other hand, kinetics of peroxynitrite isomerization catalyzed by ferric Ma-Pgb* (Ma-Pgb*-Fe(III)) is monophasic and values of the second order rate constant for peroxynitrite isomerization by Ma-Pgb*-Fe(III) and of the first order rate constant for the spontaneous conversion of peroxynitrite to nitrate are happ = 3.8×104 M–1 s–1 and h0 = 2.8×10–1 s–1 (at pH 7.4 and 20°C). The pH-dependence of hon and h0 values reflects the acid-base equilibrium of peroxynitrite (pKa = 6.7 and 6.9, respectively; at 20°C), indicating that HOONO is the species that reacts preferentially with the heme-Fe(III) atom. These results highlight the potential role of Pgbs in the biosynthesis and scavenging of reactive nitrogen and oxygen species.
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Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
- National Institute of Biostructures and Biosystems, Roma, Italy
- * E-mail:
| | - Loris Leboffe
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
| | | | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | - Diego Sbardella
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | | | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
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Shin H, Shannon CP, Fishbane N, Ruan J, Zhou M, Balshaw R, Wilson-McManus JE, Ng RT, McManus BM, Tebbutt SJ. Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion. PLoS One 2014; 9:e91041. [PMID: 24608128 PMCID: PMC3946641 DOI: 10.1371/journal.pone.0091041] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 02/08/2014] [Indexed: 12/21/2022] Open
Abstract
Background The molecular profile of circulating blood can reflect physiological and pathological events occurring in other tissues and organs of the body and delivers a comprehensive view of the status of the immune system. Blood has been useful in studying the pathobiology of many diseases. It is accessible and easily collected making it ideally suited to the development of diagnostic biomarker tests. The blood transcriptome has a high complement of globin RNA that could potentially saturate next-generation sequencing platforms, masking lower abundance transcripts. Methods to deplete globin mRNA are available, but their effect has not been comprehensively studied in peripheral whole blood RNA-Seq data. In this study we aimed to assess technical variability associated with globin depletion in addition to assessing general technical variability in RNA-Seq from whole blood derived samples. Results We compared technical and biological replicates having undergone globin depletion or not and found that the experimental globin depletion protocol employed removed approximately 80% of globin transcripts, improved the correlation of technical replicates, allowed for reliable detection of thousands of additional transcripts and generally increased transcript abundance measures. Differential expression analysis revealed thousands of genes significantly up-regulated as a result of globin depletion. In addition, globin depletion resulted in the down-regulation of genes involved in both iron and zinc metal ion bonding. Conclusions Globin depletion appears to meaningfully improve the quality of peripheral whole blood RNA-Seq data, and may improve our ability to detect true biological variation. Some concerns remain, however. Key amongst them the significant reduction in RNA yields following globin depletion. More generally, our investigation of technical and biological variation with and without globin depletion finds that high-throughput sequencing by RNA-Seq is highly reproducible within a large dynamic range of detection and provides an accurate estimation of RNA concentration in peripheral whole blood. High-throughput sequencing is thus a promising technology for whole blood transcriptomics and biomarker discovery.
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Affiliation(s)
- Heesun Shin
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Medicine (Division of Respiratory Medicine), University of British Columbia, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Casey P. Shannon
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | - Nick Fishbane
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jian Ruan
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mi Zhou
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | - Robert Balshaw
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Raymond T. Ng
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce M. McManus
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott J. Tebbutt
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Medicine (Division of Respiratory Medicine), University of British Columbia, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Matsuoka M, Fujita A, Kawai Y, Kikuchi T. Similar structures to the E-to-H helix unit in the globin-like fold are found in other helical folds. Biomolecules 2014; 4:268-88. [PMID: 24970216 PMCID: PMC4030988 DOI: 10.3390/biom4010268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 11/17/2022] Open
Abstract
A protein in the globin-like fold contains six alpha-helices, A, B, E, F, G and H. Among them, the E-to-H helix unit (E, F, G and H helices) forms a compact structure. In this study, we searched similar structures to the E-to-H helix of leghomoglobin in the whole protein structure space using the Dali program. Several similar structures were found in other helical folds, such as KaiA/RbsU domain and Type III secretion system domain. These observations suggest that the E-to-H helix unit may be a common subunit in the whole protein 3D structure space. In addition, the common conserved hydrophobic residues were found among the similar structures to the E-to-H helix unit. Hydrophobic interactions between the conserved residues may stabilize the 3D structures of the unit. We also predicted the possible compact regions of the units using the average distance method.
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Affiliation(s)
- Masanari Matsuoka
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
| | - Aoi Fujita
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
| | - Yosuke Kawai
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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Takahashi N, Watanabe S, Wakasugi K. Crucial roles of Glu60 in human neuroglobin as a guanine nucleotide dissociation inhibitor and neuroprotective agent. PLoS One 2013; 8:e83698. [PMID: 24376733 PMCID: PMC3871547 DOI: 10.1371/journal.pone.0083698] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022] Open
Abstract
Mammalian neuroglobin (Ngb) protects neuronal cells under conditions of oxidative stress. We previously showed that human Ngb acts as a guanine nucleotide dissociation inhibitor (GDI) for the α-subunits of heterotrimeric Gi/o proteins and inhibits reductions in cAMP concentration, leading to protection against cell death. In the present study, we created human E60Q Ngb mutant and clarified that Glu60 of human Ngb is a crucial residue for its GDI and neuroprotective activities. Moreover, we investigated structural and functional properties of several human Ngb mutants and demonstrated that the neuroprotective effect of human Ngb is due to its GDI activity and not due to its scavenging activity against reactive oxygen species.
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Affiliation(s)
- Nozomu Takahashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Seiji Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Keisuke Wakasugi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
- * E-mail:
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Kawada N. [Current situation and future prospect of cytoglobin research]. Nihon Rinsho 2013; 71:927-935. [PMID: 23777106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Cytoglobin was originally discovered from cultured rat hepatic stellate cells by using proteomics analysis in our laboratory in 2001. Cytoglobin is a hexacoordinate globin that is different from the traditional pentacoordinate globins like myoglobin and hemoglobin. Human cytoglobin has about 25% amino acid identity with vertebrate myoglobin and hemoglobin, and 16% with human neuroglobin that is another type of globin present specifically in the nervous system. Besides its function as O2, carbon monoxide, and nitric oxide-binding molecule, cytoglobin exhibits antioxidative properties under hypoxic condition. Recent analyses using clinical samples have indicated that cytoglobin may be a tumor suppressor gene because cytoglobin mRNA expression in cancer tissues is down-regulated through hypermethylation of cytoglobin gene promoter. In this review, the history of cytoglobin research, its current status and future prospects will be discussed.
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Affiliation(s)
- Norifumi Kawada
- Department of Hepatology, Graduate School of Medicine, Osaka City University
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Gabba M, Abbruzzetti S, Spyrakis F, Forti F, Bruno S, Mozzarelli A, Luque FJ, Viappiani C, Cozzini P, Nardini M, Germani F, Bolognesi M, Moens L, Dewilde S. CO rebinding kinetics and molecular dynamics simulations highlight dynamic regulation of internal cavities in human cytoglobin. PLoS One 2013; 8:e49770. [PMID: 23308092 PMCID: PMC3537629 DOI: 10.1371/journal.pone.0049770] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/12/2012] [Indexed: 12/03/2022] Open
Abstract
Cytoglobin (Cygb) was recently discovered in the human genome and localized in different tissues. It was suggested to play tissue-specific protective roles, spanning from scavenging of reactive oxygen species in neurons to supplying oxygen to enzymes in fibroblasts. To shed light on the functioning of such versatile machinery, we have studied the processes supporting transport of gaseous heme ligands in Cygb. Carbon monoxide rebinding shows a complex kinetic pattern with several distinct reaction intermediates, reflecting rebinding from temporary docking sites, second order recombination, and formation (and dissociation) of a bis-histidyl heme hexacoordinated reaction intermediate. Ligand exit to the solvent occurs through distinct pathways, some of which exploit temporary docking sites. The remarkable change in energetic barriers, linked to heme bis-histidyl hexacoordination by HisE7, may be responsible for active regulation of the flux of reactants and products to and from the reaction site on the distal side of the heme. A substantial change in both protein dynamics and inner cavities is observed upon transition from the CO-liganded to the pentacoordinated and bis-histidyl hexacoordinated species, which could be exploited as a signalling state. These findings are consistent with the expected versatility of the molecular activity of this protein.
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Affiliation(s)
- Matteo Gabba
- Institute of Complex Systems - Molekulare Biophysik (ICS-5) Forschungszentrum Jülich, Jülich, Germany
| | - Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, Parma, Italy
| | - Francesca Spyrakis
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Parma, Italy
- INBB, Biostructures and Biosystems National Institute, Rome, Italy
| | - Flavio Forti
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Stefano Bruno
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Cristiano Viappiani
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Pisa, Italy
- * E-mail:
| | - Pietro Cozzini
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Parma, Italy
- INBB, Biostructures and Biosystems National Institute, Rome, Italy
| | - Marco Nardini
- Dipartimento di BioScienze, CNR-IBF, and CIMAINA, Università degli Studi di Milano, Milano, Italy
| | - Francesca Germani
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Martino Bolognesi
- Dipartimento di BioScienze, CNR-IBF, and CIMAINA, Università degli Studi di Milano, Milano, Italy
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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Ramser K, Malinina E, Candefjord S. Resonance micro-Raman investigations of the rat medial preoptic nucleus: effects of a low-iron diet on the neuroglobin content. Appl Spectrosc 2012; 66:1454-1460. [PMID: 23231908 DOI: 10.1366/12-06670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The aim of this study was to investigate the medial preoptic nucleus (MPN) of the anterior hypothalamus by resonance Raman spectroscopy (514.5 nm) to determine if it is possible to enhance the Raman scattering of hemoproteins in fresh brain tissue slices. The resonance effect was compared with near-infrared Raman spectra. Two groups of male Sprague Dawley rats were studied, one control group on a normal diet and one group on a low-iron diet to evoke iron deficiency. Each group consisted of four rats, 38-41 days old. The diets lasted for 11, 12, and 15 days. The MPN regions of brain tissue slices were analyzed by monitoring raw and pre-processed mean data, by cluster analysis, and by deriving difference spectra from pre-processed mean spectra. Cluster analysis of the resonance Raman spectra could identify different hemoprotein groups, namely, hemoglobin (Hb) and neuroglobin (Ngb). Spectra from randomly distributed spots revealed high Hb content, whereas Ngb was evenly distributed in the MPN. The different spectra showed a decrease of the Ngb and lipid content for the animals on the low-iron diet. The Ngb decrease was approximately 20%. The data show that resonance Raman spectroscopy is well suited to study hemoproteins in fresh brain tissue.
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Affiliation(s)
- Kerstin Ramser
- Department of Computer Science, Electrical and Space Engineering, Luleå University of Technology, 97187 Luleå, Sweden
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Schaming D, Renault C, Tucker RT, Lau-Truong S, Aubard J, Brett MJ, Balland V, Limoges B. Spectroelectrochemical characterization of small hemoproteins adsorbed within nanostructured mesoporous ITO electrodes. Langmuir 2012; 28:14065-14072. [PMID: 22957653 DOI: 10.1021/la302913j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
3D nanostructured transparent indium tin oxide (ITO) electrodes prepared by glancing angle deposition (GLAD) were used for the spectroelectrochemical characterization of cytochrome c (Cyt c) and neuroglobin (Nb). These small hemoproteins, involved as electron-transfer partners in the prevention of apoptosis, are oppositely charged at physiological pH and can each be adsorbed within the ITO network under different pH conditions. The resulting modified electrodes were investigated by UV-visible absorption spectroscopy coupled with cyclic voltammetry. By using nondenaturating adsorption conditions, we demonstrate that both proteins are capable of direct electron transfer to the conductive ITO surface, sharing apparent standard potentials similar to those reported in solution. Preservation of the 3D protein structure upon adsorption was confirmed by resonance Raman (rR) spectroscopy. Analysis of the derivative cyclic voltabsorptograms (DCVA) monitored either in the Soret or the Q bands at scan rates up to 1 V s(-1) allowed us to investigate direct interfacial electron transfer kinetics. From the DCVA shape and scan rate dependences, we conclude that the interaction of Cyt c with the ITO surface is more specific than Nb, suggesting an oriented adsorption of Cyt c and a random adsorption of Nb on the ITO surface. At the same time, Cyt c appears more sensitive to the experimental adsorption conditions, and complete denaturation of Cyt c may occur as evidenced from cross-correlation of rR spectroscopy and spectroelectrochemistry.
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Affiliation(s)
- Delphine Schaming
- Laboratoire d'Electrochimie Moléculaire, UMR CNRS 7591, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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Abstract
In this study, the role of the globin moiety in the structure of this pigment has been evaluated, using myoglobin and hemin as model systems. After the synthesis of the cured pigment from the compounds used in this study, the absorption spectra, Fourier transform infrared spectroscopy (FTIR), and electrospray ionization (ESI)/MS spectroscopy were used to evaluate the chemical structure. Results indicated that the UV/visible, IR absorption, and mass spectroscopy of the cured pigment produced from myoglobin and its counterpart without the globin moiety, hemin, are different. Whereas myoglobin produced mononitrosylheme, hemin converted to dinitrosylheme, but probably the second nitric oxide group attached to the propionate side chain of the heme ring. It seems that the globin moiety protected heme ring against the second nitric oxide group.
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Affiliation(s)
- Nafiseh Soltanizadeh
- Department of Food Science and Technology, College of Agriculture, Isfahan University of Technology, Isfahan 84156, Iran.
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35
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Abbruzzetti S, Tilleman L, Bruno S, Viappiani C, Desmet F, Van Doorslaer S, Coletta M, Ciaccio C, Ascenzi P, Nardini M, Bolognesi M, Moens L, Dewilde S. Ligation tunes protein reactivity in an ancient haemoglobin: kinetic evidence for an allosteric mechanism in Methanosarcina acetivorans protoglobin. PLoS One 2012; 7:e33614. [PMID: 22479420 PMCID: PMC3313925 DOI: 10.1371/journal.pone.0033614] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/13/2012] [Indexed: 11/19/2022] Open
Abstract
Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin with peculiar structural properties such as a completely buried haem and two orthogonal tunnels connecting the distal cavity to the solvent. CO binding to and dissociation from MaPgb occur through a biphasic kinetics. We show that the heterogenous kinetics arises from binding to (and dissociation from) two tertiary conformations in ligation-dependent equilibrium. Ligation favours the species with high binding rate (and low dissociation rate). The equilibrium is shifted towards the species with low binding (and high dissociation) rates for the unliganded molecules. A quantitative model is proposed to describe the observed carbonylation kinetics.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Pisa, Italy
| | - Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Stefano Bruno
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Pisa, Italy
| | - Filip Desmet
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | | | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Bari, Italy
| | - Chiara Ciaccio
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Bari, Italy
| | - Paolo Ascenzi
- Dipartimento di Biologia, Università Roma Tre, Roma, Italy
| | - Marco Nardini
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, Italy
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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Abstract
BACKGROUND All globins belong to one of three families: the F (flavohemoglobin) and S (sensor) families that exhibit the canonical 3/3 α-helical fold, and the T (truncated 3/3 fold) globins characterized by a shortened 2/2 α-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins. RESULTS Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ~60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes). The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota. CONCLUSION Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote ancestor, resulting from the endosymbiotic events responsible for the origin of mitochondria and chloroplasts.
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Affiliation(s)
- David Hoogewijs
- Institute of Physiology and Zürich Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland.
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Sasakawa Y, Kominami A, Yamamoto K, Nakaoka F, Nakamura M, Nakao M, Abe M, Fukuhama C, Kagawa K. Effects of globin digest and its active ingredient Trp-Thr-Gln-Arg on galactosamine/lipopolysaccharide-induced liver injury in ICR mice. Life Sci 2011; 90:190-9. [PMID: 22154906 DOI: 10.1016/j.lfs.2011.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 10/20/2011] [Accepted: 11/08/2011] [Indexed: 12/13/2022]
Abstract
AIMS We investigated the effects of globin digest (GD) and its active ingredient Trp-Thr-Gln-Arg (WTQR) on galactosamine/lipopolysaccharide (GalN/LPS)-induced liver injury in imprinting control region (ICR) mice. MAIN METHODS The effects of WTQR and GD on the liver injury were examined by measuring the survival rate, serum aminotransferase activities, hepatic components, antioxidant enzyme activities, histopathological analysis, serum levels and hepatic gene expression of tumor necrosis factor-alpha (TNF-α), macrophage inflammatory protein-2 (MIP-2), and nitric oxide (NO) or inducible nitric oxide synthase (iNOS), and nuclear factor-kappa B (NF-κB) p65 content in GalN/LPS-treated ICR mice. RAW264 mouse macrophages were used to confirm the anti-inflammatory effects of WTQR and GD on the macrophages. KEY FINDINGS WTQR and GD increased the survival rate, suppressed the serum aminotransferase activities, serum levels and hepatic gene expression of TNF-α, MIP-2, and NO or iNOS, and nuclear NF-κB p65 content in GalN/LPS-treated mice; decreased the oxidized glutathione content, increased the superoxide dismutase activity, and decreased the histopathological grade values of the hepatocyte necrosis and lobular inflammation in GalN/LPS-injured liver; and suppressed the release levels and gene expression of TNF-α, MIP-2, and NO or iNOS, and nuclear NF-κB p65 content in LPS-stimulated RAW264 macrophages. WTQR and GD may improve the antioxidant defense system and inflammatory status in GalN/LPS-injured liver. SIGNIFICANCE These findings indicate that WTQR and GD have hepatoprotective effects on GalN/LPS-induced liver injury in ICR mice.
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Affiliation(s)
- Yuka Sasakawa
- MG Pharma Inc., 7-7-25, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.
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Oleksiewicz U, Liloglou T, Field JK, Xinarianos G. Cytoglobin: biochemical, functional and clinical perspective of the newest member of the globin family. Cell Mol Life Sci 2011; 68:3869-83. [PMID: 21744065 DOI: 10.1007/s00018-011-0764-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 06/17/2011] [Accepted: 06/21/2011] [Indexed: 02/06/2023]
Abstract
Since the discovery of cytoglobin (Cygb) a decade ago, growing amounts of data have been gathered to characterise Cygb biochemistry, functioning and implication in human pathologies. Its molecular roles remain under investigation, but nitric oxide dioxygenase and lipid peroxidase activities have been demonstrated. Cygb expression increases in response to various stress conditions including hypoxia, oxidative stress and fibrotic stimulation. When exogenously overexpressed, Cygb revealed cytoprotection against these factors. Cygb was shown to be upregulated in fibrosis and neurodegenerative disorders and downregulated in multiple cancer types. CYGB was also found within the minimal region of a hereditary tylosis with oesophageal cancer syndrome, and its expression was reduced in tylotic samples. Recently, Cygb has been shown to inhibit cancer cell growth in vitro, thus confirming its suggested tumour suppressor role. This article aims to review the biochemical and functional aspects of Cygb, its involvement in various pathological conditions and potential clinical utility.
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Affiliation(s)
- Urszula Oleksiewicz
- Cancer Research Centre, Roy Castle Lung Cancer Research Programme, University of Liverpool, UK
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39
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Li YL, Zhang Y. [The function of cytoglobin in liver and kidney fibrosis]. Sheng Li Ke Xue Jin Zhan 2011; 42:213-216. [PMID: 21932521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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40
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Kiger L, Tilleman L, Geuens E, Hoogewijs D, Lechauve C, Moens L, Dewilde S, Marden MC. Electron transfer function versus oxygen delivery: a comparative study for several hexacoordinated globins across the animal kingdom. PLoS One 2011; 6:e20478. [PMID: 21674044 PMCID: PMC3106018 DOI: 10.1371/journal.pone.0020478] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 04/27/2011] [Indexed: 11/27/2022] Open
Abstract
Caenorhabditis elegans globin GLB-26 (expressed from gene T22C1.2) has been studied in comparison with human neuroglobin (Ngb) and cytoglobin (Cygb) for its electron transfer properties. GLB-26 exhibits no reversible binding for O(2) and a relatively low CO affinity compared to myoglobin-like globins. These differences arise from its mechanism of gaseous ligand binding since the heme iron of GLB-26 is strongly hexacoordinated in the absence of external ligands; the replacement of this internal ligand, probably the E7 distal histidine, is required before binding of CO or O(2) as for Ngb and Cygb. Interestingly the ferrous bis-histidyl GLB-26 and Ngb, another strongly hexacoordinated globin, can transfer an electron to cytochrome c (Cyt-c) at a high bimolecular rate, comparable to those of inter-protein electron transfer in mitochondria. In addition, GLB-26 displays an unexpectedly rapid oxidation of the ferrous His-Fe-His complex without O(2) actually binding to the iron atom, since the heme is oxidized by O(2) faster than the time for distal histidine dissociation. These efficient mechanisms for electron transfer could indicate a family of hexacoordinated globin which are functionally different from that of pentacoordinated globins.
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Affiliation(s)
- Laurent Kiger
- INSERM U779, Universities Paris VI and XI, Le Kremlin-Bicêtre, France.
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41
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Pantiavin AA, Isheeva AK, Artiukhov VG. [Studies of physical and chemical properties of the vacuum UV-irradiated molecules of human hemoglobin and its components (heme and globin)]. Radiats Biol Radioecol 2011; 51:352-356. [PMID: 21866835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The purpose of the present work is to study the vacuum ultraviolet radiation action on the optical and chromatographic characteristics of human hemoglobin molecules and their components - haem and globin. Using the methods of spectrophotometry and thin layer chromatography (TLC), we have investigated into the structural changes of molecules of human hemoglobin, haem and globin, induced by the influence of vacuum UV light (gamma = 118-134 nm, dose - 1.2 kJ/m2). It has been shown that vacuum ultraviolet radiation induces an infringement of the higher types of the spatial organization ofglobin molecules, thus leading to the changes in the structural state of the albuminous globule.
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Watanabe S, Wakasugi K. Module M1 of zebrafish neuroglobin acts as a structural and functional protein building block for a cell-membrane-penetrating activity. PLoS One 2011; 6:e16808. [PMID: 21304818 PMCID: PMC3033418 DOI: 10.1371/journal.pone.0016808] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 12/31/2010] [Indexed: 11/18/2022] Open
Abstract
Neuroglobin (Ngb) is a recently discovered vertebrate globin that is expressed in the brain and can reversibly bind oxygen. Mammalian Ngb is involved in neuroprotection during oxidative stress that occurs, for example, during ischemia and reperfusion. Recently, we found that zebrafish, but not human, Ngb can translocate into cells. Moreover, we demonstrated that a chimeric ZHHH Ngb protein, in which the module M1 of human Ngb is replaced by the corresponding region of zebrafish Ngb, can penetrate cell membranes and protect cells against oxidative stress-induced cell death, suggesting that module M1 of zebrafish Ngb is important for protein transduction. Furthermore, we recently showed that Lys7, Lys9, Lys21, and Lys23 in module M1 of zebrafish Ngb are crucial for protein transduction activity. In the present study, we have investigated whether module M1 of zebrafish Ngb can be used as a building block to create novel cell-membrane-penetrating folded proteins. First, we engineered a chimeric myoglobin (Mb), in which module M1 of zebrafish Ngb was fused to the N-terminus of full-length human Mb, and investigated its functional and structural properties. Our results showed that this chimeric Mb protein is stable and forms almost the same heme environment and α-helical structure as human wild-type Mb. In addition, we demonstrated that chimeric Mb has a cell-membrane-penetrating activity similar to zebrafish Ngb. Moreover, we found that glycosaminoglycan is crucial for the cell-membrane-penetrating activity of chimeric Mb as well as that of zebrafish Ngb. These results enable us to conclude that such module substitutions will facilitate the design and production of novel functional proteins.
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Affiliation(s)
- Seiji Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Keisuke Wakasugi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama, Japan
- * E-mail:
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Fedyukina DV, Rajagopalan S, Sekhar A, Fulmer EC, Eun YJ, Cavagnero S. Contribution of long-range interactions to the secondary structure of an unfolded globin. Biophys J 2010; 99:L37-9. [PMID: 20816043 DOI: 10.1016/j.bpj.2010.06.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 06/07/2010] [Accepted: 06/14/2010] [Indexed: 11/19/2022] Open
Abstract
This work explores the effect of long-range tertiary contacts on the distribution of residual secondary structure in the unfolded state of an alpha-helical protein. N-terminal fragments of increasing length, in conjunction with multidimensional nuclear magnetic resonance, were employed. A protein representative of the ubiquitous globin fold was chosen as the model system. We found that, while most of the detectable alpha-helical population in the unfolded ensemble does not depend on the presence of the C-terminal region (corresponding to the native G and H helices), specific N-to-C long-range contacts between the H and A-B-C regions enhance the helical secondary structure content of the N terminus (A-B-C regions). The simple approach introduced here, based on the evaluation of N-terminal polypeptide fragments of increasing length, is of general applicability to identify the influence of long-range interactions in unfolded proteins.
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Affiliation(s)
- Daria V Fedyukina
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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44
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Astudillo L, Bernad S, Derrien V, Sebban P, Miksovska J. Probing the role of the internal disulfide bond in regulating conformational dynamics in neuroglobin. Biophys J 2010; 99:L16-8. [PMID: 20643048 PMCID: PMC2905123 DOI: 10.1016/j.bpj.2010.04.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 04/05/2010] [Accepted: 04/19/2010] [Indexed: 11/20/2022] Open
Abstract
In this report, we demonstrate that the internal disulfide bridge in human neuroglobin modulates structural changes associated with ligand photo-dissociation from the heme active site. This is evident from time-resolved photothermal studies of CO photo-dissociation, which reveal a 13.4+/-0.9 mL mol(-1) volume expansion upon ligand photo-release from human neuroglobin, whereas the CO dissociation from rat neuroglobin leads to a significantly smaller volume change (DeltaV=4.6+/-0.3 mL mol(-1)). Reduction of the internal disulfide bond in human neuroglobin leads to conformational changes (reflected by DeltaV) nearly identical to those observed for rat Ngb. Our data favor the hypothesis that the disulfide bond between Cys46 and Cys55 modulates the functioning of human neuroglobin.
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Affiliation(s)
- Luisana Astudillo
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Sophie Bernad
- University Paris-Sud, Laboratoire de Chimie-Physique, Faculté d'Orsay, Orsay cedex, France
- CNRS, Orsay, France
| | - Valérie Derrien
- University Paris-Sud, Laboratoire de Chimie-Physique, Faculté d'Orsay, Orsay cedex, France
- CNRS, Orsay, France
| | - Pierre Sebban
- University Paris-Sud, Laboratoire de Chimie-Physique, Faculté d'Orsay, Orsay cedex, France
- CNRS, Orsay, France
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
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Tandang-Silvas MRG, Fukuda T, Fukuda C, Prak K, Cabanos C, Kimura A, Itoh T, Mikami B, Utsumi S, Maruyama N. Conservation and divergence on plant seed 11S globulins based on crystal structures. Biochim Biophys Acta 2010; 1804:1432-42. [PMID: 20215054 DOI: 10.1016/j.bbapap.2010.02.016] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 02/23/2010] [Accepted: 02/24/2010] [Indexed: 11/30/2022]
Abstract
The crystal structures of two pro-11S globulins namely: rapeseed procruciferin and pea prolegumin are presented here. We have extensively compared them with the other known structures of plant seed 11S and 7S globulins. In general, the disordered regions in the crystal structures among the 11S globulins correspond to their five variable regions. Variable region III of procruciferin is relatively short and is in a loop conformation. This region is highly disordered in other pro-11S globulin crystals. Local helical and strand variations also occur across the group despite general structure conservation. We showed how these variations may alter specific physicochemical, functional and physiological properties. Aliphatic hydrophobic residues on the molecular surface correlate well with Tm values of the globulins. We also considered other structural features that were reported to influence thermal stability but no definite conclusion was drawn since each factor has additive or subtractive effect. Comparison between proA3B4 and mature A3B4 revealed an increase in r.m.s.d. values near variable regions II and IV. Both regions are on the IE face. Secondary structure based alignment of 11S and 7S globulins revealed 16 identical residues. Based on proA3B4 sequence, Pro60, Gly128, Phe163, Phe208, Leu213, Leu227, Ile237, Pro382, Val404, Pro425 and Val 466 are involved in trimer formation and stabilization. Gly28, Gly74, Asp135, Gly349 and Gly397 are involved in correct globular folding.
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Affiliation(s)
- Mary Rose G Tandang-Silvas
- Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Kyoto 611-0011, Japan
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46
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Brittain T, Skommer J, Raychaudhuri S, Birch N. An antiapoptotic neuroprotective role for neuroglobin. Int J Mol Sci 2010; 11:2306-21. [PMID: 20640154 PMCID: PMC2904918 DOI: 10.3390/ijms11062306] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 05/24/2010] [Accepted: 05/24/2010] [Indexed: 12/12/2022] Open
Abstract
Cell death associated with mitochondrial dysfunction is common in acute neurological disorders and in neurodegenerative diseases. Neuronal apoptosis is regulated by multiple proteins, including neuroglobin, a small heme protein of ancient origin. Neuroglobin is found in high concentration in some neurons, and its high expression has been shown to promote survival of neurons in vitro and to protect brain from damage by both stroke and Alzheimer's disease in vivo. Early studies suggested this protective role might arise from the protein's capacity to bind oxygen or react with nitric oxide. Recent data, however, suggests that neither of these functions is likely to be of physiological significance. Other studies have shown that neuroglobin reacts very rapidly with cytochrome c released from mitochondria during cell death, thus interfering with the intrinsic pathway of apoptosis. Systems level computational modelling suggests that the physiological role of neuroglobin is to reset the trigger level for the post-mitochondrial execution of apoptosis. An understanding of the mechanism of action of neuroglobin might thus provide a rational basis for the design of new drug targets for inhibiting excessive neuronal cell death.
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Affiliation(s)
- Thomas Brittain
- School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland, NZ, USA; E-Mails: (J.S.); (N.B.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +64-9-373-75991; Fax: +64-9-373-7414
| | - Joanna Skommer
- School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland, NZ, USA; E-Mails: (J.S.); (N.B.)
| | - Subadhip Raychaudhuri
- Department of Biomedical Engineering, 451 Health Sciences Drive, University of California, Davis, CA, USA; E-Mail:
| | - Nigel Birch
- School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland, NZ, USA; E-Mails: (J.S.); (N.B.)
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Mu J, Li L, Guo Y, Qiu Z, Tan X. Spectroscopic study on acid-induced unfolding and refolding of apo-neuroglobin. Spectrochim Acta A Mol Biomol Spectrosc 2010; 75:1600-1604. [PMID: 20227336 DOI: 10.1016/j.saa.2010.02.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2009] [Revised: 01/23/2010] [Accepted: 02/11/2010] [Indexed: 05/28/2023]
Abstract
pH-induced unfolding and refolding of apo-neuroglobin (apo-Ngb) were investigated by UV, fluorescence, circular dichroism (CD) spectra and light scattering measurements. Results revealed that apo-Ngb became partially unfolded at around pH 5.0, with evidences from a red shift in the fluorescence spectra, a decrease in the far-UV CD and a sharp peak in the light scattering intensity. Further lowering of the pH reversed these effects, suggesting that apo-Ngb folds back to a compact state. At pH 2.0, the apo-Ngb forms a folding intermediate known as molten globule (MG), which is possessed of native-like secondary structure and almost complete loss of tertiary structure. Based on these results, the acid-induced denaturation pathway of apo-Ngb can be illustrated from the native state (N), via a partially unfolded state (U(A)) to the molten globule state (MG).
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Affiliation(s)
- Jianshuai Mu
- School of Chemistry and Chemical Engineering, Liaocheng University, No. 1, Hunan Road, Liaocheng 252059, Shandong Province, PR China
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Abstract
Computer simulations in molecular biophysics describe in atomic detail the structure, dynamics, and function of biological macromolecules. To assess the quality of these models and to pick up new mechanisms, comparisons with experimental measurements are made. Most comparisons examine thermodynamic and average structural properties. Here we discuss studies of dynamics and fluctuations in a protein. The diffusion of a small ligand between internal cavities in myoglobin, and its escape to solvent are considered. Qualitative and semi-quantitative agreements between experiment and simulation are obtained for the identities of the cavities that physically trap the ligand and for the connections between them. However, experimental and computational 'doors' are at significant variance. Simulations suggest multiple gates while kinetic experiments point to one dominant exit.
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Affiliation(s)
- Ron Elber
- Department of Chemistry and Biochemistry, Institute of Computational Engineering and Sciences (ICES), 1 University Station, ICES, C0200, The University of Texas at Austin, Austin, TX 78712, USA
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Abstract
Based on the literature and our own results, this review summarizes the most recent state of nonvertebrate myoglobin (Mb) and hemoglobin (Hb) research, not as a general survey of the subject but as a case study. For this purpose, we have selected here four typical globins to discuss their unique structures and properties in detail. These include Aplysia myoglobin, which served as a prototype for the unusual globins lacking the distal histidine residue; midge larval hemoglobin showing a high degree of polymorphism; Tetrahymena hemoglobin evolved with a truncated structure; and yeast flavohemoglobin carrying an enigmatic two-domain structure. These proteins are not grouped by any common features other than the fact they have globin domains and heme groups. As a matter of course, various biochemical functions other than the conventional oxygen transport or storage have been proposed so far to these primitive or ancient hemoglobins or myoglobins, but the precise in vivo activity is still unclear. In this review, special emphasis is placed on the stability properties of the heme-bound O2. Whatever the possible roles of nonvertebrate myoglobins and hemoglobins may be (or might have been), the binding of molecular oxygen to iron(II) must be the primary event to manifest their physiological functions in vivo. However, the reversible and stable binding of O2 to iron(II) is not a simple process, since the oxygenated form of Mb or Hb is oxidized easily to its ferric met-form with the generation of superoxide anion. The metmyoglobin or methemoglobin thus produced cannot bind molecular oxygen and is therefore physiologically inactive. In this respect, protozoan ciliate myoglobin and yeast flavohemoglobin are of particular interest in their very unique structures. Indeed, both proteins have been found to have completely different strategies for overcoming many difficulties in the reversible and stable binding of molecular oxygen, as opposed to the irreversible oxidation of heme iron(II). Such comparative studies of the stability of MbO2 or HbO2 are of primary importance, not only for a full understanding of the globin evolution, but also for planning new molecular designs for synthetic oxygen carriers that may be able to function in aqueous solution and at physiological temperature.
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Affiliation(s)
- Keiji Shikama
- Biological Institute, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
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Abstract
It was recently found that the lowest-energy collective normal modes dominate the evolutionary divergence of protein structures. This was attributed to a presumed functional importance of such motions, i.e., to natural selection. In contrast to this selectionist explanation, we proposed that the observed behavior could be just the expected physical response of proteins to random mutations. This proposal was based on the success of a linearly forced elastic network model (LFENM) of mutational effects on structure to account for the observed pattern of structural divergence. Here, to further test the mutational explanation and the LFENM, we analyze the structural differences observed not only in homologous (globin-like) proteins but also in unselected experimentally engineered myoglobin mutants and in wild-type variants subject to other perturbations such as ligand-binding and pH changes. We show that the lowest normal modes dominate structural change in all the cases considered and that the LFENM reproduces this behavior quantitatively. The collective nature of the lowest normal modes results in global conformational changes that depend little on the exact nature or location of the perturbation. Significantly, the evolutionarily conserved structural core matches the regions observed to be more robust with respect to mutations, so that the core would be more conserved even under unselected random mutations. In a word, the observed patterns of structural variation can be seen as the natural response of proteins to perturbations and can be adequately modeled using the LFENM, which serves as a common framework to relate a priori different phenomena.
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Affiliation(s)
- Julián Echave
- Instituto Nacional de Investigaciones Fisicoquímicas Teóricas y Aplicadas, Consejo Nacional de Investigación Científica y Técnicas & Universidad Nacional de La Plata, La Plata, Argentina.
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