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Vasileva ID, Samgina TY, Meng Z, Zubarev RA, Lebedev AT. EThcD Benefits for the Sequencing Inside Intramolecular Disulfide Cycles of Amphibian Intact Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1979-1988. [PMID: 37525119 DOI: 10.1021/jasms.3c00127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Disulfide bonds formed by a pair of cysteine residues in the peptides' backbone represent a certain problem for their sequencing by means of mass spectrometry. As a rule, in proteomics, disulfide bonds should be cleaved before the analysis followed by some sort of chemical derivatization. That step is time-consuming and may lead to losses of minor peptides of the analyzed mixtures due to incomplete reaction, adsorption on the walls of the vials, etc. Certain problems in the de novo top-down sequencing of amphibian skin peptides are caused by the C-terminal disulfide loop, called the Rana box. Its reduction with or without subsequent derivatization was considered to be an unavoidable step before mass spectrometry. In the present study, EThcD demonstrated its efficiency in sequencing intact disulfide-containing peptides without any preliminary derivatization. Applied to the secretion of three frog species, EThcD provided the full sequence inside the intramolecular disulfide cycle for all S-S-containing peptides found in the samples, with the only exception being diarginine species. Proteolytic fragments, which are shorter than the original peptides, were helpful in some cases. HCD should be mentioned as a complementary tool to the EThcD tool, being useful as a confirmation method for some sequence details.
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Affiliation(s)
- Irina D Vasileva
- Lomonosov Moscow State University, Department of Organic Chemistry, 119991 Moscow, Russia
| | - Tatiana Yu Samgina
- Lomonosov Moscow State University, Department of Organic Chemistry, 119991 Moscow, Russia
| | - Zhaowei Meng
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Roman A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Albert T Lebedev
- Lomonosov Moscow State University, Department of Organic Chemistry, 119991 Moscow, Russia
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2
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Estrada P, Bañares-Hidalgo Á, Pérez-Gil J. Disulfide bonds in the SAPA domain of the pulmonary surfactant protein B precursor. J Proteomics 2022; 269:104722. [PMID: 36108905 DOI: 10.1016/j.jprot.2022.104722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
The disulfide bonds formed in the SAPA domain of a recombinant version of the NH2-terminal propeptide (SP-BN) from the precursor of human pulmonary surfactant protein B (SP-B) were identified through sequential digestion of SP-BN with GluC/trypsin or thermolysin/GluC, followed by mass spectrometry (MS) analysis. MS spectra allowed identification of disulfide bonds between Cys32-Cys49 and Cys40-Cys55, and we propose a disulfide connectivity pattern of 1-3 and 2-4 within the SAPA domain, with the Cys residues numbered according to their position from the N-terminus of the propeptide sequence. The peaks with m/z ∼ 2136 and ∼ 1780 in the MS spectrum of the GluC/trypsin digest were assigned to peptides 24AWTTSSLACAQGPE37 and 45QALQCR50 linked by Cys32-Cys49 and 38FWCQSLE44 and 51ALGHCLQE58 linked by Cys40-Cys55 respectively. Tandem mass spectrometry (MS/MS) analysis verified the position of the bonds. The results of the series ions, immonium ions and internal fragment ions were all compatible with the proposed 1-3/2-4 position of the disulfide bonds in the SAPA domain. This X-pattern differs from the kringle-type found in the SAPB domain of the SAPLIP proteins, where the first Cys in the sequence links to the last, the second to the penultimate and the third to the fourth one. Regarding the SAPB domain of the SP-BN propeptide, the MS analysis of both digests identified the bond Cys100-Cys112, numbered 7-8, which is coincident with the bond position in the kringle motif. SIGNIFICANCE: The SAPLIP (saposin-like proteins) family encompasses several proteins with homology to saposins (sphingolipids activator proteins). These are proteins with mainly alpha-helical folds, compact packing including well conserved disulfide bonds and ability to interact with phospholipids and membranes. There are two types of saposin-like domains termed as Saposin A (SAPA) and Saposin B (SAPB) domains. While disulfide connectivity has been well established in several SAPB domains, the position of disulfide bonds in SAPA domains is still unknown. The present study approaches a detailed proteomic study to determine disulfide connectivity in the SAPA domain of the precursor of human pulmonary surfactant-associated protein SP-B. This task has been a challenge requiring the combination of different sequential proteolytic treatments followed by MS analysis including MALDI-TOF and tandem mass MS/MS spectrometry. The determination for first time of the position of disulfide bonds in SAPA domains is an important step to understand the structural determinants defining its biological functions.
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Affiliation(s)
- Pilar Estrada
- Dept. Biochemistry and Molecular Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Ángeles Bañares-Hidalgo
- Dept. Biochemistry and Molecular Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Jesús Pérez-Gil
- Dept. Biochemistry and Molecular Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain.
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3
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Renzone G, Arena S, Scaloni A. Cross-linking reactions in food proteins and proteomic approaches for their detection. MASS SPECTROMETRY REVIEWS 2022; 41:861-898. [PMID: 34250627 DOI: 10.1002/mas.21717] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Various protein cross-linking reactions leading to molecular polymerization and covalent aggregates have been described in processed foods. They are an undesired side effect of processes designed to reduce bacterial load, extend shelf life, and modify technological properties, as well as being an expected result of treatments designed to modify raw material texture and function. Although the formation of these products is known to affect the sensory and technological properties of foods, the corresponding cross-linking reactions and resulting protein polymers have not yet undergone detailed molecular characterization. This is essential for describing how their generation can be related to food processing conditions and quality parameters. Due to the complex structure of cross-linked species, bottom-up proteomic procedures developed to characterize various amino acid modifications associated with food processing conditions currently offer a limited molecular description of bridged peptide structures. Recent progress in cross-linking mass spectrometry for the topological characterization of protein complexes has facilitated the development of various proteomic methods and bioinformatic tools for unveiling bridged species, which can now also be used for the detailed molecular characterization of polymeric cross-linked products in processed foods. We here examine their benefits and limitations in terms of evaluating cross-linked food proteins and propose future scenarios for application in foodomics. They offer potential for understanding the protein cross-linking formation mechanisms in processed foods, and how the inherent beneficial properties of treated foodstuffs can be preserved or enhanced.
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Affiliation(s)
- Giovanni Renzone
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Simona Arena
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
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4
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Stepwise oxidations play key roles in the structural and functional regulations of DJ-1. Biochem J 2021; 478:3505-3525. [PMID: 34515295 DOI: 10.1042/bcj20210245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 01/03/2023]
Abstract
DJ-1 is known to play neuroprotective roles by eliminating reactive oxygen species (ROS) as an antioxidant protein. However, the molecular mechanism of DJ-1 function has not been well elucidated. This study explored the structural and functional changes of DJ-1 in response to oxidative stress. Human DJ-1 has three cysteine residues (Cys46, Cys53 and Cys106). We found that, in addition to Cys106, Cys46 is the most reactive cysteine residue in DJ-1, which was identified employing an NPSB-B chemical probe (Ctag) that selectively reacts with redox-sensitive cysteine sulfhydryl. Peroxidatic Cys46 readily formed an intra-disulfide bond with adjacent resolving Cys53, which was identified with nanoUPLC-ESI-q-TOF tandem mass spectrometry (MS/MS) employing DBond algorithm under the non-reducing condition. Mutants (C46A and C53A), not forming Cys46-Cys53 disulfide cross-linking, increased oxidation of Cys106 to sulfinic and sulfonic acids. Furthermore, we found that DJ-1 C46A mutant has distorted unstable structure identified by biochemical assay and employing hydrogen/deuterium exchange-mass spectrometry (HDX-MS) analysis. All three Cys mutants lost antioxidant activities in SN4741 cell, a dopaminergic neuronal cell, unlike WT DJ-1. These findings suggest that all three Cys residues including Cys46-Cys53 disulfide cross-linking are required for maintaining the structural integrity, the regulation process and cellular function as an antioxidant protein. These studies broaden the understanding of regulatory mechanisms of DJ-1 that operate under oxidative conditions.
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5
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Activation of Nm23-H1 to suppress breast cancer metastasis via redox regulation. Exp Mol Med 2021; 53:346-357. [PMID: 33753879 PMCID: PMC8080780 DOI: 10.1038/s12276-021-00575-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/21/2020] [Accepted: 01/12/2021] [Indexed: 02/05/2023] Open
Abstract
Non-metastatic protein 23 H1 (Nm23-H1), a housekeeping enzyme, is a nucleoside diphosphate kinase-A (NDPK-A). It was the first identified metastasis suppressor protein. Nm23-H1 prolongs disease-free survival and is associated with a good prognosis in breast cancer patients. However, the molecular mechanisms underlying the role of Nm23-H1 in biological processes are still not well understood. This is a review of recent studies focusing on controlling NDPK activity based on the redox regulation of Nm23-H1, structural, and functional changes associated with the oxidation of cysteine residues, and the relationship between NDPK activity and cancer metastasis. Further understanding of the redox regulation of the NDPK function will likely provide a new perspective for developing new strategies for the activation of NDPK-A in suppressing cancer metastasis.
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6
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Kalinski JCJ, Krause RWM, Parker-Nance S, Waterworth SC, Dorrington RA. Unlocking the Diversity of Pyrroloiminoquinones Produced by Latrunculid Sponge Species. Mar Drugs 2021; 19:md19020068. [PMID: 33525412 PMCID: PMC7912287 DOI: 10.3390/md19020068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 12/28/2022] Open
Abstract
Sponges of the Latrunculiidae family produce bioactive pyrroloiminoquinone alkaloids including makaluvamines, discorhabdins, and tsitsikammamines. The aim of this study was to use LC-ESI-MS/MS-driven molecular networking to characterize the pyrroloiminoquinone secondary metabolites produced by six latrunculid species. These are Tsitsikamma favus, Tsitsikamma pedunculata, Cyclacanthia bellae, and Latrunculia apicalis as well as the recently discovered species, Tsitsikamma nguni and Tsitsikamma michaeli. Organic extracts of 43 sponges were analyzed, revealing distinct species-specific chemical profiles. More than 200 known and unknown putative pyrroloiminoquinones and related compounds were detected, including unprecedented makaluvamine-discorhabdin adducts and hydroxylated discorhabdin I derivatives. The chemical profiles of the new species T. nguni closely resembled those of the known T. favus (chemotype I), but with a higher abundance of tsitsikammamines vs. discorhabdins. T. michaeli sponges displayed two distinct chemical profiles, either producing mostly the same discorhabdins as T. favus (chemotype I) or non- or monobrominated, hydroxylated discorhabdins. C. bellae and L. apicalis produced similar pyrroloiminoquinone chemistry to one another, characterized by sulfur-containing discorhabdins and related adducts and oligomers. This study highlights the variability of pyrroloiminoquinone production by latrunculid species, identifies novel isolation targets, and offers fundamental insights into the collision-induced dissociation of pyrroloiminoquinones.
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Affiliation(s)
- Jarmo-Charles J. Kalinski
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140, South Africa; (J.-C.J.K.); (S.P.-N.); (S.C.W.)
| | - Rui W. M. Krause
- Department of Chemistry, Rhodes University, Makhanda 6140, South Africa;
| | - Shirley Parker-Nance
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140, South Africa; (J.-C.J.K.); (S.P.-N.); (S.C.W.)
- South African Environmental Observation Network, Elwandle Coastal Node, Port Elizabeth 6001, South Africa
- South African Institute for Aquatic Biodiversity, Makhanda 6140, South Africa
| | - Samantha C. Waterworth
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140, South Africa; (J.-C.J.K.); (S.P.-N.); (S.C.W.)
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, WI 53705, USA
| | - Rosemary A. Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140, South Africa; (J.-C.J.K.); (S.P.-N.); (S.C.W.)
- South African Institute for Aquatic Biodiversity, Makhanda 6140, South Africa
- Correspondence:
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7
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Na S, Paek E. Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions. Comput Struct Biotechnol J 2020; 18:1391-1402. [PMID: 32637038 PMCID: PMC7322682 DOI: 10.1016/j.csbj.2020.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 12/28/2022] Open
Abstract
Mass spectrometry (MS) has made enormous contributions to comprehensive protein identification and quantification in proteomics. MS is also gaining momentum for structural biology in a variety of ways, complementing conventional structural biology techniques. Here, we will review how MS-based techniques, such as hydrogen/deuterium exchange, covalent labeling, and chemical cross-linking, enable the characterization of protein structure, dynamics, and interactions, especially from a perspective of their data analyses. Structural information encoded by chemical probes in intact proteins is decoded by interpreting MS data at a peptide level, i.e., revealing conformational and dynamic changes in local regions of proteins. The structural MS data are not amenable to data analyses in traditional proteomics workflow, requiring dedicated software for each type of data. We first provide basic principles of data interpretation, including isotopic distribution and peptide sequencing. We then focus particularly on computational methods for structural MS data analyses and discuss outstanding challenges in a proteome-wide large scale analysis.
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Affiliation(s)
- Seungjin Na
- Dept. of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Eunok Paek
- Dept. of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
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8
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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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9
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Matsui R, Ferran B, Oh A, Croteau D, Shao D, Han J, Pimentel DR, Bachschmid MM. Redox Regulation via Glutaredoxin-1 and Protein S-Glutathionylation. Antioxid Redox Signal 2020; 32:677-700. [PMID: 31813265 PMCID: PMC7047114 DOI: 10.1089/ars.2019.7963] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Significance: Over the past several years, oxidative post-translational modifications of protein cysteines have been recognized for their critical roles in physiology and pathophysiology. Cells have harnessed thiol modifications involving both oxidative and reductive steps for signaling and protein processing. One of these stages requires oxidation of cysteine to sulfenic acid, followed by two reduction reactions. First, glutathione (reduced glutathione [GSH]) forms a S-glutathionylated protein, and second, enzymatic or chemical reduction removes the modification. Under physiological conditions, these steps confer redox signaling and protect cysteines from irreversible oxidation. However, oxidative stress can overwhelm protein S-glutathionylation and irreversibly modify cysteine residues, disrupting redox signaling. Critical Issues: Glutaredoxins mainly catalyze the removal of protein-bound GSH and help maintain protein thiols in a highly reduced state without exerting direct antioxidant properties. Conversely, glutathione S-transferase (GST), peroxiredoxins, and occasionally glutaredoxins can also catalyze protein S-glutathionylation, thus promoting a dynamic redox environment. Recent Advances: The latest studies of glutaredoxin-1 (Glrx) transgenic or knockout mice demonstrate important distinct roles of Glrx in a variety of pathologies. Endogenous Glrx is essential to maintain normal hepatic lipid homeostasis and prevent fatty liver disease. Further, in vivo deletion of Glrx protects lungs from inflammation and bacterial pneumonia-induced damage, attenuates angiotensin II-induced cardiovascular hypertrophy, and improves ischemic limb vascularization. Meanwhile, exogenous Glrx administration can reverse pathological lung fibrosis. Future Directions: Although S-glutathionylation modifies many proteins, these studies suggest that S-glutathionylation and Glrx regulate specific pathways in vivo, and they implicate Glrx as a potential novel therapeutic target to treat diverse disease conditions. Antioxid. Redox Signal. 32, 677-700.
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Affiliation(s)
- Reiko Matsui
- Vascular Biology Section, Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, Massachusetts
| | - Beatriz Ferran
- Vascular Biology Section, Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, Massachusetts
| | - Albin Oh
- Cardiology, Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, Massachusetts
| | - Dominique Croteau
- Cardiology, Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, Massachusetts
| | - Di Shao
- Helens Clinical Research Center, Chongqing, China
| | - Jingyan Han
- Vascular Biology Section, Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, Massachusetts
| | - David Richard Pimentel
- Cardiology, Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, Massachusetts
| | - Markus Michael Bachschmid
- Vascular Biology Section, Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, Massachusetts
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10
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Bifunctional Chloroplastic DJ-1B from Arabidopsis thaliana is an Oxidation-Robust Holdase and a Glyoxalase Sensitive to H₂O₂. Antioxidants (Basel) 2019; 8:antiox8010008. [PMID: 30609642 PMCID: PMC6356872 DOI: 10.3390/antiox8010008] [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] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 12/15/2018] [Accepted: 12/22/2018] [Indexed: 01/04/2023] Open
Abstract
Members of the DJ-1 protein family are multifunctional enzymes whose loss increases the susceptibility of the cell to oxidative stress. However, little is known about the function of the plant DJ-1 homologs. Therefore, we analyzed the effect of oxidation on the structure and function of chloroplastic AtDJ-1B and studied the phenotype of T-DNA lines lacking the protein. In vitro oxidation of AtDJ-1B with H₂O₂ lowers its glyoxalase activity, but has no effect on its holdase chaperone function. Remarkably, upon oxidation, the thermostability of AtDJ-1B increases with no significant alteration of the overall secondary structure. Moreover, we found that AtDJ-1B transcript levels are invariable, and loss of AtDJ-1B does not affect plant viability, growth and stress response. All in all, two discrete functions of AtDJ-1B respond differently to H₂O₂, and AtDJ-1B is not essential for plant development under stress.
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11
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Bonner J, Talbert LE, Akkawi N, Julian RR. Simplified identification of disulfide, trisulfide, and thioether pairs with 213 nm UVPD. Analyst 2018; 143:5176-5184. [PMID: 30264084 PMCID: PMC6197924 DOI: 10.1039/c8an01582a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Disulfide heterogeneity and other non-native crosslinks introduced during therapeutic antibody production and storage could have considerable negative effects on clinical efficacy, but tracking these modifications remains challenging. Analysis must also be carried out cautiously to avoid introduction of disulfide scrambling or reduction, necessitating the use of low pH digestion with less specific proteases. Herein we demonstrate that 213 nm ultraviolet photodissociation streamlines disulfide elucidation through bond-selective dissociation of sulfur-sulfur and carbon-sulfur bonds in combination with less specific backbone dissociation. Importantly, both types of fragmentation can be initiated in a single MS/MS activation stage. In addition to disulfide mapping, it is also shown that thioethers and trisulfides can be identified by characteristic fragmentation patterns. The photochemistry resulting from 213 nm excitation facilitates a simplified, two-tiered data processing approach that allows observation of all native disulfide bonds, scrambled disulfide bonds, and non-native sulfur-based linkages in a pepsin digest of Rituximab. Native disulfides represented the majority of bonds according to ion count, but the highly solvent-exposed heavy/light interchain disulfides were found to be most prone to modification. Production and storage methods that facilitate non-native links are discussed. Due to the importance of heavy and light chain connectivity for antibody structure and function, this region likely requires particular attention in terms of its influence on maintaining structural fidelity.
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Affiliation(s)
- James Bonner
- Department of Chemistry, University of California, Riverside, California 92521, USA.
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12
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Huang J, Niazi AK, Young D, Rosado LA, Vertommen D, Bodra N, Abdelgawwad MR, Vignols F, Wei B, Wahni K, Bashandy T, Bariat L, Van Breusegem F, Messens J, Reichheld JP. Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3491-3505. [PMID: 29194485 DOI: 10.1093/jxb/erx396] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/10/2017] [Indexed: 05/20/2023]
Abstract
Plant malate dehydrogenase (MDH) isoforms are found in different cell compartments and function in key metabolic pathways. It is well known that the chloroplastic NADP-dependent MDH activities are strictly redox regulated and controlled by light. However, redox dependence of other NAD-dependent MDH isoforms have been less studied. Here, we show by in vitro biochemical characterization that the major cytosolic MDH isoform (cytMDH1) is sensitive to H2O2 through sulfur oxidation of cysteines and methionines. CytMDH1 oxidation affects the kinetics, secondary structure, and thermodynamic stability of cytMDH1. Moreover, MS analyses and comparison of crystal structures between the reduced and H2O2-treated cytMDH1 further show that thioredoxin-reversible homodimerization of cytMDH1 through Cys330 disulfide formation protects the protein from overoxidation. Consistently, we found that cytosolic thioredoxins interact specifically with cytMDH in a yeast two-hybrid system. Importantly, we also show that cytosolic and chloroplastic, but not mitochondrial NAD-MDH activities are sensitive to H2O2 stress in Arabidopsis. NAD-MDH activities decreased both in a catalase2 mutant and in an NADP-thioredoxin reductase mutant, emphasizing the importance of the thioredoxin-reducing system to protect MDH from oxidation in vivo. We propose that the redox switch of the MDH activity contributes to adapt the cell metabolism to environmental constraints.
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Affiliation(s)
- Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Brussels Center for Redox Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Adnan Khan Niazi
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France
| | - David Young
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Brussels Center for Redox Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Leonardo Astolfi Rosado
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Brussels Center for Redox Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Nandita Bodra
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Brussels Center for Redox Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mohamed Ragab Abdelgawwad
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France
| | - Florence Vignols
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France
| | - Bo Wei
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Brussels Center for Redox Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Khadija Wahni
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Brussels Center for Redox Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Talaat Bashandy
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France
| | - Laetitia Bariat
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Brussels Center for Redox Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France
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13
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Mapping disulfide bonds from sub-micrograms of purified proteins or micrograms of complex protein mixtures. BIOPHYSICS REPORTS 2018; 4:68-81. [PMID: 29756007 PMCID: PMC5937861 DOI: 10.1007/s41048-018-0050-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 03/08/2018] [Indexed: 11/16/2022] Open
Abstract
Disulfide bonds are vital for protein functions, but locating the linkage sites has been a challenge in protein chemistry, especially when the quantity of a sample is small or the complexity is high. In 2015, our laboratory developed a sensitive and efficient method for mapping protein disulfide bonds from simple or complex samples (Lu et al. in Nat Methods 12:329, 2015). This method is based on liquid chromatography–mass spectrometry (LC–MS) and a powerful data analysis software tool named pLink. To facilitate application of this method, we present step-by-step disulfide mapping protocols for three types of samples—purified proteins in solution, proteins in SDS-PAGE gels, and complex protein mixtures in solution. The minimum amount of protein required for this method can be as low as several hundred nanograms for purified proteins, or tens of micrograms for a mixture of hundreds of proteins. The entire workflow—from sample preparation to LC–MS and data analysis—is described in great detail. We believe that this protocol can be easily implemented in any laboratory with access to a fast-scanning, high-resolution, and accurate-mass LC–MS system.
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14
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Hirata T, Mishra SK, Nakamura S, Saito K, Motooka D, Takada Y, Kanzawa N, Murakami Y, Maeda Y, Fujita M, Yamaguchi Y, Kinoshita T. Identification of a Golgi GPI-N-acetylgalactosamine transferase with tandem transmembrane regions in the catalytic domain. Nat Commun 2018; 9:405. [PMID: 29374258 PMCID: PMC5785973 DOI: 10.1038/s41467-017-02799-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/28/2017] [Indexed: 12/31/2022] Open
Abstract
Many eukaryotic proteins are anchored to the cell surface via the glycolipid glycosylphosphatidylinositol (GPI). Mammalian GPIs have a conserved core but exhibit diverse N-acetylgalactosamine (GalNAc) modifications, which are added via a yet unresolved process. Here we identify the Golgi-resident GPI-GalNAc transferase PGAP4 and show by mass spectrometry that PGAP4 knockout cells lose GPI-GalNAc structures. Furthermore, we demonstrate that PGAP4, in contrast to known Golgi glycosyltransferases, is not a single-pass membrane protein but contains three transmembrane domains, including a tandem transmembrane domain insertion into its glycosyltransferase-A fold as indicated by comparative modeling. Mutational analysis reveals a catalytic site, a DXD-like motif for UDP-GalNAc donor binding, and several residues potentially involved in acceptor binding. We suggest that a juxtamembrane region of PGAP4 accommodates various GPI-anchored proteins, presenting their acceptor residue toward the catalytic center. In summary, we present insights into the structure of PGAP4 and elucidate the initial step of GPI-GalNAc biosynthesis.
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Affiliation(s)
- Tetsuya Hirata
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Sushil K Mishra
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, Wako, Saitama, 351-0198, Japan
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazunobu Saito
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yoko Takada
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Noriyuki Kanzawa
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yoshiko Murakami
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yusuke Maeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, Wako, Saitama, 351-0198, Japan
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan.
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15
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Lakbub JC, Shipman JT, Desaire H. Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins. Anal Bioanal Chem 2017; 410:2467-2484. [PMID: 29256076 DOI: 10.1007/s00216-017-0772-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/09/2017] [Accepted: 11/17/2017] [Indexed: 12/21/2022]
Abstract
Disulfide bonds are important structural moieties of proteins: they ensure proper folding, provide stability, and ensure proper function. With the increasing use of proteins for biotherapeutics, particularly monoclonal antibodies, which are highly disulfide bonded, it is now important to confirm the correct disulfide bond connectivity and to verify the presence, or absence, of disulfide bond variants in the protein therapeutics. These studies help to ensure safety and efficacy. Hence, disulfide bonds are among the critical quality attributes of proteins that have to be monitored closely during the development of biotherapeutics. However, disulfide bond analysis is challenging because of the complexity of the biomolecules. Mass spectrometry (MS) has been the go-to analytical tool for the characterization of such complex biomolecules, and several methods have been reported to meet the challenging task of mapping disulfide bonds in proteins. In this review, we describe the relevant, recent MS-based techniques and provide important considerations needed for efficient disulfide bond analysis in proteins. The review focuses on methods for proper sample preparation, fragmentation techniques for disulfide bond analysis, recent disulfide bond mapping methods based on the fragmentation techniques, and automated algorithms designed for rapid analysis of disulfide bonds from liquid chromatography-MS/MS data. Researchers involved in method development for protein characterization can use the information herein to facilitate development of new MS-based methods for protein disulfide bond analysis. In addition, individuals characterizing biotherapeutics, especially by disulfide bond mapping in antibodies, can use this review to choose the best strategies for disulfide bond assignment of their biologic products. Graphical Abstract This review, describing characterization methods for disulfide bonds in proteins, focuses on three critical components: sample preparation, mass spectrometry data, and software tools.
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Affiliation(s)
- Jude C Lakbub
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS, 66045, USA
| | - Joshua T Shipman
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS, 66045, USA
| | - Heather Desaire
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS, 66045, USA.
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16
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Liu Y, Sun W, Shan B, Zhang K. DISC: DISulfide linkage Characterization from tandem mass spectra. Bioinformatics 2017; 33:3861-3870. [DOI: 10.1093/bioinformatics/btx667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 10/19/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yi Liu
- Department of Computer Science, The University of Western Ontario, London, ON, Canada
| | - Weiping Sun
- Department of Computer Science, The University of Western Ontario, London, ON, Canada
| | - Baozhen Shan
- Bioinformatics Solutions Inc. (BSI), Waterloo, ON, Canada
| | - Kaizhong Zhang
- Department of Computer Science, The University of Western Ontario, London, ON, Canada
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17
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Tossounian MA, Van Molle I, Wahni K, Jacques S, Gevaert K, Van Breusegem F, Vertommen D, Young D, Rosado LA, Messens J. Disulfide bond formation protects Arabidopsis thaliana glutathione transferase tau 23 from oxidative damage. Biochim Biophys Acta Gen Subj 2017; 1862:775-789. [PMID: 29031766 DOI: 10.1016/j.bbagen.2017.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/04/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Glutathione transferases play an important role as detoxifying enzymes. In A. thaliana, elevated levels of reactive oxygen species (ROS), provoked during biotic and abiotic stress, influence the activity of GSTU23. The aim of this study is to determine the impact of oxidative stress on the function and structure of GSTU23. METHODS The impact of oxidation on the function of GSTU23 was studied using a glutathione transferase biochemical assay and mass spectrometry. With kinetics, circular dichroism and thermodynamics, we compared reduced with oxidized GSTU23. X-ray crystal structures of GSTU23 visualize the impact of oxidation on methionines and cysteines. RESULTS In the presence of 100μM H2O2, oxidation of the methionine side-chain to a sulfoxide is the prominent post-translational modification, which can be reduced by C. diphtheriae MsrA and MsrB. However, increasing the level to 200μM H2O2 results in a reversible intramolecular disulfide between Cys65-Cys110, which is substrate for glutaredoxin. Under these oxidizing conditions, GSTU23 undergoes a structural change and forms a more favourable enzyme-substrate complex to overcome kcat decrease. CONCLUSIONS AND SIGNIFICANCE At lower H2O2 levels (100μM), GSTU23 forms methionine sulfoxides. Specifically, oxidation of Met14, located near the catalytic Ser13, could interfere with both GSH binding and catalytic activation. At higher H2O2 levels (200μM), the Cys65-Cys110 disulfide bond protects other cysteines and also methionines from overoxidation. This study shows the impact of oxidative stress on GSTU23 regulated by methionine sulfoxide reductases and glutaredoxin, and the mechanisms involved in maintaining its catalytic functionality under oxidizing conditions.
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Affiliation(s)
- Maria-Armineh Tossounian
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Inge Van Molle
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Khadija Wahni
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Silke Jacques
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - David Young
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Leonardo Astolfi Rosado
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium.
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18
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Maes E, Dyer JM, McKerchar HJ, Deb-Choudhury S, Clerens S. Protein-protein cross-linking and human health: the challenge of elucidating with mass spectrometry. Expert Rev Proteomics 2017; 14:917-929. [PMID: 28759730 DOI: 10.1080/14789450.2017.1362336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION In several biomedical research fields, the cross-linking of peptides and proteins has an important impact on health and wellbeing. It is therefore of crucial importance to study this class of post-translational modifications in detail. The huge potential of mass spectrometric technologies in the mapping of these protein-protein cross-links is however overshadowed by the challenges that the field has to overcome. Areas covered: In this review, we summarize the different pitfalls and challenges that the protein-protein cross-linking field is confronted with when using mass spectrometry approaches. We additionally focus on native disulfide bridges as an example and provide some examples of cross-links that are important in the biomedical field. Expert commentary: The current flow of methodological improvements, mainly from the chemical cross-linking field, has delivered a significant contribution to deciphering native and insult-induced cross-links. Although an automated data analysis of proteome-wide peptide cross-linking is currently only possible in chemical cross-linking experiments, the field is well on the way towards a more automated analysis of native and insult-induced cross-links in raw mass spectrometry data that will boost its potential in biomedical applications.
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Affiliation(s)
- Evelyne Maes
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand
| | - Jolon M Dyer
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand.,c Riddet Institute, Massey University , Palmerston North , New Zealand.,d Wine, Food & Molecular Biosciences , Lincoln University , Lincoln , New Zealand
| | - Hannah J McKerchar
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand
| | | | - Stefan Clerens
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand
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19
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Lee JJ, Yang SY, Park J, Ferrell JE, Shin DH, Lee KJ. Calcium Ion Induced Structural Changes Promote Dimerization of Secretagogin, Which Is Required for Its Insulin Secretory Function. Sci Rep 2017; 7:6976. [PMID: 28765527 PMCID: PMC5539292 DOI: 10.1038/s41598-017-07072-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/16/2017] [Indexed: 11/29/2022] Open
Abstract
Secretagogin (SCGN), a hexa EF-hand calcium binding protein, plays key roles in insulin secretion in pancreatic β-cells. It is not yet understood how the binding of Ca2+ to human SCGN (hSCGN) promotes secretion. Here we have addressed this question, using mass spectrometry combined with a disulfide searching algorithm DBond. We found that the binding of Ca2+ to hSCGN promotes the dimerization of hSCGN via the formation of a Cys193-Cys193 disulfide bond. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics studies revealed that Ca2+ binding to the EF-hands of hSCGN induces significant structural changes that affect the solvent exposure of N-terminal region, and hence the redox sensitivity of the Cys193 residue. These redox sensitivity changes were confirmed using biotinylated methyl-3-nitro-4-(piperidin-1-ylsulfonyl) benzoate (NPSB-B), a chemical probe that specifically labels reactive cysteine sulfhydryls. Furthermore, we found that wild type hSCGN overexpression promotes insulin secretion in pancreatic β cells, while C193S-hSCGN inhibits it. These findings suggest that insulin secretion in pancreatic cells is regulated by Ca2+ and ROS signaling through Ca2+-induced structural changes promoting dimerization of hSCGN.
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Affiliation(s)
- Jae-Jin Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 120-750, Korea
| | - Seo-Yun Yang
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 120-750, Korea
| | - Jimin Park
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 120-750, Korea
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA
| | - Dong-Hae Shin
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 120-750, Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 120-750, Korea.
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20
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Gu L, Robinson RAS. Proteomic approaches to quantify cysteine reversible modifications in aging and neurodegenerative diseases. Proteomics Clin Appl 2016; 10:1159-1177. [PMID: 27666938 DOI: 10.1002/prca.201600015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/13/2016] [Accepted: 09/23/2016] [Indexed: 01/11/2023]
Abstract
Cysteine is a highly reactive amino acid and is subject to a variety of reversible post-translational modifications (PTMs), including nitrosylation, glutathionylation, palmitoylation, as well as formation of sulfenic acid and disulfides. These modifications are not only involved in normal biological activities, such as enzymatic catalysis, redox signaling, and cellular homeostasis, but can also be the result of oxidative damage. Especially in aging and neurodegenerative diseases, oxidative stress leads to aberrant cysteine oxidations that affect protein structure and function leading to neurodegeneration as well as other detrimental effects. Methods that can identify cysteine modifications by type, including the site of modification, as well as the relative stoichiometry of the modification can be very helpful for understanding the role of the thiol proteome and redox homeostasis in the context of disease. Cysteine reversible modifications however, are challenging to investigate as they are low abundant, diverse, and labile especially under endogenous conditions. Thanks to the development of redox proteomic approaches, large-scale quantification of cysteine reversible modifications is possible. These approaches cover a range of strategies to enrich, identify, and quantify cysteine reversible modifications from biological samples. This review will focus on nongel-based redox proteomics workflows that give quantitative information about cysteine PTMs and highlight how these strategies have been useful for investigating the redox thiol proteome in aging and neurodegenerative diseases.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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21
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Sanagavarapu K, Weiffert T, Ní Mhurchú N, O'Connell D, Linse S. Calcium Binding and Disulfide Bonds Regulate the Stability of Secretagogin towards Thermal and Urea Denaturation. PLoS One 2016; 11:e0165709. [PMID: 27812162 PMCID: PMC5094748 DOI: 10.1371/journal.pone.0165709] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/17/2016] [Indexed: 12/18/2022] Open
Abstract
Secretagogin is a calcium-sensor protein with six EF-hands. It is widely expressed in neurons and neuro-endocrine cells of a broad range of vertebrates including mammals, fishes and amphibia. The protein plays a role in secretion and interacts with several vesicle-associated proteins. In this work, we have studied the contribution of calcium binding and disulfide-bond formation to the stability of the secretagogin structure towards thermal and urea denaturation. SDS-PAGE analysis of secretagogin in reducing and non-reducing conditions identified a tendency of the protein to form dimers in a redox-dependent manner. The denaturation of apo and Calcium-loaded secretagogin was studied by circular dichroism and fluorescence spectroscopy under conditions favoring monomer or dimer or a 1:1 monomer: dimer ratio. This analysis reveals significantly higher stability towards urea denaturation of Calcium-loaded secretagogin compared to the apo protein. The secondary and tertiary structure of the Calcium-loaded form is not completely denatured in the presence of 10 M urea. Reduced and Calcium-loaded secretagogin is found to refold reversibly after heating to 95°C, while both oxidized and reduced apo secretagogin is irreversibly denatured at this temperature. Thus, calcium binding greatly stabilizes the structure of secretagogin towards chemical and heat denaturation.
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Affiliation(s)
- Kalyani Sanagavarapu
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Tanja Weiffert
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Niamh Ní Mhurchú
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - David O'Connell
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
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22
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Sarpe V, Rafiei A, Hepburn M, Ostan N, Schryvers AB, Schriemer DC. High Sensitivity Crosslink Detection Coupled With Integrative Structure Modeling in the Mass Spec Studio. Mol Cell Proteomics 2016; 15:3071-80. [PMID: 27412762 DOI: 10.1074/mcp.o116.058685] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Indexed: 01/21/2023] Open
Abstract
The Mass Spec Studio package was designed to support the extraction of hydrogen-deuterium exchange and covalent labeling data for a range of mass spectrometry (MS)-based workflows, to integrate with restraint-driven protein modeling activities. In this report, we present an extension of the underlying Studio framework and provide a plug-in for crosslink (XL) detection. To accommodate flexibility in XL methods and applications, while maintaining efficient data processing, the plug-in employs a peptide library reduction strategy via a presearch of the tandem-MS data. We demonstrate that prescoring linear unmodified peptide tags using a probabilistic approach substantially reduces search space by requiring both crosslinked peptides to generate sparse data attributable to their linear forms. The method demonstrates highly sensitive crosslink peptide identification with a low false positive rate. Integration with a Haddock plug-in provides a resource that can combine multiple sources of data for protein modeling activities. We generated a structural model of porcine transferrin bound to TbpB, a membrane-bound receptor essential for iron acquisition in Actinobacillus pleuropneumoniae Using mutational data and crosslinking restraints, we confirm the mechanism by which TbpB recognizes the iron-loaded form of transferrin, and note the requirement for disparate sources of restraint data for accurate model construction. The software plugin is freely available at www.msstudio.ca.
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Affiliation(s)
- Vladimir Sarpe
- From the ‡Department of Biochemistry and Molecular Biology
| | | | - Morgan Hepburn
- From the ‡Department of Biochemistry and Molecular Biology
| | - Nicholas Ostan
- ¶Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Alberta, T2N 1N4, Canada
| | - Anthony B Schryvers
- From the ‡Department of Biochemistry and Molecular Biology, ¶Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Alberta, T2N 1N4, Canada
| | - David C Schriemer
- From the ‡Department of Biochemistry and Molecular Biology, §Department of Chemistry,
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23
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Arts IS, Vertommen D, Baldin F, Laloux G, Collet JF. Comprehensively Characterizing the Thioredoxin Interactome In Vivo Highlights the Central Role Played by This Ubiquitous Oxidoreductase in Redox Control. Mol Cell Proteomics 2016; 15:2125-40. [PMID: 27081212 DOI: 10.1074/mcp.m115.056440] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Indexed: 12/12/2022] Open
Abstract
Thioredoxin (Trx) is a ubiquitous oxidoreductase maintaining protein-bound cysteine residues in the reduced thiol state. Here, we combined a well-established method to trap Trx substrates with the power of bacterial genetics to comprehensively characterize the in vivo Trx redox interactome in the model bacterium Escherichia coli Using strains engineered to optimize trapping, we report the identification of a total 268 Trx substrates, including 201 that had never been reported to depend on Trx for reduction. The newly identified Trx substrates are involved in a variety of cellular processes, ranging from energy metabolism to amino acid synthesis and transcription. The interaction between Trx and two of its newly identified substrates, a protein required for the import of most carbohydrates, PtsI, and the bacterial actin homolog MreB was studied in detail. We provide direct evidence that PtsI and MreB contain cysteine residues that are susceptible to oxidation and that participate in the formation of an intermolecular disulfide with Trx. By considerably expanding the number of Trx targets, our work highlights the role played by this major oxidoreductase in a variety of cellular processes. Moreover, as the dependence on Trx for reduction is often conserved across species, it also provides insightful information on the interactome of Trx in organisms other than E. coli.
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Affiliation(s)
- Isabelle S Arts
- From the ‡WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium, §de Duve Institute, Université catholique de Louvain (UCL), Avenue Hippocrate 75, 1200 Brussels, Belgium; ¶Brussels Center for Redox Biology, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Didier Vertommen
- §de Duve Institute, Université catholique de Louvain (UCL), Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Francesca Baldin
- From the ‡WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium, §de Duve Institute, Université catholique de Louvain (UCL), Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Géraldine Laloux
- From the ‡WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium, §de Duve Institute, Université catholique de Louvain (UCL), Avenue Hippocrate 75, 1200 Brussels, Belgium; ¶Brussels Center for Redox Biology, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Jean-François Collet
- From the ‡WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium, §de Duve Institute, Université catholique de Louvain (UCL), Avenue Hippocrate 75, 1200 Brussels, Belgium; ¶Brussels Center for Redox Biology, Avenue Hippocrate 75, 1200 Brussels, Belgium
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24
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Giese SH, Fischer L, Rappsilber J. A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides. Mol Cell Proteomics 2016; 15:1094-104. [PMID: 26719564 PMCID: PMC4813691 DOI: 10.1074/mcp.m115.049296] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
Cross-linking/mass spectrometry resolves protein-protein interactions or protein folds by help of distance constraints. Cross-linkers with specific properties such as isotope-labeled or collision-induced dissociation (CID)-cleavable cross-linkers are in frequent use to simplify the identification of cross-linked peptides. Here, we analyzed the mass spectrometric behavior of 910 unique cross-linked peptides in high-resolution MS1 and MS2 from published data and validate the observation by a ninefold larger set from currently unpublished data to explore if detailed understanding of their fragmentation behavior would allow computational delivery of information that otherwise would be obtained via isotope labels or CID cleavage of cross-linkers. Isotope-labeled cross-linkers reveal cross-linked and linear fragments in fragmentation spectra. We show that fragment mass and charge alone provide this information, alleviating the need for isotope-labeling for this purpose. Isotope-labeled cross-linkers also indicate cross-linker-containing, albeit not specifically cross-linked, peptides in MS1. We observed that acquisition can be guided to better than twofold enrich cross-linked peptides with minimal losses based on peptide mass and charge alone. By help of CID-cleavable cross-linkers, individual spectra with only linear fragments can be recorded for each peptide in a cross-link. We show that cross-linked fragments of ordinary cross-linked peptides can be linearized computationally and that a simplified subspectrum can be extracted that is enriched in information on one of the two linked peptides. This allows identifying candidates for this peptide in a simplified database search as we propose in a search strategy here. We conclude that the specific behavior of cross-linked peptides in mass spectrometers can be exploited to relax the requirements on cross-linkers.
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Affiliation(s)
- Sven H Giese
- From the ‡Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Lutz Fischer
- §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Juri Rappsilber
- From the ‡Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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25
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Argo AS, Shi C, Liu F, Goshe MB. Performing protein crosslinking using gas-phase cleavable chemical crosslinkers and liquid chromatography-tandem mass spectrometry. Methods 2015; 89:64-73. [DOI: 10.1016/j.ymeth.2015.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/12/2015] [Accepted: 06/09/2015] [Indexed: 12/13/2022] Open
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26
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Makepeace KAT, Serpa JJ, Petrotchenko EV, Borchers CH. Comprehensive identification of disulfide bonds using non-specific proteinase K digestion and CID-cleavable crosslinking analysis methodology for Orbitrap LC/ESI-MS/MS data. Methods 2015; 89:74-8. [PMID: 25752848 DOI: 10.1016/j.ymeth.2015.02.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/25/2015] [Accepted: 02/26/2015] [Indexed: 10/23/2022] Open
Abstract
Disulfide bonds are valuable constraints in protein structure modeling. The Cys-Cys disulfide bond undergoes specific fragmentation under CID and, therefore, can be considered as a CID-cleavable crosslink. We have recently reported on the benefits of using non-specific digestion with proteinase K for inter-peptide crosslink determination. Here, we describe an updated application of our CID-cleavable crosslink analysis software and our crosslinking analysis with non-specific digestion methodology for the robust and comprehensive determination of disulfide bonds in proteins, using Orbitrap LC/ESI-MS/MS data.
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Affiliation(s)
- Karl A T Makepeace
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Jason J Serpa
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Evgeniy V Petrotchenko
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada; Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
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27
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Hwang J, Suh HW, Jeon YH, Hwang E, Nguyen LT, Yeom J, Lee SG, Lee C, Kim KJ, Kang BS, Jeong JO, Oh TK, Choi I, Lee JO, Kim MH. The structural basis for the negative regulation of thioredoxin by thioredoxin-interacting protein. Nat Commun 2015; 5:2958. [PMID: 24389582 PMCID: PMC3941024 DOI: 10.1038/ncomms3958] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 11/19/2013] [Indexed: 12/20/2022] Open
Abstract
The redox-dependent inhibition of thioredoxin (TRX) by thioredoxin-interacting protein (TXNIP) plays a pivotal role in various cancers and metabolic syndromes. However, the molecular mechanism of this regulation is largely unknown. Here, we present the crystal structure of the TRX-TXNIP complex and demonstrate that the inhibition of TRX by TXNIP is mediated by an intermolecular disulphide interaction resulting from a novel disulphide bond-switching mechanism. Upon binding to TRX, TXNIP undergoes a structural rearrangement that involves switching of a head-to-tail interprotomer Cys63-Cys247 disulphide between TXNIP molecules to an interdomain Cys63-Cys190 disulphide, and the formation of a de novo intermolecular TXNIP Cys247-TRX Cys32 disulphide. This disulphide-switching event unexpectedly results in a domain arrangement of TXNIP that is entirely different from those of other arrestin family proteins. We further show that the intermolecular disulphide bond between TRX and TXNIP dissociates in the presence of high concentrations of reactive oxygen species. This study provides insight into TRX and TXNIP-dependent cellular regulation.
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Affiliation(s)
- Jungwon Hwang
- 1] Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea [2] Infection and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Hyun-Woo Suh
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Young Ho Jeon
- College of Pharmacy, Korea University, Sejong 339-700, Korea
| | - Eunha Hwang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chungbuk 363-883, Korea
| | - Loi T Nguyen
- Infection and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Jeonghun Yeom
- 1] BRI, Korea Institute of Science and Technology, Seoul 136-791, Korea [2] Department of Biological Chemistry, University of Science and Technology, Daejeon 305-333, Korea
| | - Seung-Goo Lee
- Biochemicals and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Cheolju Lee
- 1] BRI, Korea Institute of Science and Technology, Seoul 136-791, Korea [2] Department of Biological Chemistry, University of Science and Technology, Daejeon 305-333, Korea
| | - Kyung Jin Kim
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701, Korea
| | - Beom Sik Kang
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701, Korea
| | - Jin-Ok Jeong
- Division of Cardiology, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon 301-721, Korea
| | - Tae-Kwang Oh
- Infection and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Inpyo Choi
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Jie-Oh Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Myung Hee Kim
- 1] Infection and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea [2] Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-333, Korea
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28
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An BC, Lee SS, Jung HS, Kim JY, Lee Y, Lee KW, Lee SY, Tripathi BN, Chung BY. An additional cysteine in a typical 2-Cys peroxiredoxin ofPseudomonaspromotes functional switching between peroxidase and molecular chaperone. FEBS Lett 2015; 589:2831-40. [DOI: 10.1016/j.febslet.2015.07.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 07/27/2015] [Indexed: 01/15/2023]
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29
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Evidence for the dimerization-mediated catalysis of methionine sulfoxide reductase A from Clostridium oremlandii. PLoS One 2015; 10:e0131523. [PMID: 26107511 PMCID: PMC4479559 DOI: 10.1371/journal.pone.0131523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/02/2015] [Indexed: 11/30/2022] Open
Abstract
Clostridium oremlandii MsrA (CoMsrA) is a natively selenocysteine-containing methionine-S-sulfoxide reductase and classified into a 1-Cys type MsrA. CoMsrA exists as a monomer in solution. Herein, we report evidence that CoMsrA can undergo homodimerization during catalysis. The monomeric CoMsrA dimerizes in the presence of its substrate methionine sulfoxide via an intermolecular disulfide bond between catalytic Cys16 residues. The dimeric CoMsrA is resolved by the reductant glutaredoxin, suggesting the relevance of dimerization in catalysis. The dimerization reaction occurs in a concentration- and time-dependent manner. In addition, the occurrence of homodimer formation in the native selenoprotein CoMsrA is confirmed. We also determine the crystal structure of the dimeric CoMsrA, having the dimer interface around the two catalytic Cys16 residues. A central cone-shaped hole is present in the surface model of dimeric structure, and the two Cys16 residues constitute the base of the hole. Collectively, our biochemical and structural analyses suggest a novel dimerization-mediated mechanism for CoMsrA catalysis that is additionally involved in CoMsrA regeneration by glutaredoxin.
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30
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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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31
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Fan SB, Meng JM, Lu S, Zhang K, Yang H, Chi H, Sun RX, Dong MQ, He SM. Using pLink to Analyze Cross-Linked Peptides. ACTA ACUST UNITED AC 2015; 49:8.21.1-8.21.19. [PMID: 25754995 DOI: 10.1002/0471250953.bi0821s49] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
pLink is a search engine for high-throughput identification of cross-linked peptides from their tandem mass spectra, which is the data-analysis step in chemical cross-linking of proteins coupled with mass spectrometry analysis. pLink has accumulated more than 200 registered users from all over the world since its first release in 2012. After 2 years of continual development, a new version of pLink has been released, which is at least 40 times faster, more versatile, and more user-friendly. Also, the function of the new pLink has been expanded to identifying endogenous protein cross-linking sites such as disulfide bonds and SUMO (Small Ubiquitin-like MOdifier) modification sites. Integrated into the new version are two accessory tools: pLabel, to annotate spectra of cross-linked peptides for visual inspection and publication, and pConfig, to assist users in setting up search parameters. Here, we provide detailed guidance on running a database search for identification of protein cross-links using the 2014 version of pLink.
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Affiliation(s)
- Sheng-Bo Fan
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jia-Ming Meng
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shan Lu
- National Institute of Biological Sciences, Beijing, China
| | - Kun Zhang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Hao Yang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Hao Chi
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Rui-Xiang Sun
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Si-Min He
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
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32
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Lee JJ, Park YS, Lee KJ. Hydrogen-deuterium exchange mass spectrometry for determining protein structural changes in drug discovery. Arch Pharm Res 2015; 38:1737-45. [PMID: 25743629 DOI: 10.1007/s12272-015-0584-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 02/25/2015] [Indexed: 12/11/2022]
Abstract
Protein structures are dynamically changed in response to post-translational modifications, ligand or chemical binding, or protein-protein interactions. Understanding the structural changes that occur in proteins in response to potential candidate drugs is important for predicting the modes of action of drugs and their functions and regulations. Recent advances in hydrogen/deuterium exchange mass spectrometry (HDX-MS) have the potential to offer a tool for obtaining such understanding similarly to other biophysical techniques, such as X-ray crystallography and high resolution NMR. We present here, a review of basic concept and methodology of HDX-MS, how it is being applied for identifying the sites and structural changes in proteins following their interactions with other proteins and small molecules, and the potential of this tool to help in drug discovery.
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Affiliation(s)
- Jae-Jin Lee
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Yeon Seung Park
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul, 120-750, Republic of Korea.
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33
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Kim HJ, Ha S, Lee HY, Lee KJ. ROSics: chemistry and proteomics of cysteine modifications in redox biology. MASS SPECTROMETRY REVIEWS 2015; 34:184-208. [PMID: 24916017 PMCID: PMC4340047 DOI: 10.1002/mas.21430] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 04/30/2013] [Accepted: 11/20/2013] [Indexed: 05/29/2023]
Abstract
Post-translational modifications (PTMs) occurring in proteins determine their functions and regulations. Proteomic tools are available to identify PTMs and have proved invaluable to expanding the inventory of these tools of nature that hold the keys to biological processes. Cysteine (Cys), the least abundant (1-2%) of amino acid residues, are unique in that they play key roles in maintaining stability of protein structure, participating in active sites of enzymes, regulating protein function and binding to metals, among others. Cys residues are major targets of reactive oxygen species (ROS), which are important mediators and modulators of various biological processes. It is therefore necessary to identify the Cys-containing ROS target proteins, as well as the sites and species of their PTMs. Cutting edge proteomic tools which have helped identify the PTMs at reactive Cys residues, have also revealed that Cys residues are modified in numerous ways. These modifications include formation of disulfide, thiosulfinate and thiosulfonate, oxidation to sulfenic, sulfinic, sulfonic acids and thiosulfonic acid, transformation to dehydroalanine (DHA) and serine, palmitoylation and farnesylation, formation of chemical adducts with glutathione, 4-hydroxynonenal and 15-deoxy PGJ2, and various other chemicals. We present here, a review of relevant ROS biology, possible chemical reactions of Cys residues and details of the proteomic strategies employed for rapid, efficient and sensitive identification of diverse and novel PTMs involving reactive Cys residues of redox-sensitive proteins. We propose a new name, "ROSics," for the science which describes the principles of mode of action of ROS at molecular levels.
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Affiliation(s)
- Hee-Jung Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans UniversitySeoul, 120-750, Korea
| | - Sura Ha
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST)Daejeon, 305-701, Korea
| | - Hee Yoon Lee
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST)Daejeon, 305-701, Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans UniversitySeoul, 120-750, Korea
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34
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Na S, Paek E. Software eyes for protein post-translational modifications. MASS SPECTROMETRY REVIEWS 2015; 34:133-147. [PMID: 24889695 DOI: 10.1002/mas.21425] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/18/2013] [Accepted: 11/20/2013] [Indexed: 06/03/2023]
Abstract
Post-translational modifications (PTMs) are critical to almost all aspects of complex processes of the cell. Identification of PTMs is one of the biggest challenges for proteomics, and there have been many computational studies for the analysis of PTMs from tandem mass spectrometry (MS/MS). Most early PTM identification studies have been performed by matching MS/MS data to protein databases, using database search tools, but they are prohibitively slow when a large number of PTMs is given as a search parameter. In this article, we present recent developments to search for more types of PTMs and to speed up the search, and discuss many computational issues and solutions in terms of identifying multiply modified peptides or searching for all possible modifications at once in unrestrictive mode. Apart from the most common type of PTMs involving covalent addition of functional groups to proteins, PTMs such as disulfide linkage require dedicated software for the analysis because they may involve cross-linking between two different parts of proteins. Finally, methods for identification of protein disulfide bonds are presented.
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Affiliation(s)
- Seungjin Na
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, 92093; Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, 92093
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35
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Wiesner J, Resemann A, Evans C, Suckau D, Jabs W. Advanced mass spectrometry workflows for analyzing disulfide bonds in biologics. Expert Rev Proteomics 2015; 12:115-23. [DOI: 10.1586/14789450.2015.1018896] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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36
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Kim MJ, Jeong J, Jeong J, Hwang KY, Lee KJ, Kim HY. Mechanism of 1-Cys type methionine sulfoxide reductase A regeneration by glutaredoxin. Biochem Biophys Res Commun 2015; 457:567-71. [PMID: 25600814 DOI: 10.1016/j.bbrc.2015.01.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 01/08/2015] [Indexed: 10/24/2022]
Abstract
Glutaredoxin (Grx), a major redox regulator, can act as a reductant of methionine sulfoxide reductase A (MsrA). However, the biochemical mechanisms involved in MsrA activity regeneration by Grx remain largely unknown. In this study, we investigated the regeneration mechanism of 1-Cys type Clostridium oremlandii MsrA (cMsrA) lacking a resolving Cys residue in a Grx-dependent assay. Kinetic analysis showed that cMsrA could be reduced by both monothiol and dithiol Grxs as efficiently as by in vitro reductant dithiothreitol. Our data revealed that the catalytic Cys sulfenic acid intermediate is not glutathionylated in the presence of the substrate, and that Grx instead directly formed a complex with cMsrA. Mass spectrometry analysis identified a disulfide bond between the N-terminal catalytic Cys of the active site of Grx and the catalytic Cys of cMsrA. This mixed disulfide bond could be resolved by glutathione. Based on these findings, we propose a model for regeneration of 1-Cys type cMsrA by Grx that involves no glutathionylation on the catalytic Cys of cMsrA. This mechanism contrasts with that of the previously known 1-Cys type MsrB.
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Affiliation(s)
- Moon-Jung Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717, Republic of Korea
| | - Jaeho Jeong
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Jihye Jeong
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701, Republic of Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea.
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717, Republic of Korea.
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37
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Lin JCY, Chiang BY, Chou CC, Chen TC, Chen YJ, Chen YJ, Lin CH. Glutathionylspermidine in the modification of protein SH groups: the enzymology and its application to study protein glutathionylation. Molecules 2015; 20:1452-74. [PMID: 25599150 PMCID: PMC6272389 DOI: 10.3390/molecules20011452] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/15/2014] [Indexed: 11/29/2022] Open
Abstract
Cysteine is very susceptible to reactive oxygen species. In response; posttranslational thiol modifications such as reversible disulfide bond formation have arisen as protective mechanisms against undesired in vivo cysteine oxidation. In Gram-negative bacteria a major defense mechanism against cysteine overoxidation is the formation of mixed protein disulfides with low molecular weight thiols such as glutathione and glutathionylspermidine. In this review we discuss some of the mechanistic aspects of glutathionylspermidine in prokaryotes and extend its potential use to eukaryotes in proteomics and biochemical applications through an example with tissue transglutaminase and its S-glutathionylation.
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Affiliation(s)
- Jason Ching-Yao Lin
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Bing-Yu Chiang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Chi-Chi Chou
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Tzu-Chieh Chen
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Chun-Hung Lin
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
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38
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Götze M, Pettelkau J, Fritzsche R, Ihling CH, Schäfer M, Sinz A. Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:83-97. [PMID: 25261217 DOI: 10.1007/s13361-014-1001-1] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 05/03/2023]
Abstract
CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .
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Affiliation(s)
- Michael Götze
- Institute for Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany,
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39
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Chou CC, Chiang BY, Lin JCY, Pan KT, Lin CH, Khoo KH. Characteristic tandem mass spectral features under various collision chemistries for site-specific identification of protein S-glutathionylation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:120-132. [PMID: 25374333 DOI: 10.1007/s13361-014-1014-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/27/2014] [Accepted: 10/02/2014] [Indexed: 06/04/2023]
Abstract
Protein S-glutathionylation is a reversible post-translational modification widely implicated in redox regulated biological functions. Conventional biochemical methods, however, often do not allow such a mixed disulfide modification to be reliably identified on specific cysteine residues or be distinguished from other related oxidized forms. To develop more efficient mass spectrometry (MS)-based analytical strategies for this purpose, we first investigated the MS/MS fragmentation pattern of S-glutathionylated peptides under various dissociation modes, including collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD), using synthetic peptides derived from protein tyrosine phosphatase as models. Our results indicate that a MALDI-based high energy CID MS/MS on a TOF/TOF affords the most distinctive spectral features that would facilitate rapid and unambiguous identification of site-specific S-glutathionylation. For more complex proteomic samples best tackled by LC-MS/MS approach, we demonstrate that HCD performed on an LTQ-Orbitrap hybrid instrument fairs better than trap-based CID and ETD in allowing more protein site-specific S-glutathionylation to be confidently identified by direct database searching of the generated MS/MS dataset using Mascot. Overall, HCD afforded more peptide sequence-informative fragment ions retaining the glutathionyl modification with less neutral losses of side chains to compromise scoring. In conjunction with our recently developed chemo-enzymatic tagging strategy, our nanoLC-HCD-MS/MS approach is sufficiently sensitive to identify endogenous S-glutathionylated peptides prepared from non-stressed cells. It is anticipated that future applications to global scale analysis of protein S-glutathionylation will benefit further from current advances in both speed and mass accuracy afforded by HCD MS/MS mode on the Orbitrap series.
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Affiliation(s)
- Chi-Chi Chou
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, 11529, Taiwan,
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40
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Huang J, Wang F, Ye M, Zou H. Enrichment and separation techniques for large-scale proteomics analysis of the protein post-translational modifications. J Chromatogr A 2014; 1372C:1-17. [DOI: 10.1016/j.chroma.2014.10.107] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022]
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41
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Reinwarth M, Avrutina O, Fabritz S, Kolmar H. Fragmentation follows structure: top-down mass spectrometry elucidates the topology of engineered cystine-knot miniproteins. PLoS One 2014; 9:e108626. [PMID: 25303319 PMCID: PMC4193770 DOI: 10.1371/journal.pone.0108626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/02/2014] [Indexed: 12/21/2022] Open
Abstract
Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS(3) spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin's folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before.
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Affiliation(s)
- Michael Reinwarth
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Olga Avrutina
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | | | - Harald Kolmar
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- * E-mail: (SF); (HK)
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42
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Petrotchenko EV, Serpa JJ, Makepeace KA, Brodie NI, Borchers CH. 14N15N DXMSMS Match program for the automated analysis of LC/ESI-MS/MS crosslinking data from experiments using 15N metabolically labeled proteins. J Proteomics 2014; 109:104-10. [DOI: 10.1016/j.jprot.2014.06.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/01/2014] [Accepted: 06/15/2014] [Indexed: 11/16/2022]
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Huang SY, Chen SF, Chen CH, Huang HW, Wu WG, Sung WC. Global Disulfide Bond Profiling for Crude Snake Venom Using Dimethyl Labeling Coupled with Mass Spectrometry and RADAR Algorithm. Anal Chem 2014; 86:8742-50. [DOI: 10.1021/ac501931t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Sheng Yu Huang
- Mithra Biotechnology
Inc., 7F, No. 104, Sec. 1, Xintai 5th
Road, Xizhi Dist., New Taipei City 221, Taiwan
| | - Sung Fang Chen
- National Taiwan Normal University, Department of
Chemistry, No. 88, Sec.
4, Tingchow Road, Taipei 116, Taiwan
| | - Chun Hao Chen
- National Taiwan Normal University, Department of
Chemistry, No. 88, Sec.
4, Tingchow Road, Taipei 116, Taiwan
| | - Hsuan Wei Huang
- National Health
Research Institutes, National Institute of Infectious Diseases and
Vaccinology, No. 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan
- National Tsing Hua University, Institute of Bioinformatics
and Structural Biology, No. 101, Sec. 2, Kuang Fu Road, Hsinchu 330, Taiwan
| | - Wen Guey Wu
- National Tsing Hua University, Institute of Bioinformatics
and Structural Biology, No. 101, Sec. 2, Kuang Fu Road, Hsinchu 330, Taiwan
| | - Wang Chou Sung
- National Health
Research Institutes, National Institute of Infectious Diseases and
Vaccinology, No. 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan
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Wheat germ in vitro translation to produce one of the most toxic sodium channel specific toxins. Biosci Rep 2014; 34:BSR20140050. [PMID: 24924257 PMCID: PMC4114062 DOI: 10.1042/bsr20140050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Envenoming following scorpion sting is a common emergency in many parts of the world. During scorpion envenoming, highly toxic small polypeptides of the venom diffuse rapidly within the victim causing serious medical problems. The exploration of toxin structure-function relationship would benefit from the generation of soluble recombinant scorpion toxins in Escherichia coli. We developed an in vitro wheat germ translation system for the expression of the highly toxic Aah (Androctonus australis hector)II protein that requires the proper formation of four disulphide bonds. Soluble, recombinant N-terminal GST (glutathione S-transferase)-tagged AahII toxin is obtained in this in vitro translation system. After proteolytic removal of the GST-tag, purified rAahII (recombinant AahII) toxin, which contains two extra amino acids at its N terminal relative to the native AahII, is highly toxic after i.c.v. (intracerebroventricular) injection in Swiss mice. An LD50 (median lethal dose)-value of 10 ng (or 1.33 pmol), close to that of the native toxin (LD50 of 3 ng) indicates that the wheat germ in vitro translation system produces properly folded and biological active rAahII. In addition, NbAahII10 (Androctonus australis hector nanobody 10), a camel single domain antibody fragment, raised against the native AahII toxin, recognizes its cognate conformational epitope on the recombinant toxin and neutralizes the toxicity of purified rAahII upon injection in mice. A wheat germ embryo derived cell-free translation system expresses a biologically active, highly toxic scorpion venom protein that is fully neutralized by a camel single domain antibody fragment raised against the native scorpion toxin.
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Borges CR, Sherma ND. Techniques for the analysis of cysteine sulfhydryls and oxidative protein folding. Antioxid Redox Signal 2014; 21:511-31. [PMID: 24383618 PMCID: PMC4076987 DOI: 10.1089/ars.2013.5559] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE Modification of cysteine thiols dramatically affects protein function and stability. Hence, the abilities to quantify specific protein sulfhydryl groups within complex biological samples and map disulfide bond structures are crucial to gaining greater insights into how proteins operate in human health and disease. RECENT ADVANCES Many different molecular probes are now commercially available to label and track cysteine residues at great sensitivity. Coupled with mass spectrometry, stable isotope-labeled sulfhydryl-specific reagents can provide previously unprecedented molecular insights into the dynamics of cysteine modification. Likewise, the combined application of modern mass spectrometers with improved sample preparation techniques and novel data mining algorithms is beginning to routinize the analysis of complex protein disulfide structures. CRITICAL ISSUES Proper application of these modern tools and techniques, however, still requires fundamental understanding of sulfhydryl chemistry as well as the assumptions that accompany sample preparation and underlie effective data interpretation. FUTURE DIRECTIONS The continued development of tools, technical approaches, and corresponding data processing algorithms will, undoubtedly, facilitate site-specific protein sulfhydryl quantification and disulfide structure analysis from within complex biological mixtures with ever-improving accuracy and sensitivity. Fully routinizing disulfide structure analysis will require an equal but balanced focus on sample preparation and corresponding mass spectral dataset reproducibility.
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Affiliation(s)
- Chad R Borges
- Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University , Tempe, Arizona
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46
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Petrotchenko EV, Borchers CH. Application of a fast sorting algorithm to the assignment of mass spectrometric cross-linking data. Proteomics 2014; 14:1987-9. [PMID: 24895266 DOI: 10.1002/pmic.201300486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 02/28/2014] [Accepted: 05/28/2014] [Indexed: 11/06/2022]
Abstract
Cross-linking combined with MS involves enzymatic digestion of cross-linked proteins and identifying cross-linked peptides. Assignment of cross-linked peptide masses requires a search of all possible binary combinations of peptides from the cross-linked proteins' sequences, which becomes impractical with increasing complexity of the protein system and/or if digestion enzyme specificity is relaxed. Here, we describe the application of a fast sorting algorithm to search large sequence databases for cross-linked peptide assignments based on mass. This same algorithm has been used previously for assigning disulfide-bridged peptides (Choi et al., ), but has not previously been applied to cross-linking studies.
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Affiliation(s)
- Evgeniy V Petrotchenko
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada
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47
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Liu F, van Breukelen B, Heck AJR. Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS. Mol Cell Proteomics 2014; 13:2776-86. [PMID: 24980484 DOI: 10.1074/mcp.o114.039057] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Disulfide bond identification is important for a detailed understanding of protein structures, which directly affect their biological functions. Here we describe an integrated workflow for the fast and accurate identification of authentic protein disulfide bridges. This novel workflow incorporates acidic proteolytic digestion using pepsin to eliminate undesirable disulfide reshuffling during sample preparation and a novel search engine, SlinkS, to directly identify disulfide-bridged peptides isolated via electron transfer higher energy dissociation (EThcD). In EThcD fragmentation of disulfide-bridged peptides, electron transfer dissociation preferentially leads to the cleavage of the S-S bonds, generating two intense disulfide-cleaved peptides as primary fragment ions. Subsequently, higher energy collision dissociation primarily targets unreacted and charge-reduced precursor ions, inducing peptide backbone fragmentation. SlinkS is able to provide the accurate monoisotopic precursor masses of the two disulfide-cleaved peptides and the sequence of each linked peptide by matching the remaining EThcD product ions against a linear peptide database. The workflow was validated using a protein mixture containing six proteins rich in natural disulfide bridges. Using this pepsin-based workflow, we were able to efficiently and confidently identify a total of 31 unique Cys-Cys bonds (out of 43 disulfide bridges present), with no disulfide reshuffling products detected. Pepsin digestion not only outperformed trypsin digestion in terms of the number of detected authentic Cys-Cys bonds, but, more important, prevented the formation of artificially reshuffled disulfide bridges due to protein digestion under neutral pH. Our new workflow therefore provides a precise and generic approach for disulfide bridge mapping, which can be used to study protein folding, structure, and stability.
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Affiliation(s)
- Fan Liu
- From the ‡Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands; §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Bas van Breukelen
- From the ‡Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands; §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands; §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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48
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Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. Mol Cell Proteomics 2014; 13:1128-36. [PMID: 24493012 DOI: 10.1074/mcp.m113.035758] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The combination of chemical cross-linking and mass spectrometry has recently been shown to constitute a powerful tool for studying protein-protein interactions and elucidating the structure of large protein complexes. However, computational methods for interpreting the complex MS/MS spectra from linked peptides are still in their infancy, making the high-throughput application of this approach largely impractical. Because of the lack of large annotated datasets, most current approaches do not capture the specific fragmentation patterns of linked peptides and therefore are not optimal for the identification of cross-linked peptides. Here we propose a generic approach to address this problem and demonstrate it using disulfide-bridged peptide libraries to (i) efficiently generate large mass spectral reference data for linked peptides at a low cost and (ii) automatically train an algorithm that can efficiently and accurately identify linked peptides from MS/MS spectra. We show that using this approach we were able to identify thousands of MS/MS spectra from disulfide-bridged peptides through comparison with proteome-scale sequence databases and significantly improve the sensitivity of cross-linked peptide identification. This allowed us to identify 60% more direct pairwise interactions between the protein subunits in the 20S proteasome complex than existing tools on cross-linking studies of the proteasome complexes. The basic framework of this approach and the MS/MS reference dataset generated should be valuable resources for the future development of new tools for the identification of linked peptides.
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Affiliation(s)
- Jian Wang
- Bioinformatics Program, University of California, San Diego, La Jolla, California
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Hugo M, Van Laer K, Reyes AM, Vertommen D, Messens J, Radi R, Trujillo M. Mycothiol/mycoredoxin 1-dependent reduction of the peroxiredoxin AhpE from Mycobacterium tuberculosis. J Biol Chem 2013; 289:5228-39. [PMID: 24379404 DOI: 10.1074/jbc.m113.510248] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis (M. tuberculosis), the pathogen responsible for tuberculosis, detoxifies cytotoxic peroxides produced by activated macrophages. M. tuberculosis expresses alkyl hydroxyperoxide reductase E (AhpE), among other peroxiredoxins. So far the system that reduces AhpE was not known. We identified M. tuberculosis mycoredoxin-1 (MtMrx1) acting in combination with mycothiol and mycothiol disulfide reductase (MR), as a biologically relevant reducing system for MtAhpE. MtMrx1, a glutaredoxin-like, mycothiol-dependent oxidoreductase, directly reduces the oxidized form of MtAhpE, through a protein mixed disulfide with the N-terminal cysteine of MtMrx1 and the sulfenic acid derivative of the peroxidatic cysteine of MtAhpE. This disulfide is then reduced by the C-terminal cysteine in MtMrx1. Accordingly, MtAhpE catalyzes the oxidation of wt MtMrx1 by hydrogen peroxide but not of MtMrx1 lacking the C-terminal cysteine, confirming a dithiolic mechanism. Alternatively, oxidized MtAhpE forms a mixed disulfide with mycothiol, which in turn is reduced by MtMrx1 using a monothiolic mechanism. We demonstrated the H2O2-dependent NADPH oxidation catalyzed by MtAhpE in the presence of MR, Mrx1, and mycothiol. Disulfide formation involving mycothiol probably competes with the direct reduction by MtMrx1 in aqueous intracellular media, where mycothiol is present at millimolar concentrations. However, MtAhpE was found to be associated with the membrane fraction, and since mycothiol is hydrophilic, direct reduction by MtMrx1 might be favored. The results reported herein allow the rationalization of peroxide detoxification actions inferred for mycothiol, and more recently, for Mrx1 in cellular systems. We report the first molecular link between a thiol-dependent peroxidase and the mycothiol/Mrx1 pathway in Mycobacteria.
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Goyder MS, Rebeaud F, Pfeifer ME, Kálmán F. Strategies in mass spectrometry for the assignment of Cys-Cys disulfide connectivities in proteins. Expert Rev Proteomics 2013; 10:489-501. [PMID: 24087910 DOI: 10.1586/14789450.2013.837663] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Elucidating disulfide linkage patterns is a crucial part of protein characterization, for which mass spectrometry (MS) is now an indispensable analytical tool. In many cases, MS-based disulfide connectivity assignment is straightforwardly achieved using one-step protein fragmentation in the unreduced form followed by mass measurement of bridged fragments. By contrast, venom proteins, which are receiving increasing interest as potential therapeutics, are a challenge for MS-based disulfide assignment due to their numerous closely spaced cysteines and knotted disulfide structure, requiring creative strategies to determine their connectivity. Today, these include the use of an array of reagents for enzymatic and/or chemical cleavage, partial reduction, differential cysteine labeling and tandem MS. This review aims to describe the toolkit of techniques available to MS users approaching both straightforward and complex disulfide bridge assignments, with a particular focus on strategies utilizing standard instrumentation found in a well-equipped analytical or proteomics laboratory.
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Affiliation(s)
- Miriam S Goyder
- Institute of Life Technologies, University of Applied Sciences Western Switzerland (HES-SO Valais/Wallis), 1950 Sion, Switzerland
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