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Fernández-Otal Á, Guío J, Sarasa-Buisan C, Peleato ML, Fillat MF, Lanas Á, Bes MT. Functional characterization of Fur from the strict anaerobe Clostridioides difficile provides insight into its redox-driven regulatory capacity. FEBS J 2024; 291:3604-3627. [PMID: 38775144 DOI: 10.1111/febs.17156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/06/2024] [Accepted: 04/29/2024] [Indexed: 08/15/2024]
Abstract
Clostridioides (formerly Clostridium) difficile is a leading cause of infectious diarrhea associated with antibiotic therapy. The ability of this anaerobic pathogen to acquire enough iron to proliferate under iron limitation conditions imposed by the host largely determines its pathogenicity. However, since high intracellular iron catalyzes formation of deleterious reactive hydroxyl radicals, iron uptake is tightly regulated at the transcriptional level by the ferric uptake regulator Fur. Several studies relate lacking a functional fur gene in C. difficile cells to higher oxidative stress sensitivity, colonization defect and less toxigenicity, although Fur does not appear to directly regulate either oxidative stress response genes or pathogenesis genes. In this work, we report the functional characterization of C. difficile Fur and describe an additional oxidation sensing Fur-mediated mechanism independent of iron, which affects Fur DNA-binding. Using electrophoretic mobility shift assays, we show that Fur binding to the promoters of fur, feoA and fldX genes, identified as iron and Fur-regulated genes in vivo, is specific and does not require co-regulator metal under reducing conditions. Fur treatment with H2O2 produces dose-dependent soluble high molecular weight species unable to bind to target promoters. Moreover, Fur oligomers are dithiotreitol sensitive, highlighting the importance of some interchain disulfide bond(s) for Fur oligomerization, and hence for activity. Additionally, the physiological electron transport chain NADPH-thioredoxin reductase/thioredoxin from Escherichia coli reduces inactive oligomerized C. difficile Fur that recovers activity. In conjunction with available transcriptomic data, these results suggest a previously underappreciated complexity in the control of some members of the Fur regulon that is based on Fur redox properties and might be fundamental for the adaptive response of C. difficile during infection.
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Affiliation(s)
- Ángela Fernández-Otal
- Department of Biochemistry & Molecular and Cellular Biology, University of Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor (Edif. I+D), Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragón), Zaragoza, Spain
| | - Jorge Guío
- Department of Biochemistry & Molecular and Cellular Biology, University of Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor (Edif. I+D), Zaragoza, Spain
| | - Cristina Sarasa-Buisan
- Department of Biochemistry & Molecular and Cellular Biology, University of Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor (Edif. I+D), Zaragoza, Spain
| | - M Luisa Peleato
- Department of Biochemistry & Molecular and Cellular Biology, University of Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor (Edif. I+D), Zaragoza, Spain
| | - María F Fillat
- Department of Biochemistry & Molecular and Cellular Biology, University of Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor (Edif. I+D), Zaragoza, Spain
| | - Ángel Lanas
- Aragon Institute for Health Research (IIS Aragón), Zaragoza, Spain
- Digestive Diseases Service, University Clinic Hospital Lozano Blesa, Zaragoza, Spain
- CIBERehd, Madrid, Spain
| | - M Teresa Bes
- Department of Biochemistry & Molecular and Cellular Biology, University of Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor (Edif. I+D), Zaragoza, Spain
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2
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Liu X, Kouassi KGW, Vanbever R, Dumoulin M. Impact of the PEG length and PEGylation site on the structural, thermodynamic, thermal, and proteolytic stability of mono-PEGylated alpha-1 antitrypsin. Protein Sci 2022; 31:e4392. [PMID: 36040264 PMCID: PMC9375436 DOI: 10.1002/pro.4392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/11/2022]
Abstract
Conjugation to polyethylene glycol (PEG) is a widely used approach to improve the therapeutic value of proteins essentially by prolonging their body residence time. PEGylation may however induce changes in the structure and/or the stability of proteins and thus on their function(s). The effects of PEGylation on the thermodynamic stability can either be positive (stabilization), negative (destabilization), or neutral (no effect). Moreover, various factors such as the PEG length and PEGylation site can influence the consequences of PEGylation on the structure and stability of proteins. In this study, the effects of PEGylation on the structure, stability, and polymerization of alpha1-antitrypsin (AAT) were investigated, using PEGs with different lengths, different structures (linear or 2-armed) and different linking chemistries (via amine or thiol) at two distinct positions of the sequence. The results show that whatever the size, position, and structure of PEG chains, PEGylation (a) does not induce significant changes in AAT structure (either at the secondary or tertiary level); (b) does not alter the stability of the native protein upon both chemical- and heat-induced denaturation; and (c) does not prevent AAT to fully refold and recover its activity following chemical denaturation. However, the propensity of AAT to aggregate upon heat treatment was significantly decreased by PEGylation, although PEGylation did not prevent the irreversible inactivation of the enzyme. Moreover, conjugation to PEG, especially 2-armed 40 kDa PEG, greatly improved the proteolytic resistance of AAT. PEGylation of AAT could be a promising strategy to prolong its half-life after infusion in AAT-deficient patients and thereby decrease the frequency of infusions.
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Affiliation(s)
- Xiao Liu
- Advanced Drug Delivery and BiomaterialsLouvain Drug Research Institute, Université catholique de Louvain (UCLouvain)BrusselsBelgium
| | - Kobenan G. W. Kouassi
- Advanced Drug Delivery and BiomaterialsLouvain Drug Research Institute, Université catholique de Louvain (UCLouvain)BrusselsBelgium
| | - Rita Vanbever
- Advanced Drug Delivery and BiomaterialsLouvain Drug Research Institute, Université catholique de Louvain (UCLouvain)BrusselsBelgium
| | - Mireille Dumoulin
- Department of Life SciencesInBios, Center for Protein Engineering, Nanobodies to Explore Protein Structure and Functions, University of LiègeLiègeBelgium
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3
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Duray E, Lejeune M, Baron F, Beguin Y, Devoogdt N, Krasniqi A, Lauwers Y, Zhao YJ, D'Huyvetter M, Dumoulin M, Caers J. A non-internalised CD38-binding radiolabelled single-domain antibody fragment to monitor and treat multiple myeloma. J Hematol Oncol 2021; 14:183. [PMID: 34727950 PMCID: PMC8561907 DOI: 10.1186/s13045-021-01171-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/22/2021] [Indexed: 12/21/2022] Open
Abstract
Background Antibody-based therapies targeting CD38 are currently used as single agents as well as in combination regimens for multiple myeloma, a malignant plasma cell disorder. In this study, we aimed to develop anti-CD38 single-domain antibodies (sdAbs) that can be used to trace CD38+ tumour cells and subsequently used for targeted radionuclide therapy. SdAbs are derived from Camelidae heavy-chain antibodies and have emerged as promising theranostic agents due to their favourable pharmacological properties. Methods Four different anti-CD38 sdAbs were produced, and their binding affinities and potential competition with the monoclonal antibody daratumumab were tested using biolayer interferometry. Their binding kinetics and potential cell internalisation were further studied after radiolabelling with the diagnostic radioisotope Indium-111. The resulting radiotracers were evaluated in vivo for their tumour-targeting potential and biodistribution through single-photon emission computed tomography (SPECT/CT) imaging and serial dissections. Finally, therapeutic efficacy of a lead anti-CD38 sdAb, radiolabelled with the therapeutic radioisotope Lutetium-177, was evaluated in a CD38+ MM xenograft model. Results We retained anti-CD38 sdAb #2F8 as lead based on its excellent affinity and superior stability, the absence of competition with daratumumab and the lack of receptor-mediated internalisation. When intravenously administered to tumour-xenografted mice, radiolabelled sdAb #2F8 revealed specific and sustained tumour retention with low accumulation in other tissues, except kidneys, resulting in high tumour-to-normal tissue ratios. In a therapeutic setting, myeloma-bearing mice received three consecutive intravenous administrations of a high (18.5 MBq) or a low radioactive dose (9.3 MBq) of 177Lu-DTPA-2F8 or an equal volume of vehicle solution. A dose-dependent tumour regression was observed, which translated into a prolonged median survival from 43 days for vehicle-treated mice, to 62 days (p = 0.027) in mice receiving the low and 65 days in mice receiving the high (p = 0.0007) radioactive dose regimen, respectively. Conclusions These results highlight the theranostic potential of radiolabelled anti-CD38 sdAbs for the monitoring and treatment of multiple myeloma. Supplementary Information The online version contains supplementary material available at 10.1186/s13045-021-01171-6.
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Affiliation(s)
- Elodie Duray
- Laboratory of Haematology, GIGA-I3, University of Liège, Liège, Belgium.,NEPTUNS, Nanobodies To Explore Protein Structure and Functions, Centre for Protein Engineering (CIP), University of Liège, Liège, Belgium
| | - Margaux Lejeune
- Laboratory of Haematology, GIGA-I3, University of Liège, Liège, Belgium
| | - Frederic Baron
- Laboratory of Haematology, GIGA-I3, University of Liège, Liège, Belgium.,Division of Haematology, Department of Medicine, University and CHU of Liège, Liège, Belgium
| | - Yves Beguin
- Laboratory of Haematology, GIGA-I3, University of Liège, Liège, Belgium.,Division of Haematology, Department of Medicine, University and CHU of Liège, Liège, Belgium
| | - Nick Devoogdt
- Department of Medical Imaging, Laboratory for In Vivo Cellular and Molecular Imaging, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ahmet Krasniqi
- Department of Medical Imaging, Laboratory for In Vivo Cellular and Molecular Imaging, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yoline Lauwers
- Department of Medical Imaging, Laboratory for In Vivo Cellular and Molecular Imaging, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yong Juan Zhao
- School of Chemical Biology and Biotechnology, University Shenzhen Graduate School, Peking, China
| | - Matthias D'Huyvetter
- Department of Medical Imaging, Laboratory for In Vivo Cellular and Molecular Imaging, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mireille Dumoulin
- NEPTUNS, Nanobodies To Explore Protein Structure and Functions, Centre for Protein Engineering (CIP), University of Liège, Liège, Belgium
| | - Jo Caers
- Laboratory of Haematology, GIGA-I3, University of Liège, Liège, Belgium. .,Division of Haematology, Department of Medicine, University and CHU of Liège, Liège, Belgium.
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4
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Kellner R, Malempré R, Vandenameele J, Brans A, Hennen AF, Rochus N, Di Paolo A, Vandevenne M, Matagne A. Protein formulation through automated screening of pH and buffer conditions, using the Robotein® high throughput facility. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:473-490. [PMID: 33611612 DOI: 10.1007/s00249-021-01510-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/26/2021] [Accepted: 02/08/2021] [Indexed: 12/30/2022]
Abstract
Among various factors, the direct environment (e.g. pH, buffer components, salts, additives, etc.…) is known to have a crucial effect on both the stability and activity of proteins. In particular, proper buffer and pH conditions can improve their stability and function significantly during purification, storage and handling, which is highly relevant for both academic and industrial applications. It can also promote data reproducibility, support the interpretation of experimental results and, finally, contribute to our general understanding of the biophysical properties of proteins. In this study, we have developed a high throughput screen of 158 different buffers/pH conditions in which we evaluated: (i) the protein stability, using differential scanning fluorimetry and (ii) the protein function, using either enzymatic assays or binding activity measurements, both in an automated manner. The modular setup of the screen allows for easy implementation of other characterization methods and parameters, as well as additional test conditions. The buffer/pH screen was validated with five different proteins used as models, i.e. two active-site serine β-lactamases, two metallo-β-lactamases (one of which is only active as a tetramer) and a single-domain dromedary antibody fragment (VHH or nanobody). The formulation screen allowed automated and fast determination of optimum buffer and pH profiles for the tested proteins. Besides the determination of the optimum buffer and pH, the collection of pH profiles of many different proteins may also allow to delineate general concepts to understand and predict the relationship between pH and protein properties.
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Affiliation(s)
- Ruth Kellner
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - Romain Malempré
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - Julie Vandenameele
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - Alain Brans
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | | | - Noémie Rochus
- Eurogentec S.A., Rue Bois Saint-Jean, 5, 4102, Seraing, Belgium
| | - Alexandre Di Paolo
- Eurogentec S.A., Rue Bois Saint-Jean, 5, 4102, Seraing, Belgium.,Xpress Biologics SA, Accessia Pharma Site, Avenue du Parc Industriel, 89, 4041, Milmort, Belgium
| | - Marylène Vandevenne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium.
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5
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Xiao Z, La Fontaine S, Bush AI, Wedd AG. Molecular Mechanisms of Glutaredoxin Enzymes: Versatile Hubs for Thiol-Disulfide Exchange between Protein Thiols and Glutathione. J Mol Biol 2018; 431:158-177. [PMID: 30552876 DOI: 10.1016/j.jmb.2018.12.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022]
Abstract
The tripeptide glutathione (GSH) and its oxidized form glutathione disulfide (GSSG) constitute a key redox couple in cells. In particular, they partner protein thiols in reversible thiol-disulfide exchange reactions that act as switches in cell signaling and redox homeostasis. Disruption of these processes may impair cellular redox signal transduction and induce redox misbalances that are linked directly to aging processes and to a range of pathological conditions including cancer, cardiovascular diseases and neurological disorders. Glutaredoxins are a class of GSH-dependent oxidoreductase enzymes that specifically catalyze reversible thiol-disulfide exchange reactions between protein thiols and the abundant thiol pool GSSG/GSH. They protect protein thiols from irreversible oxidation, regulate their activities under a variety of cellular conditions and are key players in cell signaling and redox homeostasis. On the other hand, they may also function as metal-binding proteins with a possible role in the cellular homeostasis and metabolism of essential metals copper and iron. However, the molecular basis and underlying mechanisms of glutaredoxin action remain elusive in many situations. This review focuses specifically on these aspects in the context of recent developments that illuminate some of these uncertainties.
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Affiliation(s)
- Zhiguang Xiao
- Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3052, Australia; School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Sharon La Fontaine
- Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3052, Australia; School of Life and Environmental Sciences, Deakin University, Burwood, Victoria 3125, Australia
| | - Ashley I Bush
- Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Anthony G Wedd
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
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6
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Hudson DA, Caplan JL, Thorpe C. Designing Flavoprotein-GFP Fusion Probes for Analyte-Specific Ratiometric Fluorescence Imaging. Biochemistry 2018; 57:1178-1189. [PMID: 29341594 DOI: 10.1021/acs.biochem.7b01132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The development of genetically encoded fluorescent probes for analyte-specific imaging has revolutionized our understanding of intracellular processes. Current classes of intracellular probes depend on the selection of binding domains that either undergo conformational changes on analyte binding or can be linked to thiol redox chemistry. Here we have designed novel probes by fusing a flavoenzyme, whose fluorescence is quenched on reduction by the analyte of interest, with a GFP domain to allow for rapid and specific ratiometric sensing. Two flavoproteins, Escherichia coli thioredoxin reductase and Saccharomyces cerevisiae lipoamide dehydrogenase, were successfully developed into thioredoxin and NAD+/NADH specific probes, respectively, and their performance was evaluated in vitro and in vivo. A flow cell format, which allowed dynamic measurements, was utilized in both bacterial and mammalian systems. In E. coli the first reported intracellular steady-state of the cytoplasmic thioredoxin pool was measured. In HEK293T mammalian cells, the steady-state cytosolic ratio of NAD+/NADH induced by glucose was determined. These genetically encoded fluorescent constructs represent a modular approach to intracellular probe design that should extend the range of metabolites that can be quantitated in live cells.
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Affiliation(s)
- Devin A Hudson
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Jeffrey L Caplan
- Bioimaging Center, Delaware Biotechnology Institute , Newark, Delaware 19716, United States
| | - Colin Thorpe
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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7
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Ukuwela AA, Bush AI, Wedd AG, Xiao Z. Glutaredoxins employ parallel monothiol-dithiol mechanisms to catalyze thiol-disulfide exchanges with protein disulfides. Chem Sci 2017; 9:1173-1183. [PMID: 29675162 PMCID: PMC5885593 DOI: 10.1039/c7sc04416j] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/05/2017] [Indexed: 12/02/2022] Open
Abstract
Glutaredoxins were demonstrated to be a family of versatile enzymes capable of catalyzing thiol–disulfide exchange involving GSSG/GSH via different catalytic routes either alone or in parallel.
Glutaredoxins (Grxs) are a family of glutathione (GSH)-dependent thiol–disulfide oxidoreductases. They feature GSH-binding sites that directly connect the reversible redox chemistry of protein thiols to the abundant cellular nonprotein thiol pool GSSG/GSH. This work studied the pathways for oxidation of protein dithiols P(SH)2 and reduction of protein disulfides P(SS) catalyzed by Homo sapiens HsGrx1 and Escherichia coli EcGrx1. The metal-binding domain HMA4n(SH)2 was chosen as substrate as it contains a solvent-exposed CysCys motif. Quenching of the reactions with excess iodoacetamide followed by protein speciation analysis via ESI-MS allowed interception and characterization of both substrate and enzyme intermediates. The enzymes shuttle between three catalytically-competent forms (Grx(SH)(S–), Grx(SH)(SSG) and Grx(SS)) and employ conserved parallel monothiol and dithiol mechanisms. Experiments with dithiol and monothiol versions of both Grx enzymes demonstrate which monothiol (plus GSSG or GSH) or dithiol pathways dominate a specific oxidation or reduction reaction. Grxs are shown to be a class of versatile enzymes with diverse catalytic functions that are driven by specific interactions with GSSG/GSH.
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Affiliation(s)
- Ashwinie A Ukuwela
- School of Chemistry , Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Victoria 3010 , Australia
| | - Ashley I Bush
- Melbourne Dementia Research Centre , Florey Institute of Neuroscience and Mental Health , The University of Melbourne , Parkville , Victoria 3052 , Australia .
| | - Anthony G Wedd
- School of Chemistry , Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Victoria 3010 , Australia
| | - Zhiguang Xiao
- School of Chemistry , Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Victoria 3010 , Australia.,Melbourne Dementia Research Centre , Florey Institute of Neuroscience and Mental Health , The University of Melbourne , Parkville , Victoria 3052 , Australia .
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8
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Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance. Cell Rep 2017; 19:1247-1256. [DOI: 10.1016/j.celrep.2017.04.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/14/2017] [Accepted: 04/13/2017] [Indexed: 11/17/2022] Open
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9
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Berndt C, Schwenn JD, Lillig CH. The specificity of thioredoxins and glutaredoxins is determined by electrostatic and geometric complementarity. Chem Sci 2015; 6:7049-7058. [PMID: 29861944 PMCID: PMC5947528 DOI: 10.1039/c5sc01501d] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/08/2015] [Indexed: 02/06/2023] Open
Abstract
Thiol-disulfide oxidoreductases from the thioredoxin (Trx) family of proteins have a broad range of well documented functions and possess distinct substrate specificities. The mechanisms and characteristics that control these specificities are key to the understanding of both the reduction of catalytic disulfides as well as allosteric disulfides (thiol switches). Here, we have used the catalytic disulfide of E. coli 3'-phosphoadenosine 5'-phosphosulfate (PAPS) reductase (PR) that forms between the single active site thiols of two monomers during the reaction cycle as a model system to investigate the mechanisms of Trx and Grx protein specificity. Enzyme kinetics, ΔE'0 determination, and structural analysis of various Trx and Grx family members suggested that the redox potential does not determine specificity nor efficiency of the redoxins as reductant for PR. Instead, the efficiency of PR with various redoxins correlated strongly to the extent of a negative electric field of the redoxins reaching into the solvent outside the active site, and electrostatic and geometric complementary contact surfaces. These data suggest that, in contrast to common assumption, the composition of the active site motif is less important for substrate specificity than other amino acids in or even outside the immediate contact area.
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Affiliation(s)
- Carsten Berndt
- From the Department of Neurology , Medical Faculty , Heinrich-Heine Universität , Merowingerplatz 1a , 40225 Düsseldorf , Germany
| | - Jens-Dirk Schwenn
- Biochemistry of Plants , Ruhr-Universität Bochum , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Christopher Horst Lillig
- Institute for Medical Biochemistry and Molecular Biology , Universitätsmedizin Greifswald , Ernst-Moritz-Arndt Universität , Ferdinand Sauerbruch Straße , DE-17475 Greifswald , Germany . ; ; Tel: +49 3834 86 5407
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10
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Protein flexibility and cysteine reactivity: influence of mobility on the H-bond network and effects on pKa prediction. Protein J 2015; 33:323-36. [PMID: 24809821 DOI: 10.1007/s10930-014-9564-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Thanks to its chemical plasticity, cysteine (Cys) is a very versatile player in proteins. A major determinant of Cys reactivity is pKa: the ability to predict it is deemed critical in redox bioinformatics. I considered different computational methods for pKa predictions and ultimately applied one (propka, ppka1) to various datasets; for all residues I assessed the effect of (1) hydrogen bonding, electrostatics and solvation on predictions and (2) protein mobility on pKa variability. Particularly for Cys, exposure and H-bond contributions heavily dictated propka predictions. The prominence of H-bond contributions was previously reported: this may explain the effectiveness of ppka1 (with Cys, tested in a benchmark). However ppka1 was also very sensitive to protein mobility; I assessed the effects of mobility on particularly large (compared to previous studies) datasets of structural ensembles; I found that exposed Cys presented the highest pKa variability, ascribable to correspondingly high H-bond fluctuations associated with protein flexibility. The benefit of including protein dynamics in pKa predictions was previously proposed, but empirical methods were never tested in this sense; instead, giving their outstanding speed, they could lend particularly well to this purpose. I devised a strategy combining short range molecular dynamics with ppka1; the protocol aimed to mitigate high ppka1 variability by including a "statistical view" of fast conformational changes. Tested in a benchmark, the strategy lead to improved performances. These results provide new insights on Cys bioinformatics (pKa prediction protocols) and Cys biology (effect of mobility on exposed Cys properties).
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11
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Wani R, Nagata A, Murray BW. Protein redox chemistry: post-translational cysteine modifications that regulate signal transduction and drug pharmacology. Front Pharmacol 2014; 5:224. [PMID: 25339904 PMCID: PMC4186267 DOI: 10.3389/fphar.2014.00224] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 09/17/2014] [Indexed: 12/26/2022] Open
Abstract
The perception of reactive oxygen species has evolved over the past decade from agents of cellular damage to secondary messengers which modify signaling proteins in physiology and the disease state (e.g., cancer). New protein targets of specific oxidation are rapidly being identified. One emerging class of redox modification occurs to the thiol side chain of cysteine residues which can produce multiple chemically distinct alterations to the protein (e.g., sulfenic/sulfinic/sulfonic acid, disulfides). These post-translational modifications (PTM) are shown to affect the protein structure and function. Because redox-sensitive proteins can traffic between subcellular compartments that have different redox environments, cysteine oxidation enables a spatio-temporal control to signaling. Understanding ramifications of these oxidative modifications to the functions of signaling proteins is crucial for understanding cellular regulation as well as for informed-drug discovery process. The effects of EGFR oxidation of Cys797 on inhibitor pharmacology are presented to illustrate the principle. Taken together, cysteine redox PTM can impact both cell biology and drug pharmacology.
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Affiliation(s)
- Revati Wani
- Oncology Research Unit, Pfizer Worldwide Research and Development San Diego, CA, USA
| | - Asako Nagata
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development San Diego, CA, USA
| | - Brion W Murray
- Oncology Research Unit, Pfizer Worldwide Research and Development San Diego, CA, USA
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12
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Shepherd M, Heras B, Achard MES, King GJ, Argente MP, Kurth F, Taylor SL, Howard MJ, King NP, Schembri MA, McEwan AG. Structural and functional characterization of ScsC, a periplasmic thioredoxin-like protein from Salmonella enterica serovar Typhimurium. Antioxid Redox Signal 2013; 19:1494-506. [PMID: 23642141 PMCID: PMC3797457 DOI: 10.1089/ars.2012.4939] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
AIMS The prototypical protein disulfide bond (Dsb) formation and protein refolding pathways in the bacterial periplasm involving Dsb proteins have been most comprehensively defined in Escherichia coli. However, genomic analysis has revealed several distinct Dsb-like systems in bacteria, including the pathogen Salmonella enterica serovar Typhimurium. This includes the scsABCD locus, which encodes a system that has been shown via genetic analysis to confer copper tolerance, but whose biochemical properties at the protein level are not defined. The aim of this study was to provide functional insights into the soluble ScsC protein through structural, biochemical, and genetic analyses. RESULTS Here we describe the structural and biochemical characterization of ScsC, the soluble DsbA-like component of this system. Our crystal structure of ScsC reveals a similar overall fold to DsbA, although the topology of β-sheets and α-helices in the thioredoxin domains differ. The midpoint reduction potential of the CXXC active site in ScsC was determined to be -132 mV versus normal hydrogen electrode. The reactive site cysteine has a low pKa, typical of the nucleophilic cysteines found in DsbA-like proteins. Deletion of scsC from S. Typhimurium elicits sensitivity to copper (II) ions, suggesting a potential involvement for ScsC in disulfide folding under conditions of copper stress. INNOVATION AND CONCLUSION ScsC is a novel disulfide oxidoreductase involved in protection against copper ion toxicity.
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Affiliation(s)
- Mark Shepherd
- 1 School of Biosciences, University of Kent , Canterbury, United Kingdom
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13
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Roos G, Foloppe N, Messens J. Understanding the pK(a) of redox cysteines: the key role of hydrogen bonding. Antioxid Redox Signal 2013; 18:94-127. [PMID: 22746677 DOI: 10.1089/ars.2012.4521] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many cellular functions involve cysteine chemistry via thiol-disulfide exchange pathways. The nucleophilic cysteines of the enzymes involved are activated as thiolate. A thiolate is much more reactive than a neutral thiol. Therefore, determining and understanding the pK(a)s of functional cysteines are important aspects of biochemistry and molecular biology with direct implications for redox signaling. Here, we describe the experimental and theoretical methods to determine cysteine pK(a) values, and we examine the factors that control these pK(a)s. Drawing largely on experience gained with the thioredoxin superfamily, we examine the roles of solvation, charge-charge, helix macrodipole, and hydrogen bonding interactions as pK(a)-modulating factors. The contributions of these factors in influencing cysteine pK(a)s and the associated chemistry, including the relevance for the reaction kinetics and thermodynamics, are discussed. This analysis highlights the critical role of direct hydrogen bonding to the cysteine sulfur as a key factor modulating the equilibrium between thiol S-H and thiolate S(-). This role is easily understood intuitively and provides a framework for biochemical functional insights.
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Affiliation(s)
- Goedele Roos
- General Chemistry, Vrije University Brussel, Brussels, Belgium
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14
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Abstract
Grxs (glutaredoxins) are small ubiquitous redox enzymes. They are generally involved in the reduction of oxidative modifications using glutathione. Grxs are not only able to reduce protein disulfides and the low-molecular-mass antioxidant dehydroascorbate, but also represent the major enzyme class responsible for deglutathionylation reactions. Functional proteomics, including interaction studies, comparative activity measurements using heterologous proteins and structural analysis are combined to provide important insights into the crucial function of Grxs in cellular redox networks. Summarizing the current understanding of Grxs, with a special focus on organelle-localized members across species, genus and kingdom boundaries (including cyanobacteria, plants, bacteria, yeast and humans) lead to two different classifications, one according to sequence structure that gives insights into the diversification of Grxs, and another according to function within the cell that provides a basis for assessing the different roles of Grxs.
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15
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Kurdrid P, Phuengcharoen P, Yutthanasirikul R, Roytrakul S, Paemanee A, Cheevadhanarak S, Hongsthong A. Identification of regulatory regions and regulatory protein complexes of the Spirulina desD gene under temperature stress conditions: role of thioredoxin as an inactivator of a transcriptional repressor GntR under low-temperature stress. Biochem Cell Biol 2012; 90:621-35. [PMID: 22788703 DOI: 10.1139/o2012-017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In the present study, electrophoretic mobility shift assays were used to identify temperature responsive elements in the 5' upstream region (5' UTR) of the Spirulina desD gene. Overlapping, synthetic oligonucleotides of both sense and anti-sense strands that spanned the entire 5' UTR of the gene were analyzed. The responsive DNA-binding protein complexes were identified using liquid chromatography-tandem mass spectrometry. The results indicated that the cold-responsive elements were located at -453 to -247, -197 to -151, -105 to -76, and -50 to -1, whereas the low-temperature specific regulatory regions were located at -372 to -352. Moreover, the heat-responsive elements were located at -347 to -243, -197 to -151, and -124 to -1, whereas the high-temperature specific elements were located between -130 to -101 and -30 to -1. In terms of regulatory protein complexes under the two stress conditions, Trx was only detected in the low-temperature responsive protein complex, and divalent cations were essential for the binding of the protein complex to the regulatory elements. Furthermore, Trx was shown to play a critical role as a reducing agent that inactivates the Spirulina desD repressor, GntR. Consequently, the desD gene expression is induced under the low-temperature condition.
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Affiliation(s)
- Pavinee Kurdrid
- Biochemical Engineering and Pilot Plant Research and Development Unit, National Center for Genetic Engineering and Biotechnology, King Mongkut's University of Technology-Thonburi (Bangkhuntien), 49 Soi Theintalay 25, Thakham, Bangkhuntien, Bangkok 10150, Thailand
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16
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Scarafone N, Pain C, Fratamico A, Gaspard G, Yilmaz N, Filée P, Galleni M, Matagne A, Dumoulin M. Amyloid-like fibril formation by polyQ proteins: a critical balance between the polyQ length and the constraints imposed by the host protein. PLoS One 2012; 7:e31253. [PMID: 22438863 PMCID: PMC3305072 DOI: 10.1371/journal.pone.0031253] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 01/05/2012] [Indexed: 11/18/2022] Open
Abstract
Nine neurodegenerative disorders, called polyglutamine (polyQ) diseases, are characterized by the formation of intranuclear amyloid-like aggregates by nine proteins containing a polyQ tract above a threshold length. These insoluble aggregates and/or some of their soluble precursors are thought to play a role in the pathogenesis. The mechanism by which polyQ expansions trigger the aggregation of the relevant proteins remains, however, unclear. In this work, polyQ tracts of different lengths were inserted into a solvent-exposed loop of the β-lactamase BlaP and the effects of these insertions on the properties of BlaP were investigated by a range of biophysical techniques. The insertion of up to 79 glutamines does not modify the structure of BlaP; it does, however, significantly destabilize the enzyme. The extent of destabilization is largely independent of the polyQ length, allowing us to study independently the effects intrinsic to the polyQ length and those related to the structural integrity of BlaP on the aggregating properties of the chimeras. Only chimeras with 55Q and 79Q readily form amyloid-like fibrils; therefore, similarly to the proteins associated with diseases, there is a threshold number of glutamines above which the chimeras aggregate into amyloid-like fibrils. Most importantly, the chimera containing 79Q forms amyloid-like fibrils at the same rate whether BlaP is folded or not, whereas the 55Q chimera aggregates into amyloid-like fibrils only if BlaP is unfolded. The threshold value for amyloid-like fibril formation depends, therefore, on the structural integrity of the β-lactamase moiety and thus on the steric and/or conformational constraints applied to the polyQ tract. These constraints have, however, no significant effect on the propensity of the 79Q tract to trigger fibril formation. These results suggest that the influence of the protein context on the aggregating properties of polyQ disease-associated proteins could be negligible when the latter contain particularly long polyQ tracts.
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Affiliation(s)
- Natacha Scarafone
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Coralie Pain
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Anthony Fratamico
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Gilles Gaspard
- Biological Macromolecules, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Nursel Yilmaz
- Biological Macromolecules, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Patrice Filée
- Biological Macromolecules, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Moreno Galleni
- Biological Macromolecules, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Mireille Dumoulin
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
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17
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Marino SM, Gladyshev VN. Analysis and functional prediction of reactive cysteine residues. J Biol Chem 2011; 287:4419-25. [PMID: 22157013 DOI: 10.1074/jbc.r111.275578] [Citation(s) in RCA: 198] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Cys is much different from other common amino acids in proteins. Being one of the least abundant residues, Cys is often observed in functional sites in proteins. This residue is reactive, polarizable, and redox-active; has high affinity for metals; and is particularly responsive to the local environment. A better understanding of the basic properties of Cys is essential for interpretation of high-throughput data sets and for prediction and classification of functional Cys residues. We provide an overview of approaches used to study Cys residues, from methods for investigation of their basic properties, such as exposure and pK(a), to algorithms for functional prediction of different types of Cys in proteins.
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Affiliation(s)
- Stefano M Marino
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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18
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Reeves SA, Parsonage D, Nelson KJ, Poole LB. Kinetic and thermodynamic features reveal that Escherichia coli BCP is an unusually versatile peroxiredoxin. Biochemistry 2011; 50:8970-81. [PMID: 21910476 DOI: 10.1021/bi200935d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In Escherichia coli, bacterioferritin comigratory protein (BCP) is a peroxiredoxin (Prx) that catalyzes the reduction of H(2)O(2) and organic hydroperoxides. This protein, along with plant PrxQ, is a founding member of one of the least studied subfamilies of Prxs. Recent structural data have suggested that proteins in the BCP/PrxQ group can exist as monomers or dimers; we report here that, by analytical ultracentrifugation, both oxidized and reduced E. coli BCP behave as monomers in solution at concentrations as high as 200 μM. Unexpectedly, thioredoxin (Trx1)-dependent peroxidase assays conducted by stopped-flow spectroscopy demonstrated that V(max,app) increases with increasing Trx1 concentrations, indicating a nonsaturable interaction (K(m) > 100 μM). At a physiologically reasonable Trx1 concentration of 10 μM, the apparent K(m) value for H(2)O(2) is ~80 μM, and overall, the V(max)/K(m) for H(2)O(2), which remains constant at the various Trx1 concentrations (consistent with a ping-pong mechanism), is ~1.3 × 10(4) M(-1) s(-1). Our kinetic analyses demonstrated that BCP can utilize a variety of reducing substrates, including Trx1, Trx2, Grx1, and Grx3. BCP exhibited a high redox potential of -145.9 ± 3.2 mV, the highest to date observed for a Prx. Moreover, BCP exhibited a broad peroxide specificity, with comparable rates for H(2)O(2) and cumene hydroperoxide. We determined a pK(a) of ~5.8 for the peroxidatic cysteine (Cys45) using both spectroscopic and activity titration data. These findings support an important role for BCP in interacting with multiple substrates and remaining active under highly oxidizing cellular conditions, potentially serving as a defense enzyme of last resort.
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Affiliation(s)
- Stacy A Reeves
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
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19
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Jacob C, Kriznik A, Boschi-Muller S, Branlant G. Thioredoxin 2 from Escherichia coli is not involved in vivo in the recycling process of methionine sulfoxide reductase activities. FEBS Lett 2011; 585:1905-9. [PMID: 21570393 DOI: 10.1016/j.febslet.2011.04.070] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/22/2011] [Accepted: 04/26/2011] [Indexed: 11/17/2022]
Abstract
Thioredoxins (Trx) 1 and 2, and three methionine sulfoxide reductases (Msr) whose activities are Trx-dependent, are expressed in Escherichia coli. A metB(1)trxA mutant was shown to be unable to grow on methionine sulfoxide (Met-O) suggesting that Trx2 is not essential in the Msr-recycling process. In the present study, we have determined the kinetic parameters of the recycling process of the three Msrs by Trx2 and the in vivo expression of Trx2 in a metB(1)trxA mutant. The data demonstrate that the lack of growth of the metB(1)trxA mutant on Met-O is due to low in vivo expression of Trx2 and not to the lower catalytic efficiency of Msrs for Trx2.
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Affiliation(s)
- Christophe Jacob
- Nancy-Université-Université Henri Poincaré, UMR CNRS-UHP 7214, ARN-RNP, Enzymologie Moléculaire et Structurale, Nancy Université, Faculté des Sciences et Technologies, Vandoeuvre-lès-Nancy, France
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20
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Abstract
Thioredoxins are ubiquitous antioxidant enzymes that play important roles in many health-related cellular processes. As such, the fundamental knowledge of how these enzymes work is of prime importance for understanding cellular redox mechanisms and for laying the ground for the development of future therapeutic approaches. Over the past 40 years, a really impressive amount of data has been published on thioredoxins. Here, we review the most significant results that have contributed to our knowledge regarding the structure, the function, and the mechanism of these crucial enzymes.
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21
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Mutational analysis of VIM-2 reveals an essential determinant for metallo-beta-lactamase stability and folding. Antimicrob Agents Chemother 2010; 54:3197-204. [PMID: 20498317 DOI: 10.1128/aac.01336-09] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Metallo-beta-lactamase (MBL)-producing bacteria are emerging worldwide and represent a formidable threat to the efficacy of relevant beta-lactams, including carbapenems, expanded-spectrum cephalosporins, and beta-lactamase inactivator/beta-lactam combinations. VIM-2 is currently the most widespread MBL and represents a primary target for MBL inhibitor research, the clinical need for which is expected to further increase in the future. Using a saturation mutagenesis approach, we probed the importance of four residues (Phe-61, Ala-64, Tyr-67, and Trp-87) located close to the VIM-2 active site and putatively relevant to the enzyme activity based on structural knowledge of the enzyme and on structure-activity relationships of the subclass B1 MBLs. The ampicillin MIC values shown by the various mutants were affected very differently depending on the randomized amino acid position. Position 64 appeared to be rather tolerant to substitution, and kinetic studies showed that the A64W mutation did not significantly affect substrate hydrolysis or binding, representing an important difference from IMP-type enzymes. Phe-61 and Tyr-67 could be replaced with several amino acids without the ampicillin MIC being significantly affected, but in contrast, Trp-87 was found to be critical for ampicillin resistance. Further kinetic and biochemical analyses of W87A and W87F variants showed that this residue is apparently important for the structure and proper folding of the enzyme but, surprisingly, not for its catalytic activity. These data support the critical role of residue 87 in the stability and folding of VIM-2 and might have strong implications for MBL inhibitor design, as this residue would represent an ideal target for interaction with small molecules.
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Wouters MA, Fan SW, Haworth NL. Disulfides as redox switches: from molecular mechanisms to functional significance. Antioxid Redox Signal 2010; 12:53-91. [PMID: 19634988 DOI: 10.1089/ars.2009.2510] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The molecular mechanisms underlying thiol-based redox control are poorly defined. Disulfide bonds between Cys residues are commonly thought to confer extra rigidity and stability to their resident protein, forming a type of proteinaceous spot weld. Redox biologists have been redefining the role of disulfides over the last 30-40 years. Disulfides are now known to form in the cytosol under conditions of oxidative stress. Isomerization of extracellular disulfides is also emerging as an important regulator of protein function. The current paradigm is that the disulfide proteome consists of two subproteomes: a structural group and a redox-sensitive group. The redox-sensitive group is less stable and often associated with regions of stress in protein structures. Some characterized redox-active disulfides are the helical CXXC motif, often associated with thioredoxin-fold proteins; and forbidden disulfides, a group of metastable disulfides that disobey elucidated rules of protein stereochemistry. Here we discuss the role of redox-active disulfides as switches in proteins.
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Affiliation(s)
- Merridee A Wouters
- Structural & Computational Biology Division, Victor Chang Cardiac Research Institute, Sydney, Australia.
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23
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Ma Z, Jacobsen FE, Giedroc DP. Coordination chemistry of bacterial metal transport and sensing. Chem Rev 2009; 109:4644-81. [PMID: 19788177 PMCID: PMC2783614 DOI: 10.1021/cr900077w] [Citation(s) in RCA: 433] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zhen Ma
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128 USA
| | - Faith E. Jacobsen
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
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24
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Abstract
The dissociation mechanism of the thioredoxin (Trx) mixed disulfide complexes is unknown and has been debated for more than twenty years. Specifically, opposing arguments for the activation of the nucleophilic cysteine as a thiolate during the dissociation of the complex have been put forward. As a key model, the complex between Trx and its endogenous substrate, arsenate reductase (ArsC), was used. In this structure, a Cys29Trx-Cys89ArsC intermediate disulfide is formed by the nucleophilic attack of Cys29Trx on the exposed Cys82ArsC-Cys89ArsC in oxidized ArsC. With theoretical reactivity analysis, molecular dynamics simulations, and biochemical complex formation experiments with Cys-mutants, Trx mixed disulfide dissociation was studied. We observed that the conformational changes around the intermediate disulfide bring Cys32Trx in contact with Cys29Trx. Cys32Trx is activated for its nucleophilic attack by hydrogen bonds, and Cys32Trx is found to be more reactive than Cys82ArsC. Additionally, Cys32Trx directs its nucleophilic attack on the more susceptible Cys29Trx and not on Cys89ArsC. This multidisciplinary approach provides fresh insights into a universal thiol/disulfide exchange reaction mechanism that results in reduced substrate and oxidized Trx. Thioredoxins are found in all types of cells and control several essential functions of life, including promotion of cell growth, inhibition of apoptosis, and modulation of inflammation. Thioredoxin has two ‘free’ cysteines in its active site, which are used to break disulfide bonds in oxidized substrate proteins. In the first step, an intermediate thioredoxin-protein complex is formed, which is broken in the second step, releasing the substrate protein in its reduced state. In other words, the disulfide is being transferred from the substrate protein to thioredoxin, or the electrons coming from thioredoxin are shuttled to the protein substrate. The exact reaction mechanism, i.e., the detailed succession of steps in which the reaction takes place, of how this mixed disulfide is broken is not known and has been debated over the last twenty years. With a multidisciplinary approach, combining computational and experimental work, we provide fresh insights into how conformational changes activate the catalytic cysteines with which this universal reduction mechanism is completed with the correct regioselectivity. This work illustrates the strengths of computational approaches in probing phenomena which are otherwise very difficult to investigate experimentally.
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