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Pittalà MGG, Reina S, Cucina A, Cunsolo V, Guarino F, Di Francesco A, Foti S, De Pinto V, Saletti R. Intramolecular Disulfide Bridges in Voltage-Dependent Anion Channel 2 (VDAC2) Protein from Rattus norvegicus Revealed by High-Resolution Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1422-1433. [PMID: 38832804 DOI: 10.1021/jasms.4c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Voltage-Dependent Anion Channel isoforms (VDAC1, VDAC2, and VDAC3) are relevant components of the outer mitochondrial membrane (OMM) and play a crucial role in regulation of metabolism and in survival pathways. As major players in the regulation of cellular metabolism and apoptosis, VDACs can be considered at the crossroads between two broad families of pathologies, namely, cancer and neurodegeneration, the former being associated with elevated glycolytic rate and suppression of apoptosis in cancer cells, the latter characterized by mitochondrial dysfunction and increased cell death. Recently, we reported the characterization of the oxidation pattern of methionine and cysteines in rat and human VDACs showing that each cysteine in these proteins is present with a preferred oxidation state, ranging from the reduced to the trioxidized form, and such an oxidation state is remarkably conserved between rat and human VDACs. However, the presence and localization of disulfide bonds in VDACs, a key point for their structural characterization, have so far remained undetermined. Herein we have investigated by nanoUHPLC/High-Resolution nanoESI-MS/MS the position of intramolecular disulfide bonds in rat VDAC2 (rVDAC2), a protein that contains 11 cysteines. To this purpose, extraction, purification, and enzymatic digestions were carried out at slightly acidic or neutral pH in order to minimize disulfide bond interchange. The presence of six disulfide bridges was unequivocally determined, including a disulfide bridge linking the two adjacent cysteines 4 and 5, a disulfide bridge linking cysteines 9 and 14, and the alternative disulfide bridges between cysteines 48, 77, and 104. A disulfide bond, which is very resistant to reduction, between cysteines 134 and 139 was also detected. In addition to the previous findings, these results significantly extend the characterization of the oxidation state of cysteines in rVDAC2 and show that it is highly complex and presents unusual features. Data are available via ProteomeXchange with the identifier PXD044041.
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Affiliation(s)
- Maria Gaetana Giovanna Pittalà
- Department of Chemical Sciences, Organic Mass Spectrometry Laboratory, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Simona Reina
- Department of Biomedical Sciences and Biotechnology, Section of Biology and Genetics, University of Catania, via S. Sofia, 97, 95123 Catania, Italy
| | - Annamaria Cucina
- Department of Chemical Sciences, Organic Mass Spectrometry Laboratory, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Vincenzo Cunsolo
- Department of Chemical Sciences, Organic Mass Spectrometry Laboratory, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Francesca Guarino
- Department of Biomedical Sciences and Biotechnology, Section of Biology and Genetics, University of Catania, via S. Sofia, 97, 95123 Catania, Italy
| | - Antonella Di Francesco
- Department of Chemical Sciences, Organic Mass Spectrometry Laboratory, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Salvatore Foti
- Department of Chemical Sciences, Organic Mass Spectrometry Laboratory, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Vito De Pinto
- Department of Biomedical Sciences and Biotechnology, Section of Biology and Genetics, University of Catania, via S. Sofia, 97, 95123 Catania, Italy
| | - Rosaria Saletti
- Department of Chemical Sciences, Organic Mass Spectrometry Laboratory, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
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2
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Seo WM, Ballesteros M, Tsui EY. Sulfane Decreases the Nucleophilic Reactivity of Zinc Thiolates: Implications for Biological Reactive Sulfur Species. J Am Chem Soc 2022; 144:20630-20640. [DOI: 10.1021/jacs.2c07380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- W.T. Michael Seo
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556, United States
| | - Moises Ballesteros
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556, United States
| | - Emily Y. Tsui
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556, United States
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3
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Brücksken KA, Loreto Palacio P, Hanschmann EM. Thiol Modifications in the Extracellular Space-Key Proteins in Inflammation and Viral Infection. Front Immunol 2022; 13:932525. [PMID: 35833136 PMCID: PMC9271835 DOI: 10.3389/fimmu.2022.932525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Posttranslational modifications (PTMs) allow to control molecular and cellular functions in response to specific signals and changes in the microenvironment of cells. They regulate structure, localization, stability, and function of proteins in a spatial and temporal manner. Among them, specific thiol modifications of cysteine (Cys) residues facilitate rapid signal transduction. In fact, Cys is unique because it contains the highly reactive thiol group that can undergo different reversible and irreversible modifications. Upon inflammation and changes in the cellular microenvironment, many extracellular soluble and membrane proteins undergo thiol modifications, particularly dithiol-disulfide exchange, S-glutathionylation, and S-nitrosylation. Among others, these thiol switches are essential for inflammatory signaling, regulation of gene expression, cytokine release, immunoglobulin function and isoform variation, and antigen presentation. Interestingly, also the redox state of bacterial and viral proteins depends on host cell-mediated redox reactions that are critical for invasion and infection. Here, we highlight mechanistic thiol switches in inflammatory pathways and infections including cholera, diphtheria, hepatitis, human immunodeficiency virus (HIV), influenza, and coronavirus disease 2019 (COVID-19).
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Affiliation(s)
| | | | - Eva-Maria Hanschmann
- Department of Neurology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
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4
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Honer J, Niemeyer KM, Fercher C, Diez Tissera AL, Jaberolansar N, Jafrani YMA, Zhou C, Caramelo JJ, Shewan AM, Schulz BL, Brodsky JL, Zacchi LF. TorsinA folding and N-linked glycosylation are sensitive to redox homeostasis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119073. [PMID: 34062155 PMCID: PMC8889903 DOI: 10.1016/j.bbamcr.2021.119073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 01/03/2023]
Abstract
The Endoplasmic Reticulum (ER) is responsible for the folding and post-translational modification of secretory proteins, as well as for triaging misfolded proteins. During folding, there is a complex yet only partially understood interplay between disulfide bond formation, which is an enzyme catalyzed event in the oxidizing environment of the ER, along with other post-translational modifications (PTMs) and chaperone-supported protein folding. Here, we used the glycoprotein torsinA as a model substrate to explore the impact of ER redox homeostasis on PTMs and protein biogenesis. TorsinA is a AAA+ ATPase with unusual oligomeric properties and controversial functions. The deletion of a C-terminal glutamic acid residue (∆E) is associated with the development of Early-Onset Torsion Dystonia, a severe movement disorder. TorsinA differs from other AAA+ ATPases since it is an ER resident, and as a result of its entry into the ER torsinA contains two N-linked glycans and at least one disulfide bond. The role of these PTMs on torsinA biogenesis and function and the identity of the enzymes that catalyze them are poorly defined. Using a yeast torsinA expression system, we demonstrate that a specific protein disulfide isomerase, Pdi1, affects the folding and N-linked glycosylation of torsinA and torsinA∆E in a redox-dependent manner, suggesting that the acquisition of early torsinA folding intermediates is sensitive to perturbed interactions between Cys residues and the quality control machinery. We also highlight the role of specific Cys residues during torsinA biogenesis and demonstrate that torsinA∆E is more sensitive than torsinA when these Cys residues are mutated.
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Affiliation(s)
- Jonas Honer
- Department of Biological Sciences, A320 Langley Hall, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Katie M Niemeyer
- Department of Biological Sciences, A320 Langley Hall, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Christian Fercher
- Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Ana L Diez Tissera
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), 1405 Buenos Aires, Argentina
| | - Noushin Jaberolansar
- Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Yohaann M A Jafrani
- Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Chun Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Julio J Caramelo
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), 1405 Buenos Aires, Argentina
| | - Annette M Shewan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Benjamin L Schulz
- Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Jeffrey L Brodsky
- Department of Biological Sciences, A320 Langley Hall, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Lucía F Zacchi
- Department of Biological Sciences, A320 Langley Hall, University of Pittsburgh, Pittsburgh, PA 15260, United States of America; Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia; Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), 1405 Buenos Aires, Argentina; School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia.
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5
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Opuni KFM, Koy C, Russ M, Reepmeyer M, Danquah BD, Weresow M, Alef A, Lorenz P, Thiesen HJ, Glocker MO. ITEM-THREE analysis of a monoclonal anti-malaria antibody reveals its assembled epitope on the pfMSP1 19 antigen. J Biol Chem 2020; 295:14987-14997. [PMID: 32848020 DOI: 10.1074/jbc.ra120.014802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/18/2020] [Indexed: 11/06/2022] Open
Abstract
Rapid diagnostic tests are first-line assays for diagnosing infectious diseases, such as malaria. To minimize false positive and false negative test results in population-screening assays, high-quality reagents and well-characterized antigens and antibodies are needed. An important property of antigen-antibody binding is recognition specificity, which best can be estimated by mapping an antibody's epitope on the respective antigen. We have cloned a malarial antigen-containing fusion protein, MBP-pfMSP119, in Escherichia coli, which then was structurally and functionally characterized before and after high pressure-assisted enzymatic digestion. We then used our previously developed method, intact transition epitope mapping-targeted high-energy rupture of extracted epitopes (ITEM-THREE), to map the area on the MBP-pfMSP119 antigen surface that is recognized by the anti-pfMSP119 antibody G17.12. We identified three epitope-carrying peptides, 386GRNISQHQCVKKQCPQNSGCFRHLDE411, 386GRNISQHQCVKKQCPQNSGCFRHLDEREE414, and 415CKCLLNYKQE424, from the GluC-derived peptide mixture. These peptides belong to an assembled (conformational) epitope on the MBP-pfMSP119 antigen whose identification was substantiated by positive and negative control experiments. In conclusion, our data help to establish a workflow to obtain high-quality control data for diagnostic assays, including the use of ITEM-THREE as a powerful analytical tool. Data are available via ProteomeXchange: PXD019717.
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Affiliation(s)
- Kwabena F M Opuni
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany; Department of Pharmaceutical Chemistry, School of Pharmacy, College of Health, University of Ghana, Legon, Ghana
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | - Manuela Russ
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | - Maren Reepmeyer
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | - Bright D Danquah
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | | | | | - Peter Lorenz
- Institute for Immunology, University Medicine Rostock, Rostock, Germany
| | | | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany.
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6
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Abstract
Neutrophils kill invading microbes and therefore represent the first line of defense of the innate immune response. Activated neutrophils assemble NADPH oxidase to convert substantial amounts of molecular oxygen into superoxide, which, after dismutation into peroxide, serves as the substrate for the generation of the potent antimicrobial hypochlorous acid (HOCl) in the phagosomal space. In this minireview, we explore the most recent insights into physiological consequences of HOCl stress. Not surprisingly, Gram-negative bacteria have evolved diverse posttranslational defense mechanisms to protect their proteins, the main targets of HOCl, from HOCl-mediated damage. We discuss the idea that oxidation of conserved cysteine residues and partial unfolding of its structure convert the heat shock protein Hsp33 into a highly active chaperone holdase that binds unfolded proteins and prevents their aggregation. We examine two novel members of the Escherichia coli chaperone holdase family, RidA and CnoX, whose thiol-independent activation mechanism differs from that of Hsp33 and requires N-chlorination of positively charged amino acids during HOCl exposure. Furthermore, we summarize the latest findings with respect to another bacterial defense strategy employed in response to HOCl stress, which involves the accumulation of the universally conserved biopolymer inorganic polyphosphate. We then discuss sophisticated adaptive strategies that bacteria have developed to enhance their survival during HOCl stress. Understanding bacterial defense and survival strategies against one of the most powerful neutrophilic oxidants may provide novel insights into treatment options that potentially compromise the ability of pathogens to resist HOCl stress and therefore may increase the efficacy of the innate immune response.
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7
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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8
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Goemans CV, Collet JF. Stress-induced chaperones: a first line of defense against the powerful oxidant hypochlorous acid. F1000Res 2019; 8. [PMID: 31583082 PMCID: PMC6758839 DOI: 10.12688/f1000research.19517.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2019] [Indexed: 01/12/2023] Open
Abstract
Hypochlorous acid (HOCl; bleach) is a powerful weapon used by our immune system to eliminate invading bacteria. Yet the way HOCl actually kills bacteria and how they defend themselves from its oxidative action have only started to be uncovered. As this molecule induces both protein oxidation and aggregation, bacteria need concerted efforts of chaperones and antioxidants to maintain proteostasis during stress. Recent advances in the field identified several stress-activated chaperones, like Hsp33, RidA, and CnoX, which display unique structural features and play a central role in protecting the bacterial proteome during HOCl stress.
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Affiliation(s)
- Camille V Goemans
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
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Chakraborty S, Ganguli S, Chowdhury A, Ibba M, Banerjee R. Reversible inactivation of yeast mitochondrial phenylalanyl-tRNA synthetase under oxidative stress. Biochim Biophys Acta Gen Subj 2018; 1862:1801-1809. [DOI: 10.1016/j.bbagen.2018.04.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 04/18/2018] [Accepted: 04/27/2018] [Indexed: 12/28/2022]
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10
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Goemans CV, Vertommen D, Agrebi R, Collet JF. CnoX Is a Chaperedoxin: A Holdase that Protects Its Substrates from Irreversible Oxidation. Mol Cell 2018; 70:614-627.e7. [PMID: 29754824 DOI: 10.1016/j.molcel.2018.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/22/2018] [Accepted: 04/03/2018] [Indexed: 02/01/2023]
Abstract
Bleach (HOCl) is a powerful oxidant that kills bacteria in part by causing protein aggregation. It inactivates ATP-dependent chaperones, rendering cellular proteins mostly dependent on holdases. Here we identified Escherichia coli CnoX (YbbN) as a folding factor that, when activated by bleach via chlorination, functions as an efficient holdase, protecting the substrates of the major folding systems GroEL/ES and DnaK/J/GrpE. Remarkably, CnoX uniquely combines this function with the ability to prevent the irreversible oxidation of its substrates. This dual activity makes CnoX the founding member of a family of proteins, the "chaperedoxins." Because CnoX displays a thioredoxin fold and a tetratricopeptide (TPR) domain, two structural motifs conserved in all organisms, this investigation sets the stage for the discovery of additional chaperedoxins in bacteria and eukaryotes that could cooperate with proteins from both the Hsp60 and Hsp70 families.
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Affiliation(s)
- Camille V Goemans
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Didier Vertommen
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Rym Agrebi
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Jean-François Collet
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
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11
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Mukhopadyay R, Sudasinghe N, Schaub T, Yukl ET. Heme-independent Redox Sensing by the Heme-Nitric Oxide/Oxygen-binding Protein (H-NOX) from Vibrio cholerae. J Biol Chem 2016; 291:17547-56. [PMID: 27358409 DOI: 10.1074/jbc.m116.733337] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 11/06/2022] Open
Abstract
Heme nitric oxide/oxygen (H-NOX)-binding proteins act as nitric oxide (NO) sensors among various bacterial species. In several cases, they act to mediate communal behavior such as biofilm formation, quorum sensing, and motility by influencing the activity of downstream signaling proteins such as histidine kinases (HisKa) in a NO-dependent manner. An H-NOX/HisKa regulatory circuit was recently identified in Vibrio cholerae, and the H-NOX protein has been spectroscopically characterized. However, the influence of the H-NOX protein on HisKa autophosphorylation has not been evaluated. This process may be important for persistence and pathogenicity in this organism. Here, we have expressed and purified the V. cholerae HisKa (HnoK) and H-NOX in its heme-bound (holo) and heme-free (apo) forms. Autophosphorylation assays of HnoK in the presence of H-NOX show that the holoprotein in the Fe(II)-NO and Fe(III) forms is a potent inhibitor of HnoK. Activity of the Fe(III) form and aerobic instability of the Fe(II) form suggested that Vibrio cholerae H-NOX may act as a sensor of the redox state as well as NO. Remarkably, the apoprotein also showed robust HnoK inhibition that was dependent on the oxidation of cysteine residues to form disulfide bonds at a highly conserved zinc site. The importance of cysteine in this process was confirmed by mutagenesis, which also showed that holo Fe(III), but not Fe(II)-NO, H-NOX relied heavily upon cysteine for activation. These results highlight a heme-independent mechanism for activation of V. cholerae H-NOX that implicates this protein as a dual redox/NO sensor.
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Affiliation(s)
| | - Nilusha Sudasinghe
- Chemical Analysis and Instrumentation Laboratory, New Mexico State University, Las Cruces, New Mexico 88003
| | - Tanner Schaub
- Chemical Analysis and Instrumentation Laboratory, New Mexico State University, Las Cruces, New Mexico 88003
| | - Erik T Yukl
- From the Department of Chemistry and Biochemistry and
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12
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Lebrun V, Ravanat JL, Latour JM, Sénèque O. Near diffusion-controlled reaction of a Zn(Cys) 4 zinc finger with hypochlorous acid. Chem Sci 2016; 7:5508-5516. [PMID: 30034691 PMCID: PMC6021785 DOI: 10.1039/c6sc00974c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/14/2016] [Indexed: 11/22/2022] Open
Abstract
Reaction rate constants of HOCl with zinc-bound cysteines are determined, demonstrating that zinc fingers are potent targets for HOCl and may serve as HOCl sensors.
Hypochlorous acid (HOCl) is one of the strongest oxidants produced in mammals to kill invading microorganisms. The bacterial response to HOCl involves proteins that are able to sense HOCl using methionine, free cysteines or zinc-bound cysteines of zinc finger sites. Although the reactivity of methionine or free cysteine with HOCl is well documented at the molecular level, this is not the case for zinc-bound cysteines. We present here a study that aims at filling this gap. Using a model peptide of the Zn(Cys)4 zinc finger site of the chaperone Hsp33, a protein involved in the defence against HOCl in bacteria, we show that HOCl oxidation of this model leads to the formation of two disulfides. A detailed mechanistic and kinetic study of this reaction, relying on stopped-flow measurements and competitive oxidation with methionine, reveals very high rate constants: the absolute second-order rate constants for the reaction of the model zinc finger with HOCl and its conjugated base ClO– are (9.3 ± 0.8) × 108 M–1 s–1 and (1.2 ± 0.2) × 104 M–1 s–1, the former approaching the diffusion limit. Revised values of the second-order rate constants for the reaction of methionine with HOCl and ClO– were also determined to be (5.5 ± 0.8) × 108 M–1 s–1 and (7 ± 5) × 102 M–1 s–1, respectively. At physiological pH, the zinc finger site reacts faster with HOCl than methionine and glutathione or cysteine. This study demonstrates that zinc fingers are potent targets for HOCl and confirms that they may serve as HOCl sensors as proposed for Hsp33.
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Affiliation(s)
- Vincent Lebrun
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France . ;
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes , INAC-SyMMES , F-38000 Grenoble , France.,CEA , INAC-SyMMES , F-38000 Grenoble , France
| | - Jean-Marc Latour
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France . ;
| | - Olivier Sénèque
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France . ;
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13
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Laitaoja M, Tossavainen H, Pihlajamaa T, Valjakka J, Viiri K, Lohi O, Permi P, Jänis J. Redox-dependent disulfide bond formation in SAP30L corepressor protein: Implications for structure and function. Protein Sci 2015; 25:572-86. [PMID: 26609676 DOI: 10.1002/pro.2849] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 11/14/2015] [Indexed: 11/08/2022]
Abstract
Sin3A-associated protein 30-like (SAP30L) is one of the key proteins in a multi-subunit protein complex involved in transcriptional regulation via histone deacetylation. SAP30L, together with a highly homologous SAP30 as well as other SAP proteins (i.e., SAP25, SAP45, SAP130, and SAP180), is an essential component of the Sin3A corepressor complex, although its actual role has remained elusive. SAP30L is thought to function as an important stabilizing and bridging molecule in the complex and to mediate its interactions with other corepressors. SAP30L has been previously shown to contain an N-terminal Cys3 His type zinc finger (ZnF) motif, which is responsible for the key protein-protein, protein-DNA, and protein-lipid interactions. By using high-resolution mass spectrometry, we studied a redox-dependent disulfide bond formation in SAP30L ZnF as a regulatory mechanism for its structure and function. We showed that upon oxidative stress SAP30L undergoes the formation of two specific disulfide bonds, a vicinal Cys29-Cys30 and Cys38-Cys74, with a concomitant release of the coordinated zinc ion. The oxidized protein was shown to remain folded in solution and to bind signaling phospholipids. We also determined a solution NMR structure for SAP30L ZnF that showed an overall fold similar to that of SAP30, determined earlier. The NMR titration experiments with lipids and DNA showed that the binding is mediated by the C-terminal tail as well as both α-helices of SAP30L ZnF. The implications of these results for the structure and function of SAP30L are discussed.
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Affiliation(s)
- Mikko Laitaoja
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | | | - Tero Pihlajamaa
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Keijo Viiri
- Center for Child Health Research and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Olli Lohi
- Center for Child Health Research and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Perttu Permi
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
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14
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Lee YS, Lee J, Ryu KS, Lee Y, Jung TG, Jang JH, Sim DW, Kim EH, Seo MD, Lee KW, Won HS. Semi-Empirical Structure Determination of Escherichia coli Hsp33 and Identification of Dynamic Regulatory Elements for the Activation Process. J Mol Biol 2015; 427:3850-61. [DOI: 10.1016/j.jmb.2015.09.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 11/27/2022]
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15
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Wang S, Kaltashov IA. Identification of reduction-susceptible disulfide bonds in transferrin by differential alkylation using O(16)/O(18) labeled iodoacetic acid. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:800-807. [PMID: 25716754 PMCID: PMC4401651 DOI: 10.1007/s13361-015-1082-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 06/04/2023]
Abstract
Stabilization of native three-dimensional structure has been considered for decades to be the main function of disulfide bonds in proteins. More recently, it was becoming increasingly clear that in addition to this static role, disulfide bonds are also important for many other aspects of protein behavior, such as regulating protein function in a redox-sensitive fashion. Dynamic disulfide bonds can be taken advantage of as candidate anchor sites for site-specific modification (such as PEGylation of conjugation to a drug molecule), but are also frequently implicated in protein aggregation (through disulfide bond scrambling leading to formation of intermolecular covalent linkages). A common feature of all these labile disulfide bonds is their high susceptibility to reduction, as they need to be selectively regulated by either specific local redox conditions in vivo or well-controlled experimental conditions in vitro. The ability to identify labile disulfide bonds in a cysteine-rich protein can be extremely beneficial for a variety of tasks ranging from understanding the mechanistic aspects of protein function to identification of troublesome "hot spots" in biopharmaceutical products. Herein, we describe a mass spectrometry (MS)-based method for reliable identification of labile disulfide bonds, which consists of limited reduction, differential alkylation with an O(18)-labeled reagent, and LC-MS/MS analysis. Application of this method to a cysteine-rich protein transferrin allows the majority of its native disulfide bonds to be measured for their reduction susceptibility, which appears to reflect both solvent accessibility and bond strain energy.
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Affiliation(s)
| | - Igor A. Kaltashov
- address correspondence to: Igor A. Kaltashov, Department of Chemistry, University of Massachusetts-Amherst, 140 Thatcher Drive, LSL N369, Amherst, MA 01003, Tel: (413) 545-1460, Fax: (413) 545-4490,
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16
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Na S, Paek E, Choi JS, Kim D, Lee SJ, Kwon J. Characterization of disulfide bonds by planned digestion and tandem mass spectrometry. MOLECULAR BIOSYSTEMS 2015; 11:1156-64. [PMID: 25703060 PMCID: PMC4410109 DOI: 10.1039/c4mb00688g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The identification of disulfide bonds provides critical information regarding the structure and function of a protein and is a key aspect in understanding signaling cascades in biological systems. Recent proteomic approaches using digestion enzymes have facilitated the characterization of disulfide-bonds and/or oxidized products from cysteine residues, although these methods have limitations in the application of MS/MS. For example, protein digestion to obtain the native form of disulfide bonds results in short lengths of amino acids, which can cause ambiguous MS/MS analysis due to false positive identifications. In this study we propose a new approach, termed planned digestion, to obtain sufficient amino acid lengths after cleavage for proteomic approaches. Application of the DBond software to planned digestion of specific proteins accurately identified disulfide-linked peptides. RNase A was used as a model protein in this study because the disulfide bonds of this protein have been well characterized. Application of this approach to peptides digested with Asp-N/C (chemical digestion) and trypsin under acid hydrolysis conditions identified the four native disulfide bonds of RNase A. Missed cleavages introduced by trypsin treatment for only 3 hours generated sufficient lengths of amino acids for identification of the disulfide bonds. Analysis using MS/MS successfully showed additional fragmentation patterns that are cleavage products of S-S and C-S bonds of disulfide-linkage peptides. These fragmentation patterns generate thioaldehydes, persulfide, and dehydroalanine. This approach of planned digestion with missed cleavages using the DBond algorithm could be applied to other proteins to determine their disulfide linkage and the oxidation patterns of cysteine residues.
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Affiliation(s)
- Seungjin Na
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, United States of America
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA 92093, United States of America
| | - Eunok Paek
- Division of Computer Science and Engineering, Hanyang University, Seoul 133-791, Rep. of Korea
| | - Jong-Soon Choi
- Division of Life Science, Korea Basic Science Institute, Daejeon 350-333, Rep. of Korea
| | - Duwoon Kim
- Department of Food Science and Technology and Function Food Research Center, Chonnam National University, Gwangju 500-757, Rep. of Korea
| | - Seung Jae Lee
- Department of Chemistry and Research Center for Physics and Chemistry, Chonbuk National University, Jeonju 561-756, Rep. of Korea
| | - Joseph Kwon
- Division of Life Science, Korea Basic Science Institute, Daejeon 350-333, Rep. of Korea
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17
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Diabetes and Alzheimer disease, two overlapping pathologies with the same background: oxidative stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:985845. [PMID: 25815110 PMCID: PMC4357132 DOI: 10.1155/2015/985845] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/10/2015] [Indexed: 01/06/2023]
Abstract
There are several oxidative stress-related pathways interconnecting Alzheimer's disease and type II diabetes, two public health problems worldwide. Coincidences are so compelling that it is attractive to speculate they are the same disorder. However, some pathological mechanisms as observed in diabetes are not necessarily the same mechanisms related to Alzheimer's or the only ones related to Alzheimer's pathology. Oxidative stress is inherent to Alzheimer's and feeds a vicious cycle with other key pathological features, such as inflammation and Ca2+ dysregulation. Alzheimer's pathology by itself may lead to insulin resistance in brain, insulin resistance being an intervening variable in the neurodegenerative disorder. Hyperglycemia and insulin resistance from diabetes, overlapping with the Alzheimer's pathology, aggravate the progression of the neurodegenerative processes, indeed. But the same pathophysiological background is behind the consequences, oxidative stress. We emphasize oxidative stress and its detrimental role in some key regulatory enzymes.
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18
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Theoretical insights into the mechanism of redox switch in heat shock protein Hsp33. J Biol Inorg Chem 2015; 20:555-62. [PMID: 25637463 DOI: 10.1007/s00775-015-1240-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/10/2015] [Indexed: 10/24/2022]
Abstract
Heat shock protein 33 (Hsp33) is activated in the presence of H2O2 by a very interesting redox switch based on a tetra-coordinated zinc-cysteine complex present in the fully reduced and inactive protein form. The oxidation of this zinc center by H2O2 induces formation of two S-S bridges and the zinc release followed by the protein unfolding. We report here a theoretical study of the step-by-step sequence of the overall process starting with the oxidation of the first cysteine residue and ending with the zinc release. Each reaction step is characterized by its Gibbs free energy barrier (∆G (‡)). It is predicted that the first reaction step consists in the oxidation of Cys263 by H2O2 which is by far the most reactive cysteine (∆G (‡) = 15.4 kcal mol(-1)). The next two reaction steps are the formation of the first S-S bridge between Cys263 and Cys266 (∆G (‡) = 13.6 kcal mol(-1)) and the oxidation of Cys231 by H2O2 (∆G (‡) = 20.4 kcal mol(-1)). It is then shown that the formation of the second S-S bridge (Cys231-Cys233) before the zinc release is most unlikely (∆G (‡) = 34.8 kcal mol(-1)). Instead, the release of zinc just after the oxidation of the third cysteine (Cys231) is shown to be thermodynamically (dissociation Gibbs free energy ∆G d = 6.0 kcal mol(-1)) and kinetically (reaction rate constant k d ≈ 10(6) s(-1)) favored. This result is in good agreement with the experimental data on the oxidation mechanism of Hsp33 zinc center available to date.
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19
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Groitl B, Jakob U. Thiol-based redox switches. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1844:1335-43. [PMID: 24657586 PMCID: PMC4059413 DOI: 10.1016/j.bbapap.2014.03.007] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/04/2014] [Accepted: 03/11/2014] [Indexed: 11/30/2022]
Abstract
Regulation of protein function through thiol-based redox switches plays an important role in the response and adaptation to local and global changes in the cellular levels of reactive oxygen species (ROS). Redox regulation is used by first responder proteins, such as ROS-specific transcriptional regulators, chaperones or metabolic enzymes to protect cells against mounting levels of oxidants, repair the damage and restore redox homeostasis. Redox regulation of phosphatases and kinases is used to control the activity of select eukaryotic signaling pathways, making reactive oxygen species important second messengers that regulate growth, development and differentiation. In this review we will compare different types of reversible protein thiol modifications, elaborate on their structural and functional consequences and discuss their role in oxidative stress response and ROS adaptation. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.
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Affiliation(s)
- Bastian Groitl
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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20
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Isom CE, Turner JL, Lessner DJ, Karr EA. Redox-sensitive DNA binding by homodimeric Methanosarcina acetivorans MsvR is modulated by cysteine residues. BMC Microbiol 2013; 13:163. [PMID: 23865844 PMCID: PMC3729527 DOI: 10.1186/1471-2180-13-163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 07/12/2013] [Indexed: 11/16/2022] Open
Abstract
Background Methanoarchaea are among the strictest known anaerobes, yet they can survive exposure to oxygen. The mechanisms by which they sense and respond to oxidizing conditions are unknown. MsvR is a transcription regulatory protein unique to the methanoarchaea. Initially identified and characterized in the methanogen Methanothermobacter thermautotrophicus (Mth), MthMsvR displays differential DNA binding under either oxidizing or reducing conditions. Since MthMsvR regulates a potential oxidative stress operon in M. thermautotrophicus, it was hypothesized that the MsvR family of proteins were redox-sensitive transcription regulators. Results An MsvR homologue from the methanogen Methanosarcina acetivorans, MaMsvR, was overexpressed and purified. The two MsvR proteins bound the same DNA sequence motif found upstream of all known MsvR encoding genes, but unlike MthMsvR, MaMsvR did not bind the promoters of select genes involved in the oxidative stress response. Unlike MthMsvR that bound DNA under both non-reducing and reducing conditions, MaMsvR bound DNA only under reducing conditions. MaMsvR appeared as a dimer in gel filtration chromatography analysis and site-directed mutagenesis suggested that conserved cysteine residues within the V4R domain were involved in conformational rearrangements that impact DNA binding. Conclusions Results presented herein suggest that homodimeric MaMsvR acts as a transcriptional repressor by binding Ma PmsvR under non-reducing conditions. Changing redox conditions promote conformational changes that abrogate binding to Ma PmsvR which likely leads to de-repression.
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Affiliation(s)
- Catherine E Isom
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
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21
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Mitrea DM, Kriwacki RW. Regulated unfolding of proteins in signaling. FEBS Lett 2013; 587:1081-8. [PMID: 23454209 DOI: 10.1016/j.febslet.2013.02.024] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 02/12/2013] [Accepted: 02/13/2013] [Indexed: 11/27/2022]
Abstract
The transduction of biological signals often involves structural rearrangements of proteins in response to input signals, which leads to functional outputs. This review discusses the role of regulated partial and complete protein unfolding as a mechanism of controlling protein function and the prevalence of this regulatory mechanism in signal transduction pathways. The principles of regulated unfolding, the stimuli that trigger unfolding, and the coupling of unfolding with other well characterized regulatory mechanism are discussed.
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Affiliation(s)
- Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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22
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Zhang X, Zhang Q, Xin Q, Yu L, Wang Z, Wu W, Jiang L, Wang G, Tian W, Deng Z, Wang Y, Liu Z, Long J, Gong Z, Chen Z. Complex Structures of the Abscisic Acid Receptor PYL3/RCAR13 Reveal a Unique Regulatory Mechanism. Structure 2012; 20:780-90. [DOI: 10.1016/j.str.2012.02.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 02/20/2012] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
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23
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Disulfide bond formation and activation of Escherichia coli β-galactosidase under oxidizing conditions. Appl Environ Microbiol 2012; 78:2376-85. [PMID: 22286993 DOI: 10.1128/aem.06923-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Escherichia coli β-galactosidase is probably the most widely used reporter enzyme in molecular biology, cell biology, and biotechnology because of the easy detection of its activity. Its large size and tetrameric structure make this bacterial protein an interesting model for crystallographic studies and atomic mapping. In the present study, we investigate a version of Escherichia coli β-galactosidase produced under oxidizing conditions, in the cytoplasm of an Origami strain. Our data prove the activation of this microbial enzyme under oxidizing conditions and clearly show the occurrence of a disulfide bond in the β-galactosidase structure. Additionally, the formation of this disulfide bond is supported by the analysis of a homology model of the protein that indicates that two cysteines located in the vicinity of the catalytic center are sufficiently close for disulfide bond formation.
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24
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Bourlès E, Isaac M, Lebrun C, Latour JM, Sénèque O. Oxidation of Zn(Cys)4 zinc finger peptides by O2 and H2O2: products, mechanism and kinetics. Chemistry 2011; 17:13762-72. [PMID: 22052717 DOI: 10.1002/chem.201101913] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Indexed: 11/10/2022]
Abstract
The reactivity of a series of Zn(Cys)(4) zinc finger model peptides towards H(2)O(2) and O(2) has been investigated. The oxidation products were identified by HPLC and ESI-MS analysis. At pH<7.5, the zinc complexes and the free peptides are oxidised to bis-disulfide-containing peptides. Above pH 7.5, the oxidation of the zinc complexes by H(2)O(2) also yields sulfinate- and sulfonate-containing overoxidised peptides. At pH 7.0, monitoring of the reactions between the zinc complexes and H(2)O(2) by HPLC revealed the sequential formation of two disulfides. Several techniques for the determination of the rate constant for the first oxidation step corresponding to the attack of H(2)O(2) by the Zn(Cys)(4) site have been compared. This rate constant can be reliably determined by monitoring the oxidation by HPLC, fluorescence, circular dichroism or absorption spectroscopy in the presence of excess ethyleneglycol bis(2-aminoethyl ether)tetraacetic acid. In contrast, monitoring of the release of zinc with 4-(2-pyridylazo)resorcinol or of the thiol content with 5,5'-dithiobis(2-nitrobenzoate) did not yield reliable values of this rate constant for the case in which the formation of the second disulfide is slower than the formation of the first. The kinetic measurements clearly evidence a protective effect of zinc on the oxidation of the cysteines by both H(2)O(2) and O(2), which points to the fact that zinc binding diminishes the nucleophilicity of the thiolates. In addition, the reaction between the zinc finger and H(2)O(2) is too slow to consider zinc fingers as potential sensors for H(2)O(2) in cells.
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Affiliation(s)
- Emilie Bourlès
- Laboratoire de Chimie et Biologie des Métaux, UMR 5249 CNRS/CEA/Université Joseph Fourier, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France
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25
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Giron P, Dayon L, Sanchez JC. Cysteine tagging for MS-based proteomics. MASS SPECTROMETRY REVIEWS 2011; 30:366-395. [PMID: 21500242 DOI: 10.1002/mas.20285] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 11/13/2009] [Accepted: 11/13/2009] [Indexed: 05/30/2023]
Abstract
Amino acid-tagging strategies are widespread in proteomics. Because of the central role of mass spectrometry (MS) as a detection technique in protein sciences, the term "mass tagging" was coined to describe the attachment of a label, which serves MS analysis and/or adds analytical value to the measurements. These so-called mass tags can be used for separation, enrichment, detection, and quantitation of peptides and proteins. In this context, cysteine is a frequent target for modifications because the thiol function can react specifically by nucleophilic substitution or addition. Furthermore, cysteines present natural modifications of biological importance and a low occurrence in the proteome that justify the development of strategies to specifically target them in peptides or proteins. In the present review, the mass-tagging methods directed to cysteine residues are comprehensively discussed, and the advantages and drawbacks of these strategies are addressed. Some concrete applications are given to underline the relevance of cysteine-tagging techniques for MS-based proteomics.
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Affiliation(s)
- Priscille Giron
- Biomedical Proteomics Research Group, Structural Biology and Bioinformatics Department, University of Geneva, Geneva, Switzerland
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26
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Addepalli B, Limbach PA, Hunt AG. A disulfide linkage in a CCCH zinc finger motif of an Arabidopsis CPSF30 ortholog. FEBS Lett 2010; 584:4408-12. [PMID: 20888817 DOI: 10.1016/j.febslet.2010.09.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 09/24/2010] [Indexed: 10/19/2022]
Abstract
The Arabidopsis ortholog of the 30kDa subunit of the cleavage and polyadenylation factor (AtCPSF30) is an RNA binding endonuclease, and the endonuclease activity is inhibited by reducing agents. Here, we report the presence of a disulfide linkage in the endonuclease motif based on comparative mass spectrometry (MS) analysis of reduced and non-reduced but carbamidomethylated protein. This analysis reveals that this disulfide bond involves a CCCH zinc finger motif, one that is associated with the endonuclease activity of AtCPSF30. This finding raises the possibility that redox regulation of AtCPSF30 may occur through oxidation and reduction of the disulfide linkage.
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27
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Waypa GB, Schumacker PT. Hypoxia-induced changes in pulmonary and systemic vascular resistance: where is the O2 sensor? Respir Physiol Neurobiol 2010; 174:201-11. [PMID: 20713189 DOI: 10.1016/j.resp.2010.08.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 08/05/2010] [Accepted: 08/06/2010] [Indexed: 01/06/2023]
Abstract
Pulmonary arteries (PA) constrict in response to alveolar hypoxia, whereas systemic arteries (SA) undergo dilation. These physiological responses reflect the need to improve gas exchange in the lung, and to enhance the delivery of blood to hypoxic systemic tissues. An important unresolved question relates to the underlying mechanism by which the vascular cells detect a decrease in oxygen tension and translate that into a signal that triggers the functional response. A growing body of work implicates the mitochondria, which appear to function as O2 sensors by initiating a redox-signaling pathway that leads to the activation of downstream effectors that regulate vascular tone. However, the direction of this redox signal has been the subject of controversy. Part of the problem has been the lack of appropriate tools to assess redox signaling in live cells. Recent advancements in the development of redox sensors have led to studies that help to clarify the nature of the hypoxia-induced redox signaling by reactive oxygen species (ROS). Moreover, these studies provide valuable insight regarding the basis for discrepancies in earlier studies of the hypoxia-induced mechanism of redox signaling. Based on recent work, it appears that the O2 sensing mechanism in both the PA and SA are identical, that mitochondria function as the site of O2 sensing, and that increased ROS release from these organelles leads to the activation of cell-specific, downstream vascular responses.
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Affiliation(s)
- Gregory B Waypa
- Department of Pediatrics, Division of Neonatology, Northwestern University, Morton Building 4-685, 310 East Superior St, Chicago, IL 60611, USA.
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28
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Xu Y, Schmitt S, Tang L, Jakob U, Fitzgerald MC. Thermodynamic analysis of a molecular chaperone binding to unfolded protein substrates. Biochemistry 2010; 49:1346-53. [PMID: 20073505 DOI: 10.1021/bi902010t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Molecular chaperones are a highly diverse group of proteins that recognize and bind unfolded proteins to facilitate protein folding and prevent nonspecific protein aggregation. The mechanisms by which chaperones bind their protein substrates have been studied for decades. However, there are few reports about the affinity of molecular chaperones for their unfolded protein substrates. Thus, little is known about the relative binding affinities of different chaperones and about the relative binding affinities of chaperones for different unfolded protein substrates. Here we describe the application of SUPREX (stability of unpurified proteins from rates of H-D exchange), an H-D exchange and MALDI-based technique, in studying the binding interaction between the molecular chaperone Hsp33 and four different unfolded protein substrates, including citrate synthase, lactate dehydrogenase, malate dehydrogenase, and aldolase. The results of our studies suggest that the cooperativity of the Hsp33 folding-unfolding reaction increases upon binding with denatured protein substrates. This is consistent with the burial of significant hydrophobic surface area in Hsp33 when it interacts with its substrate proteins. The SUPREX-derived K(d) values for Hsp33 complexes with four different substrates were all found to be within the range of 3-300 nM.
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Affiliation(s)
- Ying Xu
- Department of Chemistry, Duke University, Durham, North Carolina 27708-0346, USA
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29
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Mendoza VL, Vachet RW. Probing protein structure by amino acid-specific covalent labeling and mass spectrometry. MASS SPECTROMETRY REVIEWS 2009; 28:785-815. [PMID: 19016300 PMCID: PMC2768138 DOI: 10.1002/mas.20203] [Citation(s) in RCA: 270] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies.
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Affiliation(s)
- Vanessa Leah Mendoza
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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30
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Kim Y, Kang K, Kim I, Lee YJ, Oh C, Ryoo J, Jeong E, Ahn K. Molecular mechanisms of MHC class I-antigen processing: redox considerations. Antioxid Redox Signal 2009; 11:907-36. [PMID: 19178136 DOI: 10.1089/ars.2008.2316] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Major histocompatibility complex (MHC) class I molecules present antigenic peptides to the cell surface for screening by CD8(+) T cells. A number of ER-resident chaperones assist the assembly of peptides onto MHC class I molecules, a process that can be divided into several steps. Early folding of the MHC class I heavy chain is followed by its association with beta(2)-microglobulin (beta(2)m). The MHC class I heavy chain-beta(2)m heterodimer is incorporated into the peptide-loading complex, leading to peptide loading, release of the peptide-filled MHC class I molecules from the peptide-loading complex, and exit of the complete MHC class I complex from the ER. Because proper antigen presentation is vital for normal immune responses, the assembly of MHC class I molecules requires tight regulation. Emerging evidence indicates that thiol-based redox regulation plays critical roles in MHC class I-restricted antigen processing and presentation, establishing an unexpected link between redox biology and antigen processing. We review the influences of redox regulation on antigen processing and presentation. Because redox signaling pathways are a rich source of validated drug targets, newly discovered redox biology-mediated mechanisms of antigen processing may facilitate the development of more selective and therapeutic drugs or vaccines against immune diseases.
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Affiliation(s)
- Youngkyun Kim
- National Creative Research Center for Antigen Presentation, Department of Biological Sciences, Seoul National University, Seoul, South Korea
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31
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Zhang L, Xu H, Chen CL, Green-Church KB, Freitas MA, Chen YR. Mass spectrometry profiles superoxide-induced intramolecular disulfide in the FMN-binding subunit of mitochondrial Complex I. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1875-1886. [PMID: 18789718 PMCID: PMC2614441 DOI: 10.1016/j.jasms.2008.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 08/01/2008] [Accepted: 08/01/2008] [Indexed: 05/26/2023]
Abstract
Protein thiols with regulatory functions play a critical role in maintaining the homeostasis of the redox state in mitochondria. One major host of regulatory cysteines in mitochondria is Complex I, with the thiols primarily located on its 51 kDa FMN-binding subunit. In response to oxidative stress, these thiols are expected to form intramolecular disulfide bridges as one of their oxidative post-translational modifications. Here, to test this hypothesis and gain insights into the molecular pattern of disulfide in Complex I, the isolated bovine Complex I was prepared. Superoxide (O(2)(.-)) is generated by Complex I under the conditions of enzyme turnover. O(2)(.-)-induced intramolecular disulfide formation at the 51, kDa subunit was determined by tandem mass spectrometry and database searching, with the latter accomplished by adaptation of the in-house developed database search engine, MassMatrix [Xu, H., et al., J. Proteome Res. 2008, 7, 138-144]. LC/MS/MS analysis of tryptic/chymotryptic digests of the 51 kDa subunit from alkylated Complex I revealed that four specific cysteines (C(125), C(142), C(187), and C(206)) of the 51 kDa subunit were involved in the formation of mixed intramolecular disulfide linkages. In all, three cysteine pairs were observed: C(125)/C(142), C(187)/C(206), and C(142)/C(206). The formation of disulfide bond was subsequently inhibited by superoxide dismutase, indicating the involvement of O(2)(.-). These results elucidated by mass spectrometry indicate that the residues of C(125), C(142), C(187), and C(206) are the specific regulatory cysteines of Complex I and they participate in the oxidative modification with disulfide formation under the physiological or pathophysiological conditions of oxidative stress.
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Affiliation(s)
- Liwen Zhang
- Campus Chemical Instrument Center, Proteomics and Mass Spectrometry Facility, The Ohio State University, Columbus, OH 43210
| | - Hua Xu
- Department of Molecular Virology Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210
| | - Chwen-Lih Chen
- Davis Heart & Lung Research Institute, Division of Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210
| | - Kari B. Green-Church
- Department of Molecular and Cellular Biochemistry, College of Medicine, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, Proteomics and Mass Spectrometry Facility, The Ohio State University, Columbus, OH 43210
| | - Michael A. Freitas
- Department of Molecular Virology Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210
| | - Yeong-Renn Chen
- Davis Heart & Lung Research Institute, Division of Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210
- Department of Molecular and Cellular Biochemistry, College of Medicine, The Ohio State University, Columbus, OH 43210
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Leelakriangsak M, Huyen NTT, Töwe S, van Duy N, Becher D, Hecker M, Antelmann H, Zuber P. Regulation of quinone detoxification by the thiol stress sensing DUF24/MarR-like repressor, YodB in Bacillus subtilis. Mol Microbiol 2008; 67:1108-24. [PMID: 18208493 DOI: 10.1111/j.1365-2958.2008.06110.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, we showed that the MarR-type repressor YkvE (MhqR) regulates multiple dioxygenases/glyoxalases, oxidoreductases and the azoreductase encoding yvaB (azoR2) gene in response to thiol-specific stress conditions, such as diamide, catechol and 2-methylhydroquinone (MHQ). Here we report on the regulation of the yocJ (azoR1) gene encoding another azoreductase by the novel DUF24/MarR-type repressor, YodB after exposure to thiol-reactive compounds. DNA binding activity of YodB is directly inhibited by thiol-reactive compounds in vitro. Mass spectrometry identified YodB-Cys-S-adducts that are formed upon exposure of YodB to MHQ and catechol in vitro. This confirms that catechol and MHQ are auto-oxidized to toxic ortho- and para-benzoquinones which act like diamide as thiol-reactive electrophiles. Mutational analyses further showed that the conserved Cys6 residue of YodB is required for optimal repression in vivo and in vitro while substitution of all three Cys residues of YodB affects induction of azoR1 transcription. Finally, phenotype analyses revealed that both azoreductases, AzoR1 and AzoR2 confer resistance to catechol, MHQ, 1,4-benzoquinone and diamide. Thus, both azoreductases that are controlled by different regulatory mechanisms have common functions in quinone and azo-compound reduction to protect cells against the thiol reactivity of electrophiles.
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Affiliation(s)
- Montira Leelakriangsak
- Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering, Oregon Health and Science University, Beaverton, OR, USA
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Waypa GB, Schumacker PT. Oxygen sensing in hypoxic pulmonary vasoconstriction: using new tools to answer an age-old question. Exp Physiol 2007; 93:133-8. [PMID: 17993507 DOI: 10.1113/expphysiol.2007.041236] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hypoxic pulmonary vasoconstriction (HPV) becomes activated in response to alveolar hypoxia and, although the characteristics of HPV have been well described, the underlying mechanism of O(2) sensing which initiates the HPV response has not been fully established. Mitochondria have long been considered as a putative site of oxygen sensing because they consume O(2) and therefore represent the intracellular site with the lowest oxygen tension. However, two opposing theories have emerged regarding mitochondria-dependent O(2) sensing during hypoxia. One model suggests that there is a decrease in mitochondrial reactive oxygen species (ROS) levels during the transition from normoxia to hypoxia, resulting in the shift in cytosolic redox to a more reduced state. An alternative model proposes that hypoxia paradoxically increases mitochondrial ROS signalling in pulmonary arterial smooth muscle. Experimental resolution of the question of whether the mitochondrial ROS levels increase or decrease during hypoxia has been problematic owing to the technical limitations of the tools used to assess oxidant stress as well as the pharmacological agents used to inhibit the mitochondrial electron transport chain. However, recent developments in genetic techniques and redox-sensitive probes may allow us eventually to reach a consensus concerning the O(2) sensing mechanism underlying HPV.
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Affiliation(s)
- Gregory B Waypa
- Department of Pediatrics, North-western University, Ward Building 12-191, 303 East Chicago Avenue, Chicago, IL 60611, USA
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34
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Marcus NY, Marcus RA, Schmidt BZ, Haslam DB. Contribution of the HEDJ/ERdj3 cysteine-rich domain to substrate interactions. Arch Biochem Biophys 2007; 468:147-58. [PMID: 17976514 DOI: 10.1016/j.abb.2007.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2007] [Revised: 09/27/2007] [Accepted: 10/01/2007] [Indexed: 10/22/2022]
Abstract
Cytoplasmic type I DnaJ/Hsp40 chaperones contain a Cys-rich domain consisting of four CXXCXG motifs that are in a reduced state and coordinate zinc, stabilizing the intervening sequence in a loop structure. However, the Cys-rich region of the endoplasmic reticulum localized HEDJ (ERdj3/ERj3p), is considerably different in sequence and arrangement. Unlike the typical type I molecule, the HEDJ CXC, and CXXC motifs were demonstrated in this study to be predominantly oxidized in intramolecular disulfide bonds. In the native state, HEDJ bound to immobilized, denatured thyroglobulin. Unlike its binding partner GRP78, redox conditions affected the interaction of HEDJ with substrate. Substitution of the Cys-rich domain cysteine residues with serine diminished or abolished HEDJ binding in the in vitro assay. These findings suggest that the Cys-rich region of HEDJ and its oxidation state are important in maintaining the substrate interaction domain in a binding-competent conformation.
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Affiliation(s)
- Nancy Y Marcus
- Department of Pediatrics and Molecular Microbiology, Washington University School of Medicine, 660 South Euclid, St. Louis, MO 63110, USA.
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35
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Zou LF, Shen K, Fu Y, Guo QX. Initiation of petroleum formation and antioxidant function - a DFT study of sulfursulfur bond dissociation enthalpies. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ilbert M, Horst J, Ahrens S, Winter J, Graf PCF, Lilie H, Jakob U. The redox-switch domain of Hsp33 functions as dual stress sensor. Nat Struct Mol Biol 2007; 14:556-63. [PMID: 17515905 PMCID: PMC2782886 DOI: 10.1038/nsmb1244] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Accepted: 04/04/2007] [Indexed: 11/09/2022]
Abstract
The redox-regulated chaperone Hsp33 is specifically activated upon exposure of cells to peroxide stress at elevated temperatures. Here we show that Hsp33 harbors two interdependent stress-sensing regions located in the C-terminal redox-switch domain of Hsp33: a zinc center sensing peroxide stress conditions and an adjacent linker region responding to unfolding conditions. Neither of these sensors works sufficiently in the absence of the other, making the simultaneous presence of both stress conditions a necessary requirement for Hsp33's full activation. Upon activation, Hsp33's redox-switch domain adopts a natively unfolded conformation, thereby exposing hydrophobic surfaces in its N-terminal substrate-binding domain. The specific activation of Hsp33 by the oxidative unfolding of its redox-switch domain makes this chaperone optimally suited to quickly respond to oxidative stress conditions that lead to protein unfolding.
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Affiliation(s)
- Marianne Ilbert
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N-University, Ann Arbor, Michigan 48109-1048, USA
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37
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Alam MS, Garg SK, Agrawal P. Molecular function of WhiB4/Rv3681c of Mycobacterium tuberculosis H37Rv: a [4Fe?4S] cluster co-ordinating protein disulphide reductase. Mol Microbiol 2007; 63:1414-31. [PMID: 17302817 DOI: 10.1111/j.1365-2958.2007.05589.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The genome sequence of Mycobacterium tuberculosis H37Rv revealed the presence of seven whiB-like open reading frames. In spite of several genetic studies on whiB genes, the biochemical properties of WhiB proteins are poorly understood. All WhiB-like proteins have four conserved cysteine residues, out of which two are present in a CXXC motif. We report for the first time the detailed biochemical and biophysical properties of M. tuberculosis WhiB4/Rv3681c and demonstrate the functional relevance of four conserved cysteines and the CXXC motif. UV-visible absorption spectra of freshly purified mWhiB4 showed the presence of a [2Fe-2S] cluster, whereas the electron paramagnetic resonance (EPR) spectra of reconstituted protein showed the presence of a [4Fe-4S] cluster. The iron-sulphur cluster was redox sensitive but stably co-ordinated to the protein even in the presence of high concentration of chaotropic agents. Despite primary sequence divergence from thioredoxin family proteins, the apo mWhiB4 has properties similar to thioredoxins and functions as a protein disulphide reductase, whereas holo mWhiB4 is enzymatically inactive. Apart from the cysteine thiol of CXXC motif the distantly placed thiol pair also contributes equally to the enzymatic activity of mWhiB4. A functional model of mWhiB4 in redox signaling during oxidative stress in M. tuberculosis has been presented.
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Affiliation(s)
- Md Suhail Alam
- Institute of Microbial Technology, Sector-39A, Chandigarh, 160 036, India
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38
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Traoré DAK, El Ghazouani A, Ilango S, Dupuy J, Jacquamet L, Ferrer JL, Caux-Thang C, Duarte V, Latour JM. Crystal structure of the apo-PerR-Zn protein from Bacillus subtilis. Mol Microbiol 2006; 61:1211-9. [PMID: 16925555 DOI: 10.1111/j.1365-2958.2006.05313.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteria adapt to elevated levels of Reactive Oxygen Species (ROS) by increasing the expression of defence and repair proteins, which is regulated by ROS responsive transcription factors. In Bacillus subtilis the zinc protein PerR, a peroxide sensor that binds DNA in the presence of a regulatory metal Mn2+ or Fe2+, mediates the adaptive response to H2O2. This study presents the first crystal structure of apo-PerR-Zn which shows that all four cysteine residues of the protein are involved in zinc co-ordination. The Zn(Cys)4 site locks the dimerization domain and stabilizes the dimer. Sequence alignment of PerR-like proteins supports that this structural site may constitute a distinctive feature of this class of peroxide stress regulators.
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Affiliation(s)
- Daouda A K Traoré
- DRDC/Laboratoire de Physicochimie des Métaux en Biologie, UMR 5155 CEA-CNRS-UJF, CEA-Grenoble, 38054 Grenoble Cedex 9, France
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39
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Waypa GB, Guzy R, Mungai PT, Mack MM, Marks JD, Roe MW, Schumacker PT. Increases in mitochondrial reactive oxygen species trigger hypoxia-induced calcium responses in pulmonary artery smooth muscle cells. Circ Res 2006; 99:970-8. [PMID: 17008601 DOI: 10.1161/01.res.0000247068.75808.3f] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mitochondria have been implicated as a potential site of O(2) sensing underlying hypoxic pulmonary vasoconstriction (HPV), but 2 disparate models have been proposed to explain their reaction to hypoxia. One model proposes that hypoxia-induced increases in mitochondrial reactive oxygen species (ROS) generation activate HPV through an oxidant-signaling pathway, whereas the other proposes that HPV is a result of decreased oxidant signaling. In an attempt to resolve this debate, we use a novel, ratiometric, redox-sensitive fluorescence resonance energy transfer (HSP-FRET) probe, in concert with measurements of reduced/oxidized glutathione (GSH/GSSG), to assess cytosolic redox responses in cultured pulmonary artery smooth muscle cells (PASMCs). Superfusion of PASMCs with hypoxic media increases the HSP-FRET ratio and decreases GSH/GSSG, indicating an increase in oxidant stress. The antioxidants pyrrolidinedithiocarbamate and N-acetyl-l-cysteine attenuated this response, as well as the hypoxia-induced increases in cytosolic calcium ([Ca(2+)](i)), assessed by the Ca(2+)-sensitive FRET sensor YC2.3. Adenoviral overexpression of glutathione peroxidase or cytosolic or mitochondrial catalase attenuated the hypoxia-induced increase in ROS signaling and [Ca(2+)](i). Adenoviral overexpression of cytosolic Cu, Zn-superoxide dismutase (SOD-I) had no effect on the hypoxia-induced increase in ROS signaling and [Ca(2+)](i), whereas mitochondrial matrix-targeted Mn-SOD (SOD-II) augmented [Ca(2+)](i). The mitochondrial inhibitor myxothiazol attenuated the hypoxia-induced changes in the ROS signaling and [Ca(2+)](i), whereas cyanide augmented the increase in [Ca(2+)](i). Finally, simultaneous measurement of ROS and Ca(2+) signaling in the same cell revealed that the initial increase in these 2 signals could not be distinguished temporally. These results demonstrate that hypoxia triggers increases in PASMC [Ca(2+)](i) by augmenting ROS signaling from the mitochondria.
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Affiliation(s)
- Gregory B Waypa
- Department of Pediatrics, Division of Neonatology, Northwestern University, Chicago, IL 60611, USA.
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40
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Abstract
Zinc plays a vital role in various cellular functions. Zinc deprivation is associated with severe disorders related to growth, maturation, and stress responses. In the heart, zinc affects differentiation and regeneration of cardiac muscle, cardiac conductance, acute stress responses, and recovery of heart transplants. Recent discoveries of the molecular players in zinc homeostasis revealed that the amount of intracellular free zinc is tightly controlled on the level of uptake, intracellular sequestration, redistribution, storage, and elimination, consequently creating a narrow window of optimal zinc concentration in the cells. Most of intracellular zinc is bound to numerous structural and regulatory proteins, with metabolically active, labile zinc present in picoto nanomolar concentrations. The central position of zinc in the redox signaling network is built on its unique chemical nature. The redox inert zinc creates a redox active environment when it binds to a sulfur ligand. The reversible oxidation of the sulfur ligand is coupled to the reversible zinc release from the protein, thereby executing the task of so-called protein "redox zinc switch." Clearly, the impairment of zinc homeostasis will have far reaching physiological consequences.
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Affiliation(s)
- Irina Korichneva
- Department of Medicine, Division of Cardiovascular Diseases and Hypertension, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, USA.
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41
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Modelli A, Jones D. Temporary Anion States and Dissociative Electron Attachment in Diphenyl Disulfide. J Phys Chem A 2006; 110:10219-24. [PMID: 16928111 DOI: 10.1021/jp0628683] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The temporary anion states of gas-phase diphenyl disulfide are characterized by means of electron transmission (ET) and dissociative electron attachment (DEA) spectroscopies. The measured energies of vertical electron attachment are compared to the virtual orbital energies of the neutral state molecule supplied by MP2 and B3LYP calculations with the 6-31G basis set. The calculated energies, scaled with empirical equations, reproduce satisfactorily the attachment energies measured in the ET spectrum. The first anion state of diphenyl disulfide is stable, thus escaping detection in ETS. The vertical and adiabatic electron affinities, evaluated with B3LYP/6-31+G calculations as the energy difference between the neutral and anion states, are predicted to be 0.37 and 1.38 eV, respectively. The anion current displayed in the DEA spectrum has a sharp and intense peak at zero energy, essentially due to the C6H5S- negative fragment. In agreement, according to the calculations, the localization properties of the first anion state are strongly S-S antibonding, and the energetic requirement for its dissociation along the S-S bond is fulfilled even at zero energy.
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Affiliation(s)
- Alberto Modelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, 40126 Bologna, Italy.
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42
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Abstract
Oxidative stress affects a wide variety of different cellular processes. Now, an increasing number of proteins have been identified that use the presence of reactive oxygen species or alterations in the cellular thiol-disulfide state as regulators of their protein function. This review focuses on two members of this growing group of redox-regulated proteins that utilize a cysteine-containing zinc center as the redox switch: Hsp33, the first molecular chaperone, whose ability to protect cells against stress-induced protein unfolding depends on the presence of reactive oxygen species and RsrA, the first anti-sigma factor that uses a cysteine-containing zinc center to sense and respond to cellular disulfide stress.
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Affiliation(s)
- Marianne Ilbert
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, 48109-1048, USA
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43
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Winter J, Jakob U. Beyond transcription--new mechanisms for the regulation of molecular chaperones. Crit Rev Biochem Mol Biol 2005; 39:297-317. [PMID: 15763707 DOI: 10.1080/10409230490900658] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Molecular chaperones are an essential part of the universal heat shock response that allows organisms to survive stress conditions that cause intracellular protein unfolding. During the past few years, two new mechanisms have been found to control the activity of several chaperones under stress conditions-the regulation of chaperone activity by the redox state and by the temperature of the environment. Hsp33, for example, is redox-regulated. Hsp33 is specifically activated by disulfide bond formation during oxidative stress, where it becomes a highly efficient chaperone holdase that binds tightly to unfolding proteins. Certain small heat shock proteins, such as Hsp26 and Hsp16.9, on the other hand, are temperature regulated. Exposure to heat shock temperatures causes these oligomeric proteins to disassemble, thereby changing them into highly efficient chaperones. The ATP-dependent chaperone folding system DnaK/DnaJ/GrpE also appears to be temperature regulated, switching from a folding to a holding mode during heat stress. Both of these novel post-translational regulatory strategies appear to have one ultimate goal: to significantly increase the substrate binding affinity of the affected chaperones under exactly those stress conditions that require their highest chaperone activity. This ensures that protein folding intermediates remain bound to the chaperones under stress conditions and are released only after the cells return to non-stress conditions.
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Affiliation(s)
- Jeannette Winter
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
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44
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Janda I, Devedjiev Y, Derewenda U, Dauter Z, Bielnicki J, Cooper DR, Graf PC, Joachimiak A, Jakob U, Derewenda ZS. The crystal structure of the reduced, Zn2+-bound form of the B. subtilis Hsp33 chaperone and its implications for the activation mechanism. Structure 2005; 12:1901-7. [PMID: 15458638 PMCID: PMC3691021 DOI: 10.1016/j.str.2004.08.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2004] [Revised: 08/06/2004] [Accepted: 08/08/2004] [Indexed: 11/19/2022]
Abstract
The bacterial heat shock protein Hsp33 is a redox-regulated chaperone activated by oxidative stress. In response to oxidation, four cysteines within a Zn2+ binding C-terminal domain form two disulfide bonds with concomitant release of the metal. This leads to the formation of the biologically active Hsp33 dimer. The crystal structure of the N-terminal domain of the E. coli protein has been reported, but neither the structure of the Zn2+ binding motif nor the nature of its regulatory interaction with the rest of the protein are known. Here we report the crystal structure of the full-length B. subtilis Hsp33 in the reduced form. The structure of the N-terminal, dimerization domain is similar to that of the E. coli protein, although there is no domain swapping. The Zn2+ binding domain is clearly resolved showing the details of the tetrahedral coordination of Zn2+ by four thiolates. We propose a structure-based activation pathway for Hsp33.
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Affiliation(s)
- Izabela Janda
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Yancho Devedjiev
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Urszula Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, NCI, Brookhaven National Laboratory, Upton, New York 11973
| | - Jakub Bielnicki
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Paul C.F. Graf
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Andrzej Joachimiak
- Biosciences Division and Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, Illinois 60439
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Zygmunt S. Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
- Correspondence:
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45
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Akhtar MW, Srinivas V, Raman B, Ramakrishna T, Inobe T, Maki K, Arai M, Kuwajima K, Rao CM. Oligomeric Hsp33 with Enhanced Chaperone Activity. J Biol Chem 2004; 279:55760-9. [PMID: 15494414 DOI: 10.1074/jbc.m406333200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hsp33, an Escherichia coli cytosolic chaperone, is inactive under normal conditions but becomes active upon oxidative stress. It was previously shown to dimerize upon activation in a concentration- and temperature-dependent manner. This dimer was thought to bind to aggregation-prone target proteins, preventing their aggregation. In the present study, we report small angle x-ray scattering (SAXS), steady state and time-resolved fluorescence, gel filtration, and glutaraldehyde cross-linking analysis of full-length Hsp33. Our circular dichroism and fluorescence results show that there are significant structural changes in oxidized Hsp33 at different temperatures. SAXS, gel filtration, and glutaraldehyde cross-linking results indicate, in addition to the dimers, the presence of oligomeric species. Oxidation in the presence of physiological salt concentration leads to significant increases in the oligomer population. Our results further show that under conditions that mimic the crowded milieu of the cytosol, oxidized Hsp33 exists predominantly as an oligomeric species. Interestingly, chaperone activity studies show that the oligomeric species is much more efficient compared with the dimers in preventing aggregation of target proteins. Taken together, these results indicate that in the cell, Hsp33 undergoes conformational and quaternary structural changes leading to the formation of oligomeric species in response to oxidative stress. Oligomeric Hsp33 thus might be physiologically relevant under oxidative stress.
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46
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Won HS, Low LY, Guzman RD, Martinez-Yamout M, Jakob U, Dyson HJ. The Zinc-dependent Redox Switch Domain of the Chaperone Hsp33 has a Novel Fold. J Mol Biol 2004; 341:893-9. [PMID: 15328602 DOI: 10.1016/j.jmb.2004.06.046] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The Escherichia coli chaperone Hsp33 contains a C-terminal zinc-binding domain that modulates activity by a so-called "redox switch". The oxidized form in the absence of zinc is active, while the reduced form in the presence of zinc is inactive. X-ray crystal structures of Hsp33 invariably omit details of the C-terminal domain, which is truncated in protein constructs that are capable of forming crystals. We report the solution structure of a recombinant 61-residue protein containing the zinc-binding domain (residues 227-287) of Hsp33, in the presence of stoichiometric amounts of Zn2+. The zinc-bound protein is well folded, and forms a novel structure unlike other published zinc-binding domains. The structure consists of two helices at right-angles to each other, a two-stranded B-hairpin and a third helix at the C terminus. The zinc site comprises the side-chains of the conserved cysteine residues 232, 234, 262 and 265, and connects a short sequence before the first helix with the tight turn in the middle of the B-hairpin. The structure of the C-terminal zinc-binding domain suggests a mechanism for the operation of the redox switch: loss of the bound zinc ion disrupts the folded structure, allowing the ligand cysteine residues to be oxidized, probably to disulfide bonds. The observation that the C-terminal domain is poorly structured in the active oxidized form suggests that the loss of zinc and unfolding of the domain precedes the oxidation of the thiolate groups of the cysteine residues, since the formation of disulfides between distant parts of the domain sequence would presumably promote the formation of stable three-dimensional structure in the oxidized form.Hsp33 provides an example of a redox signaling system that utilizes protein folding and unfolding together with chemical modification for transduction of external stimuli, in this case oxidative stress, to activate the machinery of the cell that is designed to deal with that stress.
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Affiliation(s)
- Hyung-Sik Won
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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47
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Graf PCF, Martinez-Yamout M, VanHaerents S, Lilie H, Dyson HJ, Jakob U. Activation of the Redox-regulated Chaperone Hsp33 by Domain Unfolding. J Biol Chem 2004; 279:20529-38. [PMID: 15023991 DOI: 10.1074/jbc.m401764200] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The molecular chaperone Hsp33 in Escherichia coli responds to oxidative stress conditions with the rapid activation of its chaperone function. On its activation pathway, Hsp33 progresses through three major conformations, starting as a reduced, zinc-bound inactive monomer, proceeding through an oxidized zinc-free monomer, and ending as a fully active oxidized dimer. While it is known that Hsp33 senses oxidative stress through its C-terminal four-cysteine zinc center, the nature of the conformational changes in Hsp33 that must take place to accommodate this activation process is largely unknown. To investigate these conformational rearrangements, we constructed constitutively monomeric Hsp33 variants as well as fragments consisting of the redox regulatory C-terminal domain of Hsp33. These proteins were studied by a combination of biochemical and NMR spectroscopic techniques. We found that in the reduced, monomeric conformation, zinc binding stabilizes the C terminus of Hsp33 in a highly compact, alpha-helical structure. This appears to conceal both the substrate-binding site as well as the dimerization interface. Zinc release without formation of the two native disulfide bonds causes the partial unfolding of the C terminus of Hsp33. This is sufficient to unmask the substrate-binding site, but not the dimerization interface, rendering reduced zinc-free Hsp33 partially active yet monomeric. Critical for the dimerization is disulfide bond formation, which causes the further unfolding of the C terminus of Hsp3 and allows the association of two oxidized Hsp33 monomers. This then leads to the formation of active Hsp33 dimers, which are capable of protecting cells against the severe consequences of oxidative heat stress.
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Affiliation(s)
- Paul C F Graf
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109-1048, USA
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Melkani GC, McNamara C, Zardeneta G, Mendoza JA. Hydrogen peroxide induces the dissociation of GroEL into monomers that can facilitate the reactivation of oxidatively inactivated rhodanese. Int J Biochem Cell Biol 2004; 36:505-18. [PMID: 14687928 DOI: 10.1016/j.biocel.2003.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although, several studies have been reported on the effects of oxidants on the structure and function of other molecular chaperones, no reports have been made so far for the chaperonin GroEL. The ability of GroEL to function under oxidative stress was investigated in this report by monitoring the effects of hydrogen peroxide (H(2)O(2)) on the structure and refolding activity of this protein. Using fluorescence spectroscopy and light scattering, we observed that GroEL showed increases in exposed hydrophobic sites and changes in tertiary and quaternary structure. Differential sedimentation, gel electrophoresis, and circular dichroism showed that H(2)O(2) treated GroEL underwent irreversible dissociation into monomers with partial loss of secondary structure. Relative to other proteins, GroEL was found to be highly resistant to oxidative damage. Interestingly, GroEL monomers produced under these conditions can facilitate the reactivation of H(2)O(2)-inactivated rhodanese but not urea-denatured rhodanese. Recovery of approximately 84% active rhodanese was obtained with either native or oxidized GroEL in the absence of GroES or ATP. In comparison, urea-denatured GroEL, BSA and the refolding mixture in the absence of proteins resulted in the recovery of 72, 50, and 49% rhodanese activity, respectively. Previous studies have shown that GroEL monomers can reactivate rhodanese. Here, we show that oxidized monomeric GroEL can reactivate oxidized rhodanese suggesting that GroEL retains the ability to protect proteins during oxidative stress.
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Affiliation(s)
- Girish C Melkani
- Department of Chemistry and Biochemistry, California State University, San Marcos, CA 92096-0001, USA
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Hoffmann JH, Linke K, Graf PCF, Lilie H, Jakob U. Identification of a redox-regulated chaperone network. EMBO J 2003; 23:160-8. [PMID: 14685279 PMCID: PMC1271656 DOI: 10.1038/sj.emboj.7600016] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Accepted: 10/20/2003] [Indexed: 11/08/2022] Open
Abstract
We have identified and reconstituted a multicomponent redox-chaperone network that appears to be designed to protect proteins against stress-induced unfolding and to refold proteins when conditions return to normal. The central player is Hsp33, a redox-regulated molecular chaperone. Hsp33, which is activated by disulfide bond formation and subsequent dimerization, works as an efficient chaperone holdase that binds to unfolding protein intermediates and maintains them in a folding competent conformation. Reduction of Hsp33 is catalyzed by the glutaredoxin and thioredoxin systems in vivo, and leads to the formation of highly active, reduced Hsp33 dimers. Reduction of Hsp33 is necessary but not sufficient for substrate protein release. Substrate dissociation from Hsp33 is linked to the presence of the DnaK/DnaJ/GrpE foldase system, which alone, or in concert with the GroEL/GroES system, then supports the refolding of the substrate proteins. Upon substrate release, reduced Hsp33 dimers dissociate into inactive monomers. This regulated substrate transfer ultimately links substrate release and Hsp33 inactivation to the presence of available DnaK/DnaJ/GrpE, and, therefore, to the return of cells to non-stress conditions.
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Affiliation(s)
- Jörg H Hoffmann
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Katrin Linke
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Paul CF Graf
- Program in Cellular and Molecular Biology, University of Michigan, MI, USA
| | - Hauke Lilie
- Department of Biotechnology, University of Halle, Halle, Germany
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N-University, Ann Arbor, MI 48109, USA. Tel.: +1 734 615 1286; Fax: +1 734 647 0884; E-mail:
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Abstract
Thiol-based regulatory switches play central roles in cellular responses to oxidative stress, nitrosative stress, and changes in the overall thiol-disulfide redox balance. Protein sulfhydryls offer a great deal of flexibility in the different types of modification they can undergo and the range of chemical signals they can perceive. For example, recent work on OhrR and OxyR has clearly established that disulfide bonds are not the only cysteine oxidation products that are likely to be relevant to redox sensing in vivo. Furthermore, different stresses can result in distinct modifications to the same protein; in OxyR it seems that distinct modifications can occur at the same cysteine, and in Yap1 a partner protein ensures that the disulfide bond induced by peroxide stress is different from the disulfide bond induced by other stresses. These kinds of discoveries have also led to the intriguing suggestion that different modifications to the same protein can create multiple activation states and thus deliver discrete regulatory outcomes. In this review, we highlight these issues, focusing on seven well-characterized microbial proteins controlled by thiol-based switches, each of which exhibits unique regulatory features.
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Affiliation(s)
- Mark S B Paget
- Department of Biochemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom.
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