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Peris-Díaz MD, Orzeł A, Wu S, Mosna K, Barran PE, Krężel A. Combining Native Mass Spectrometry and Proteomics to Differentiate and Map the Metalloform Landscape in Metallothioneins. J Proteome Res 2024; 23:3626-3637. [PMID: 38993068 PMCID: PMC11301679 DOI: 10.1021/acs.jproteome.4c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/13/2024]
Abstract
Within the intricate landscape of the proteome, approximately 30% of all proteins bind metal ions. This repertoire is even larger when considering all the different forms of a protein, known as proteoforms. Here, we propose the term "metalloforms" to refer to different structural or functional variations of a protein resulting from the binding of various hetero- or homogeneous metal ions. Using human Cu(I)/Zn(II)-metallothionein-3 as a representative model, we developed a chemical proteomics strategy to simultaneously differentiate and map Zn(II) and Cu(I) metal binding sites. In the first labeling step, N-ethylmaleimide reacts with Cysteine (Cys), resulting in the dissociation of all Zn(II) ions while Cu(I) remains bound to the protein. In the second labeling step, iodoacetamide is utilized to label Cu(I)-bound Cys residues. Native mass spectrometry (MS) was used to determine the metal/labeling protein stoichiometries, while bottom-up/top-down MS was used to map the Cys-labeled residues. Next, we used a developed methodology to interrogate an isolated rabbit liver metallothionein fraction containing three metallothionein-2 isoforms and multiple Cd(II)/Zn(II) metalloforms. The approach detailed in this study thus holds the potential to decode the metalloproteoform diversity within other proteins.
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Affiliation(s)
- Manuel David Peris-Díaz
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Alicja Orzeł
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Sylwia Wu
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Karolina Mosna
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Artur Krężel
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
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2
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Weggen JT, Bean R, Hui K, Wendeler M, Hubbuch J. Kinetic models towards an enhanced understanding of diverse ADC conjugation reactions. Front Bioeng Biotechnol 2024; 12:1403644. [PMID: 39070164 PMCID: PMC11274341 DOI: 10.3389/fbioe.2024.1403644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/07/2024] [Indexed: 07/30/2024] Open
Abstract
The conjugation reaction is the central step in the manufacturing process of antibody-drug conjugates (ADCs). This reaction generates a heterogeneous and complex mixture of differently conjugated sub-species depending on the chosen conjugation chemistry. The parametrization of the conjugation reaction through mechanistic kinetic models offers a chance to enhance valuable reaction knowledge and ensure process robustness. This study introduces a versatile modeling framework for the conjugation reaction of cysteine-conjugated ADC modalities-site-specific and interchain disulfide conjugation. Various conjugation kinetics involving different maleimide-functionalized payloads were performed, while controlled gradual payload feeding was employed to decelerate the conjugation, facilitating a more detailed investigation of the reaction mechanism. The kinetic data were analyzed with a reducing reversed phase (RP) chromatography method, that can readily be implemented for the accurate characterization of ADCs with diverse drug-to-antibody ratios, providing the conjugation trajectories of the single chains of the monoclonal antibody (mAb). Possible kinetic models for the conjugation mechanism were then developed and selected based on multiple criteria. When calibrating the established model to kinetics involving different payloads, conjugation rates were determined to be payload-specific. Further conclusions regarding the kinetic comparability across the two modalities could also be derived. One calibrated model was used for an exemplary in silico screening of the initial concentrations offering valuable insights for profound understanding of the conjugation process in ADC development.
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Affiliation(s)
- Jan Tobias Weggen
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Ryan Bean
- Purification Process Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Kimberly Hui
- Purification Process Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Michaela Wendeler
- Purification Process Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Jürgen Hubbuch
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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3
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Smythers AL, Joseph KM, O'Dell HM, Clark TA, Crislip JR, Flinn BB, Daughtridge MH, Stair ER, Mubarek SN, Lewis HC, Salas AA, Hnilica ME, Kolling DRJ, Hicks LM. Chemobiosis reveals tardigrade tun formation is dependent on reversible cysteine oxidation. PLoS One 2024; 19:e0295062. [PMID: 38232097 DOI: 10.1371/journal.pone.0295062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/14/2023] [Indexed: 01/19/2024] Open
Abstract
Tardigrades, commonly known as 'waterbears', are eight-legged microscopic invertebrates renowned for their ability to withstand extreme stressors, including high osmotic pressure, freezing temperatures, and complete desiccation. Limb retraction and substantial decreases to their internal water stores results in the tun state, greatly increasing their ability to survive. Emergence from the tun state and/or activity regain follows stress removal, where resumption of life cycle occurs as if stasis never occurred. However, the mechanism(s) through which tardigrades initiate tun formation is yet to be uncovered. Herein, we use chemobiosis to demonstrate that tardigrade tun formation is mediated by reactive oxygen species (ROS). We further reveal that tuns are dependent on reversible cysteine oxidation, and that this reversible cysteine oxidation is facilitated by the release of intracellular reactive oxygen species (ROS). We provide the first empirical evidence of chemobiosis and map the initiation and survival of tardigrades via osmobiosis, chemobiosis, and cryobiosis. In vivo electron paramagnetic spectrometry suggests an intracellular release of reactive oxygen species following stress induction; when this release is quenched through the application of exogenous antioxidants, the tardigrades can no longer survive osmotic stress. Together, this work suggests a conserved dependence of reversible cysteine oxidation across distinct tardigrade cryptobioses.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Kara M Joseph
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Hayden M O'Dell
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Trace A Clark
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Jessica R Crislip
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Brendin B Flinn
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Meredith H Daughtridge
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Evan R Stair
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Saher N Mubarek
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Hailey C Lewis
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Abel A Salas
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Megan E Hnilica
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Derrick R J Kolling
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
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4
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Koo TY, Lai H, Nomura DK, Chung CYS. N-Acryloylindole-alkyne (NAIA) enables imaging and profiling new ligandable cysteines and oxidized thiols by chemoproteomics. Nat Commun 2023; 14:3564. [PMID: 37322008 PMCID: PMC10272157 DOI: 10.1038/s41467-023-39268-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Cysteine has been exploited as the binding site of covalent drugs. Its high sensitivity to oxidation is also important for regulating cellular processes. To identify new ligandable cysteines which can be hotspots for therapy and to better study cysteine oxidations, we develop cysteine-reactive probes, N-acryloylindole-alkynes (NAIAs), which have superior cysteine reactivity owing to delocalization of π electrons of the acrylamide warhead over the whole indole scaffold. This allows NAIAs to probe functional cysteines more effectively than conventional iodoacetamide-alkyne, and to image oxidized thiols by confocal fluorescence microscopy. In mass spectrometry experiments, NAIAs successfully capture new oxidized cysteines, as well as a new pool of ligandable cysteines and proteins. Competitive activity-based protein profiling experiments further demonstrate the ability of NAIA to discover lead compounds targeting these cysteines and proteins. We show the development of NAIAs with activated acrylamide for advancing proteome-wide profiling and imaging ligandable cysteines and oxidized thiols.
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Affiliation(s)
- Tin-Yan Koo
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Hinyuk Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Clive Yik-Sham Chung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China.
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong, P. R. China.
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5
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Disulfide bond and crosslinking analyses reveal inter-domain interactions that contribute to the rigidity of placental malaria VAR2CSA structure and formation of CSA binding channel. Int J Biol Macromol 2023; 226:143-158. [PMID: 36470436 DOI: 10.1016/j.ijbiomac.2022.11.258] [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: 08/26/2022] [Revised: 11/15/2022] [Accepted: 11/24/2022] [Indexed: 12/11/2022]
Abstract
VAR2CSA, a multidomain Plasmodium falciparum protein, mediates the adherence of parasite-infected red blood cells to chondroitin 4-sulfate (C4S) in the placenta, contributing to placental malaria. Therefore, detailed understanding of VAR2CSA structure likely help developing strategies to treat placental malaria. The VAR2CSA ectodomain consists of an N-terminal segment (NTS), six Duffy binding-like (DBL) domains, and three interdomains (IDs) present in sequence NTS-DBL1x-ID1-DBL2x-ID2-DBL3x-DBL4ε-ID3-DBL5ε-DBL6ε. Recent electron microscopy studies showed that VAR2CSA is compactly organized into a globular structure containing C4S-binding channel, and that DBL5ε-DBL6ε arm is attached to the NTS-ID3 core structure. However, the structural elements involved in inter-domain interactions that stabilize the VAR2CSA structure remain largely not understood. Here, limited proteolysis and peptide mapping by mass spectrometry showed that VAR2CSA contains several inter-domain disulfide bonds that stabilize its compact structure. Chemical crosslinking-mass spectrometry showed that all IDs interact with DBL4ε; additionally, IDs interact with other DBL domains, demonstrating that IDs are the key structural scaffolds that shape the functional NTS-ID3 core. Ligand binding analysis suggested that NTS considerably restricts the C4S binding. Overall, our study revealed that inter-domain disulfide bonds and interactions between IDs and DBL domains contribute to the stability of VAR2CSA structural architecture and formation of C4S-binding channel.
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6
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Herrero-Galán E, Martínez-Martín I, Sánchez-González C, Vicente N, Bonzón-Kulichenko E, Calvo E, Suay-Corredera C, Pricolo MR, Fernández-Trasancos Á, Velázquez-Carreras D, Careaga CB, Abdellatif M, Sedej S, Rainer PP, Giganti D, Pérez-Jiménez R, Vázquez J, Alegre-Cebollada J. Basal oxidation of conserved cysteines modulates cardiac titin stiffness and dynamics. Redox Biol 2022; 52:102306. [PMID: 35367810 PMCID: PMC8971355 DOI: 10.1016/j.redox.2022.102306] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/11/2023] Open
Abstract
Titin, as the main protein responsible for the passive stiffness of the sarcomere, plays a key role in diastolic function and is a determinant factor in the etiology of heart disease. Titin stiffness depends on unfolding and folding transitions of immunoglobulin-like (Ig) domains of the I-band, and recent studies have shown that oxidative modifications of cryptic cysteines belonging to these Ig domains modulate their mechanical properties in vitro. However, the relevance of this mode of titin mechanical modulation in vivo remains largely unknown. Here, we describe the high evolutionary conservation of titin mechanical cysteines and show that they are remarkably oxidized in murine cardiac tissue. Mass spectrometry analyses indicate a similar landscape of basal oxidation in murine and human myocardium. Monte Carlo simulations illustrate how disulfides and S-thiolations on these cysteines increase the dynamics of the protein at physiological forces, while enabling load- and isoform-dependent regulation of titin stiffness. Our results demonstrate the role of conserved cysteines in the modulation of titin mechanical properties in vivo and point to potential redox-based pathomechanisms in heart disease.
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Affiliation(s)
| | | | | | - Natalia Vicente
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Elena Bonzón-Kulichenko
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Enrique Calvo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | | | | | | | | | | | | | - Simon Sedej
- Division of Cardiology, Medical University of Graz, Graz, Austria; Faculty of Medicine, University of Maribor, Maribor, Slovenia; BioTechMed Graz, Graz, Austria
| | - Peter P Rainer
- Division of Cardiology, Medical University of Graz, Graz, Austria; BioTechMed Graz, Graz, Austria
| | - David Giganti
- Department of Biochemistry & Molecular Pharmacology and Institute for Systems Genetics, NYU Langone Health, New York, NY, United States
| | - Raúl Pérez-Jiménez
- CIC NanoGUNE BRTA, San Sebastian, Spain; Ikerbasque Foundation for Science, Bilbao, Spain
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
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7
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Yang M, Flaumenhaft R. Oxidative Cysteine Modification of Thiol Isomerases in Thrombotic Disease: A Hypothesis. Antioxid Redox Signal 2021; 35:1134-1155. [PMID: 34121445 PMCID: PMC8817710 DOI: 10.1089/ars.2021.0108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Significance: Oxidative stress is a characteristic of many systemic diseases associated with thrombosis. Thiol isomerases are a family of oxidoreductases important in protein folding and are exquisitely sensitive to the redox environment. They are essential for thrombus formation and represent a previously unrecognized layer of control of the thrombotic process. Yet, the mechanisms by which thiol isomerases function in thrombus formation are unknown. Recent Advances: The oxidoreductase activity of thiol isomerases in thrombus formation is controlled by the redox environment via oxidative changes to active site cysteines. Specific alterations can now be detected owing to advances in the chemical biology of oxidative cysteine modifications. Critical Issues: Understanding of the role of thiol isomerases in thrombus formation has focused largely on identifying single disulfide bond modifications in isolated proteins (e.g., αIIbβ3, tissue factor, vitronectin, or glycoprotein Ibα [GPIbα]). An alternative approach is to conceptualize thiol isomerases as effectors in redox signaling pathways that control thrombotic potential by modifying substrate networks. Future Directions: Cysteine-based chemical biology will be employed to study thiol-dependent dynamics mediated by the redox state of thiol isomerases at the systems level. This approach could identify thiol isomerase-dependent modifications of the disulfide landscape that are prothrombotic.
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Affiliation(s)
- Moua Yang
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
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8
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Blood Plasma Quality Control by Plasma Glutathione Status. Antioxidants (Basel) 2021; 10:antiox10060864. [PMID: 34072235 PMCID: PMC8226592 DOI: 10.3390/antiox10060864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 11/17/2022] Open
Abstract
Timely centrifugation of blood for plasma preparation is a key step to ensure high plasma quality for analytics. Delays during preparation can significantly influence readouts of key clinical parameters. However, in a routine clinical environment, a strictly controlled timeline is often not feasible. The next best approach is to control for sample preparation delays by a marker that provides a readout of the time-dependent degradation of the sample. In this study, we explored the usefulness of glutathione status as potential marker of plasma preparation delay. As the concentration of glutathione in erythrocytes is at least two orders of magnitude higher than in plasma, even the slightest leakage of glutathione from the cells can be readily observed. Over the 3 h observation period employed in this study, we observed a linear increase of plasma concentrations of both reduced (GSH) and oxidized glutathione (GSSG). Artificial oxidation of GSH is prevented by rapid alkylation with N-ethylmaleimide directly in the blood sampling vessel as recently published. The observed relative leakage of GSH was significantly higher than that of GSSG. A direct comparison with plasma lactate dehydrogenase activity, a widely employed hemolysis marker, clearly demonstrated the superiority of our approach for quality control. Moreover, we show that the addition of the thiol alkylating reagent NEM directly to the blood tubes does not influence downstream analysis of other clinical parameters. In conclusion, we report that GSH gives an excellent readout of the duration of plasma preparation and the associated pre-analytical errors.
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9
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Murphy EL, Joy AP, Ouellette RJ, Barnett DA. Optimization of cysteine residue alkylation using an on-line LC-MS strategy: Benefits of using a cocktail of haloacetamide reagents. Anal Biochem 2021; 619:114137. [PMID: 33582115 DOI: 10.1016/j.ab.2021.114137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/31/2022]
Abstract
Several common reagents for the alkylation of cysteine residues of model intact proteins were evaluated for reaction speed, yield of alkylated product and degree of over-alkylation using an online LC-MS platform. The efficiency of the alkylation reaction is found to be dependent on the (1) reagent, (2) peptide/protein, (3) reagent concentration and (4) reaction time. At high reagent concentrations, iodoacetic acid was found to produce significant levels of over-alkylation products wherein methionine residues become modified. For optimal performance of the alkylation reaction, we found the use of a cocktail of chloroacetamide, bromoacetamide and iodoacetamide worked best. The alkylating efficiency of each haloacetamide is a balance between the characteristics of the halogen leaving group and the steric hindrance of the alkylation site on the peptide or protein. A key aspect of using a cocktail of haloacetamides is that they all produce the same modification (+57.0209 Da) to the cysteine residues of the protein while the alkylation efficiency of each site may differ for each of the three reagents. Over-alkylation effects appear to be lower with the cocktail due to a lower concentration of each reagent. The haloacetamide cocktail could be useful when considering complex mixtures of proteins.
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Affiliation(s)
- EmmaRae L Murphy
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada; Department of Process Engineering and Applied Science, Dalhousie University, Sexton Campus Chemical Engineering Building, PO Box 15000, Halifax, Nova Scotia, B3H4R2, Canada
| | - Andrew P Joy
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada
| | - Rodney J Ouellette
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada
| | - David A Barnett
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada; Department of Chemistry and Biochemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L1G8, Canada.
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10
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Peris-Díaz M, Guran R, Zitka O, Adam V, Krężel A. Metal- and Affinity-Specific Dual Labeling of Cysteine-Rich Proteins for Identification of Metal-Binding Sites. Anal Chem 2020; 92:12950-12958. [PMID: 32786475 PMCID: PMC7547867 DOI: 10.1021/acs.analchem.0c01604] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023]
Abstract
Here, using human metallothionein (MT2) as an example, we describe an improved strategy based on differential alkylation coupled to MS, assisted by zinc probe monitoring, for identification of cysteine-rich binding sites with nanomolar and picomolar metal affinity utilizing iodoacetamide (IAM) and N-ethylmaleimide reagents. We concluded that an SN2 reaction provided by IAM is more suitable to label free Cys residues, avoiding nonspecific metal dissociation. Afterward, metal-bound Cys can be easily labeled in a nucleophilic addition reaction after separation by reverse-phase C18 at acidic pH. Finally, we evaluated the efficiency of the method by mapping metal-binding sites of Zn7-xMT species using a bottom-up MS approach with respect to metal-to-protein affinity and element(al) resolution. The methodology presented might be applied not only for MT2 but to identify metal-binding sites in other Cys-containing proteins.
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Affiliation(s)
- Manuel
David Peris-Díaz
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Roman Guran
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Ondrej Zitka
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Vojtech Adam
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Artur Krężel
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
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11
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Mthembu SN, Sharma A, Albericio F, de la Torre BG. Breaking a Couple: Disulfide Reducing Agents. Chembiochem 2020; 21:1947-1954. [PMID: 32196882 DOI: 10.1002/cbic.202000092] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/19/2020] [Indexed: 01/20/2023]
Abstract
Cysteine is present in a large number of natural and synthetic (bio)molecules. Although the thiol side chain of Cys can be in a free form, in most cases it forms a disulfide bond either with a second Cys (bridge) or with another thiol, as in the case of protecting groups. Efficient reduction of these disulfide bridges is a requirement for many applications of Cys-containing molecules in the fields of chemistry and biochemistry. Here we review reducing methods for disulfide bonds, taking into consideration the solubility of the substrates when selecting the appropriate reducing reagent.
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Affiliation(s)
- Sinenhlanhla N Mthembu
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa.,KRISP, School of Laboratory of Medicine and Medical Sciences College of Health Sciences, University of KwaZulu-Natal Westville, Durban, 4001, South Africa
| | - Anamika Sharma
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa.,KRISP, School of Laboratory of Medicine and Medical Sciences College of Health Sciences, University of KwaZulu-Natal Westville, Durban, 4001, South Africa
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa.,Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, Barcelona, 08028, Spain.,CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine IQAC, CSIC, Jordi Girona, Barcelona, 08028, Spain
| | - Beatriz G de la Torre
- KRISP, School of Laboratory of Medicine and Medical Sciences College of Health Sciences, University of KwaZulu-Natal Westville, Durban, 4001, South Africa
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12
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McConnell EW, Smythers AL, Hicks LM. Maleimide-Based Chemical Proteomics for Quantitative Analysis of Cysteine Reactivity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1697-1705. [PMID: 32573231 DOI: 10.1021/jasms.0c00116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cysteine is the most intrinsically nucleophilic residue in proteins and serves as a mediator against increasing reactive oxygen species (ROS) via reversible thiol oxidation. Despite the importance of cysteine oxidation in understanding biological stress response, cysteine sites most reactive toward ROS remain largely unknown and are a major analytical challenge. Herein, a chemical proteomic method to quantify site-specific cysteine reactivity using a maleimide-activated, thiol-reactive probe (N-propargylmaleimide, NPM) is described. Implementation of a gel-based approach via conjugation of rhodamine-azide to NPM-labeled cysteine residues by copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry allowed simple and highly sensitive fluorescence profiling. Relative quantification of >1500 unique cysteine sites from greater than 800 proteins was achieved by conjugating dialkoxydiphenylsilane (DADPS) biotin-azide by the CuAAC reaction and subsequently performing biotin-streptavidin affinity purification and mass-spectrometry-based proteomics. Taken together, this work defines a novel role for the NPM probe in chemical proteomics and presents a robust method for determination of cysteine reactivity during oxidative stress response.
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Affiliation(s)
- Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Amanda L Smythers
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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13
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Kuznetsova KG, Solovyeva EM, Kuzikov AV, Gorshkov MV, Moshkovskii SA. [Modification of cysteine residues for mass spectrometry-based proteomic analysis: facts and artifacts]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2020; 66:18-29. [PMID: 32116223 DOI: 10.18097/pbmc20206601018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mass spectrometric proteomic analysis at the sample preparation stage involves the artificial reduction of disulfide bonds in proteins formed between cysteine residues. Such bonds, when preserved in their native state, complicate subsequent enzymatic hydrolysis and interpretation of the research results. To prevent the re-formation of the disulfide bonds, cysteine residues are protected by special groups, most often by alkylation. In this review, we consider the methods used to modify cysteine residues during sample preparation, as well as possible artifacts of this stage. Particularly, adverse reactions of the alkylating agents with other amino acid residues are described. The most common alkylating compound used to protect cysteine residues in mass spectrometric proteomic analysis is iodoacetamide. However, an analysis of the literature in this area indicates that this reagent causes more adverse reactions than other agents used, such as chloroacetamide and acrylamide. The latter can be recommended for wider use. In the review we also discuss the features of the cysteine residue modifications and their influence on the efficiency of the search for post-translational modifications and protein products of single nucleotide substitutions.
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Affiliation(s)
| | - E M Solovyeva
- Talrose Institute for Energy Problems of Chemical Physics, Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, Russia; Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - A V Kuzikov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - M V Gorshkov
- Talrose Institute for Energy Problems of Chemical Physics, Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - S A Moshkovskii
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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Tomin T, Schittmayer M, Birner-Gruenberger R. Addressing Glutathione Redox Status in Clinical Samples by Two-Step Alkylation with N-ethylmaleimide Isotopologues. Metabolites 2020; 10:metabo10020071. [PMID: 32079090 PMCID: PMC7074022 DOI: 10.3390/metabo10020071] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/13/2020] [Accepted: 02/15/2020] [Indexed: 01/10/2023] Open
Abstract
Determination of the ratio of reduced to oxidized glutathione is of profound clinical interest in assessing the oxidative status of tissues and body fluids. However, this ratio is not yet a routine clinical parameter due to the analytically challenging interconversion of reduced (free) glutathione to oxidized (bound) glutathione. We aimed to facilitate this ratio determination in order to aid its incorporation as a routine clinical parameter. To this end, we developed a simple derivatization route that yields different isotopologues of N-ethylmaleimide alkylated glutathione from reduced and oxidized glutathione (after its chemical reduction) for mass spectrometric analysis. A third isotopologue can be used as isotopic standard for simultaneous absolute quantification. As all isotopologues have similar chromatographic properties, matrix effects arising from different sample origins can only impact method sensitivity but not quantification accuracy. Robustness, simplified data analysis, cost effectiveness by one common standard, and highly improved mass spectrometric sensitivity by conversion of oxidized glutathione to an alkylated glutathione isotopologue are the main advantages of our approach. We present a method fully optimized for blood, plasma, serum, cell, and tissue samples. In addition, we propose production of N-ethylmaleimide customized blood collection tubes to even further facilitate the analysis in a clinical setting.
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Affiliation(s)
- Tamara Tomin
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology—TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Matthias Schittmayer
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology—TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
- Correspondence: (M.S.); (R.B.-G.)
| | - Ruth Birner-Gruenberger
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology—TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
- Correspondence: (M.S.); (R.B.-G.)
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15
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Comparison of N-ethyl maleimide and N-(1-phenylethyl) maleimide for derivatization of biological thiols using liquid chromatography-mass spectrometry. Anal Bioanal Chem 2020; 412:1639-1652. [PMID: 32016570 DOI: 10.1007/s00216-020-02398-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/18/2019] [Accepted: 01/08/2020] [Indexed: 01/13/2023]
Abstract
The ratio between reduced and oxidized thiols, mainly glutathione and oxidized glutathione, is one of the biomarkers for the evaluation of oxidative stress. The accurate measurement of thiol concentrations is challenging because reduced thiols are easily oxidized during sample manipulation. Derivatization is commonly used to protect thiols from oxidation. The objective of this work was to systematically compare two cell-permeable derivatizing agents: N-ethyl maleimide (NEM) and (R)-(+)-N-(1-phenylethyl)maleimide (NPEM) in terms of derivatization efficiency, ionization enhancement, side product formation, reaction selectivity for thiols, pH dependence of the reaction, and derivative stability. All thiol measurements and the characterization of side products were performed using a biphenyl reversed phase liquid chromatography-high-resolution mass spectrometry (LC-HRMS). Four thiols, cysteine (CYS), homocysteine, N-acetylcysteine (NAC), and glutathione (GSH), were used for the evaluation. Using 1:10 ratio of thiol:derivatizing agent, complete derivatization was obtained within 30 min for both agents tested with the exception of CYS-NEM, where 97% efficiency was obtained. The more hydrophobic NPEM provided better ionization of the thiols, with enhancement ranging from 2.1x for GSH to 5.7x for CYS in comparison to NEM. NPEM derivatization led to more extensive side reactions, such as double derivatization and ring opening, which hindered the accurate measurement of the thiol concentrations. Both NEM and NPEM also showed poor stability of CYS derivative due to its time-dependent conversion to cyclic cysteine-maleimide derivative. Both reagents also showed significant reactivity with amine-containing metabolites depending on the pH used during derivatization, but overall NEM was found to be more selective towards thiol group than NPEM. Taking into account all evaluation criteria, NEM was selected as a more suitable reagent for the thiol protection and derivatization, but strict control of pH 7.0 is recommended to minimize the side reactions. This work illustrates the importance of the characterization of side products and derivative stability during the evaluation of thiol derivatizing agents and contributes fundamental understanding to improve the accuracy of thiol determinations. The key sources of errors during maleimide derivatization include the derivatization of amine-containing metabolites, poor derivative stability of certain thiols (CYS and NAC), and the side reactions especially if ring opening of the reagent is not minimized. Graphical abstract.
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Wiśniewski JR, Zettl K, Pilch M, Rysiewicz B, Sadok I. 'Shotgun' proteomic analyses without alkylation of cysteine. Anal Chim Acta 2019; 1100:131-137. [PMID: 31987133 DOI: 10.1016/j.aca.2019.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/12/2019] [Accepted: 12/01/2019] [Indexed: 12/29/2022]
Abstract
It is a common belief that reduction of disulfide bridges and alkylation of thiols in proteins are indispensable steps in proteomic sample preparation. Since this chemical procedure is often incomplete and prone to side reactions we reexamined its importance. We found that reduction and alkylation do not increase the depth of analysis and quality of proteomic quantification and therefore these steps are not essential in 'shotgun'-type investigations of proteomes. Moreover, we found that compared to a standard procedure using iodoacetamide for thiol-alkylation, sample preparation under conditions protecting thiols from oxidation improves quality of peptides and allows identifying of 10-20% more peptides and proteins. Excluding thiol-alkylation from proteomic sample preparation shortens the workflows and decreases the probability of biases resulting from occurrence of artificially modified peptides.
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Affiliation(s)
- Jacek R Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.
| | - Katharina Zettl
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany
| | - Magdalena Pilch
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.
| | - Beata Rysiewicz
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.
| | - Ilona Sadok
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.
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17
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Ford MM, Smythers AL, McConnell EW, Lowery SC, Kolling DRJ, Hicks LM. Inhibition of TOR in Chlamydomonas reinhardtii Leads to Rapid Cysteine Oxidation Reflecting Sustained Physiological Changes. Cells 2019; 8:cells8101171. [PMID: 31569396 PMCID: PMC6829209 DOI: 10.3390/cells8101171] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/16/2019] [Accepted: 09/26/2019] [Indexed: 12/16/2022] Open
Abstract
The target of rapamycin (TOR) kinase is a master metabolic regulator with roles in nutritional sensing, protein translation, and autophagy. In Chlamydomonas reinhardtii, a unicellular green alga, TOR has been linked to the regulation of increased triacylglycerol (TAG) accumulation, suggesting that TOR or a downstream target(s) is responsible for the elusive “lipid switch” in control of increasing TAG accumulation under nutrient limitation. However, while TOR has been well characterized in mammalian systems, it is still poorly understood in photosynthetic systems, and little work has been done to show the role of oxidative signaling in TOR regulation. In this study, the TOR inhibitor AZD8055 was used to relate reversible thiol oxidation to the physiological changes seen under TOR inhibition, including increased TAG content. Using oxidized cysteine resin-assisted capture enrichment coupled with label-free quantitative proteomics, 401 proteins were determined to have significant changes in oxidation following TOR inhibition. These oxidative changes mirrored characterized physiological modifications, supporting the role of reversible thiol oxidation in TOR regulation of TAG production, protein translation, carbohydrate catabolism, and photosynthesis through the use of reversible thiol oxidation. The delineation of redox-controlled proteins under TOR inhibition provides a framework for further characterization of the TOR pathway in photosynthetic eukaryotes.
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Affiliation(s)
- Megan M Ford
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Amanda L Smythers
- Department of Chemistry, Marshall University, Huntington, WV 25755, USA.
| | - Evan W McConnell
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Sarah C Lowery
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | | | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Solis N, Parambath A, Abbina S, Kizhakkedathu J, Overall CM. Simplified high yield TAILS terminomics using a new HPG-ALD 800K-2000 polymer with precipitation. Methods Enzymol 2019; 626:429-446. [PMID: 31606086 DOI: 10.1016/bs.mie.2019.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Identification of the N terminus of proteins in complex samples has been accelerated in recent years by the increased power of mass spectrometers, bioinformatic tools and biochemical methods. We developed Terminal Amine Isotopic Labeling of Substrates (TAILS), a powerful method for the isolation, identification and quantification of N terminal peptides comprising the N terminome from proteome in vitro analyses, cultured cells and tissues. TAILS depletes internal tryptic peptides so enriching for the natural and cleaved neo N-terminal peptides present in complex proteome samples. To do so N-terminal peptides are blocked at the protein level by isotopically labeled amine reactive reagents, then digested with trypsin. TAILS relies on a water-soluble 100-kDa highly-branched polyglycerol polymer (HPG-ALD) developed in our laboratories to bind and deplete the sample of tryptic peptides. Polymer-bound internal tryptic peptides are separated from the blocked N-terminal peptides by spin filters. Here we describe a revised TAILS protocol that uses a newly developed 800-kDa HPG-ALD polymer that allows precipitation of the polymer post-depletion. Precipitation has multiple advantages over spin filters including maximal N-terminal peptide recovery and faster high-throughput N-terminome identification and quantification in any sample type.
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Affiliation(s)
- Nestor Solis
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Anilkumar Parambath
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Srinivas Abbina
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jayachandran Kizhakkedathu
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Christopher M Overall
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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19
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Bègue H, Besson-Bard A, Blanchard C, Winckler P, Bourque S, Nicolas V, Wendehenne D, Rosnoblet C. The chaperone-like protein CDC48 regulates ascorbate peroxidase in tobacco. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2665-2681. [PMID: 30821322 PMCID: PMC6506776 DOI: 10.1093/jxb/erz097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 02/14/2019] [Accepted: 02/27/2019] [Indexed: 06/09/2023]
Abstract
There is increasing evidence that the chaperone-like protein CDC48 (cell division cycle 48) plays a role in plant immunity. Cytosolic ascorbate peroxidase (cAPX), which is a major regulator of the redox status of plant cells, has previously been shown to interact with CDC48. In this study, we examined the regulation of cAPX by the ATPase NtCDC48 during the cryptogein-induced immune response in tobacco cells. Our results not only confirmed the interaction between the proteins but also showed that it occurs in the cytosol. cAPX accumulation was modified in cells overexpressing NtCDC48, a process that was shown to involve post-translational modification of cAPX. In addition, cryptogein-induced increases in cAPX activity were suppressed in cells overexpressing NtCDC48 and the abundance of the cAPX dimer was below the level of detection. Furthermore, the levels of both reduced (GSH) and oxidized glutathione (GSSG) and the GSH/GSSG ratio decreased more rapidly in response to the elicitor in these cells than in controls. A decrease in cAPX activity was also observed in response to heat shock in the cells overexpressing NtCDC48, indicating that the regulation of cAPX by NtCDC48 is not specific to the immune response.
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Affiliation(s)
- Hervé Bègue
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Angélique Besson-Bard
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Cécile Blanchard
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Pascale Winckler
- Plateforme Dimacell/Imagerie spectroscopique UMR Procédés Alimentaires et Microbiologiques Equipe Procédés Microbiologiques et Biotechnologiques, AgroSup Dijon Nord, Dijon, France
| | - Stéphane Bourque
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Valérie Nicolas
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - David Wendehenne
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Claire Rosnoblet
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
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20
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Reducing Complexity? Cysteine Reduction and S-Alkylation in Proteomic Workflows: Practical Considerations. Methods Mol Biol 2019; 1977:83-97. [PMID: 30980324 DOI: 10.1007/978-1-4939-9232-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Reduction and alkylation are common processing steps in sample preparation for qualitative and quantitative proteomic analyses. In principle, these steps mitigate the limitations resulting from the presence of disulfide bridges. There has been recurring debate in the proteomics community around their use, with concern over negative impacts that result from overalkylation (off-target, non-thiol sites) or incomplete reduction and/or S-alkylation of cysteine. This chapter integrates findings from a number of studies on different reduction and alkylation strategies, to guide users in experimental design for their optimal use in proteomic workflows.
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21
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Emery SJ, Baker L, Ansell BRE, Mirzaei M, Haynes PA, McConville MJ, Svärd SG, Jex AR. Differential protein expression and post-translational modifications in metronidazole-resistant Giardia duodenalis. Gigascience 2018; 7:4931738. [PMID: 29688452 PMCID: PMC5913674 DOI: 10.1093/gigascience/giy024] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 03/06/2018] [Indexed: 01/20/2023] Open
Abstract
Background Metronidazole (Mtz) is the frontline drug treatment for multiple anaerobic pathogens, including the gastrointestinal protist, Giardia duodenalis. However, treatment failure is common and linked to in vivo drug resistance. In Giardia, in vitro drug-resistant lines allow controlled experimental interrogation of resistance mechanisms in isogenic cultures. However, resistance-associated changes are inconsistent between lines, phenotypic data are incomplete, and resistance is rarely genetically fixed, highlighted by reversion to sensitivity after drug selection ceases or via passage through the life cycle. Comprehensive quantitative approaches are required to resolve isolate variability, fully define Mtz resistance phenotypes, and explore the role of post-translational modifications therein. Findings We performed quantitative proteomics to describe differentially expressed proteins in 3 seminal Mtz-resistant lines compared to their isogenic, Mtz-susceptible, parental line. We also probed changes in post-translational modifications including protein acetylation, methylation, ubiquitination, and phosphorylation via immunoblotting. We quantified more than 1,000 proteins in each genotype, recording substantial genotypic variation in differentially expressed proteins between isotypes. Our data confirm substantial changes in the antioxidant network, glycolysis, and electron transport and indicate links between protein acetylation and Mtz resistance, including cross-resistance to deacetylase inhibitor trichostatin A in Mtz-resistant lines. Finally, we performed the first controlled, longitudinal study of Mtz resistance stability, monitoring lines after cessation of drug selection, revealing isolate-dependent phenotypic plasticity. Conclusions Our data demonstrate understanding that Mtz resistance must be broadened to post-transcriptional and post-translational responses and that Mtz resistance is polygenic, driven by isolate-dependent variation, and is correlated with changes in protein acetylation networks.
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Affiliation(s)
- Samantha J Emery
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Louise Baker
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Brendan R E Ansell
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Mehdi Mirzaei
- Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, North Ryde, NSW, Australia.,Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW, Australia
| | - Paul A Haynes
- Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, North Ryde, NSW, Australia
| | - Malcom J McConville
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Aaron R Jex
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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22
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Zhang Y, Kang A, Deng H, Shi L, Su S, Yu L, Xie T, Shan J, Wen H, Chi Y, Han S, Su R, Song Y, Chen X, Shaikh AB. Simultaneous determination of sulfur compounds from the sulfur pathway in rat plasma by liquid chromatography tandem mass spectrometry: application to the study of the effect of Shao Fu Zhu Yu decoction. Anal Bioanal Chem 2018; 410:3743-3755. [PMID: 29632971 DOI: 10.1007/s00216-018-1038-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/17/2018] [Accepted: 03/20/2018] [Indexed: 02/07/2023]
Abstract
A sensitive, accurate, and time-saving approach was developed for the simultaneous quantification of eight sulfur compounds in the sulfur pathway, which could reflect the status of an organism, including oxidative stress, signal transduction, enzyme reaction, and so on. In order to overcome the instability of highly reactive sulfhydryl compounds, N-ethylmaleimide derivatization was adopted to effectively protect sulfhydryl-containing samples. Using isotope-labeled glutathione (GSH-13C2, 15N), the validated method was demonstrated to offer satisfactory linearity, accuracy, and precision. Separation was done by UHPLC, using a BEH amide column. Accordingly, 0.1% formic acid acetonitrile was selected as the precipitant. A tandem mass spectrometer was coupled to the chromatographic system and afforded a detection limit of 0.2 ng/mL. Good linearity was maintained over a wide concentration range (r2 > 0.994), and the accuracy was in the range of 86.6-114% for all the studied compounds. The precision, expressed in RSD%, ranged from 1.1% to 9.4% as intraday variability and less than 13% as interday precision for all of the analytes. The approach was applied to study the potential therapeutic mechanism of a well-known traditional Chinese medicine, Shao Fu Zhu Yu decoction. The results suggested that Shao Fu Zhu Yu decoction might protect against oxidative damage by increasing the concentrations of sulfhydryl compounds. Graphical abstract An approach to quantitatively determining sulfur compounds in the sulfur pathway simultaneously wasestablished and applied to the study of the effect of Shao Fu Zhu Yu decoction.
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Affiliation(s)
- Yue Zhang
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
- Section in Pharmaceutical Analysis, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - An Kang
- Section in Pharmaceutical Analysis, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - Haishan Deng
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China.
- Section in Pharmaceutical Analysis, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China.
| | - Le Shi
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - Shulan Su
- Jiangsu Key Laboratory for TCM Formulae Research, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - Li Yu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - Tong Xie
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - Jinjun Shan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China.
| | - Hongmei Wen
- Section in Pharmaceutical Analysis, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - Yumei Chi
- Section in Pharmaceutical Analysis, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - Shuying Han
- Section in Pharmaceutical Analysis, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - Ruilin Su
- Section in Pharmaceutical Analysis, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - Yilin Song
- Section in Pharmaceutical Analysis, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - Xi Chen
- Section in Pharmaceutical Analysis, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China
| | - Armaan Basheer Shaikh
- Jurong Country Garden School, 2 Qiuzhi Road, Jurong Economic Development Zone, Zhenjiang, 212426, Jiangsu, China
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Nazari M, Bokhart MT, Loziuk PL, Muddiman DC. Quantitative mass spectrometry imaging of glutathione in healthy and cancerous hen ovarian tissue sections by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI). Analyst 2018; 143:654-661. [PMID: 29323367 PMCID: PMC5788707 DOI: 10.1039/c7an01828b] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A quantitative mass spectrometry imaging (QMSI) method for absolute quantification of glutathione (GSH) in healthy and cancerous hen ovarian tissues using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is presented. Using this technique, the ion abundance of GSH was normalized to that of a structural analogue, which was sprayed on the slide prior to mounting the tissue sections. This normalization strategy significantly improved the voxel-to-voxel variability; the variability is attributed to the overall ionization process. Subsequently, a series of calibration spots of stable isotope-labeled (SIL) GSH were pipetted on top of the tissue to construct a spatial calibration curve, and calculate the concentration of GSH in both tissue sections. The QMSI results were verified by LC-MS/MS quantification of GSH for the same tissues. GSH was extracted from tissue sections in a slightly acidic buffer and was then alkylated using N-ethylmaleimide to minimize autoxidation of GSH to glutathione disulfide. The alkylated GSH was separated from other contaminants using reversed phase liquid chromatography (RPLC) coupled to a triple quadrupole mass spectrometer, and the z-ion transition of NEM-GSH was used to quantify GSH in each tissue section. While the absolute values obtained using IR-MALDESI QMSI and LC-MS/MS were different, a ∼2-fold increase in the concentration of GSH in cancer tissue compared to the healthy tissue was observed using both techniques. Possible reasons for the difference between absolute concentration values obtained using IR-MALDESI QMSI and LC-MS/MS are also discussed.
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Affiliation(s)
- Milad Nazari
- Department of Chemistry and Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC 27695, USA.
| | - Mark T Bokhart
- Department of Chemistry and Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC 27695, USA.
| | - Philip L Loziuk
- Department of Chemistry and Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC 27695, USA.
| | - David C Muddiman
- Department of Chemistry and Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC 27695, USA.
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24
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Suttapitugsakul S, Xiao H, Smeekens J, Wu R. Evaluation and optimization of reduction and alkylation methods to maximize peptide identification with MS-based proteomics. MOLECULAR BIOSYSTEMS 2017; 13:2574-2582. [PMID: 29019370 PMCID: PMC5698164 DOI: 10.1039/c7mb00393e] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mass spectrometry (MS) has become an increasingly important technique to analyze proteins. In popular bottom-up MS-based proteomics, reduction and alkylation are routine steps to facilitate peptide identification. However, incomplete reactions and side reactions may occur, which compromise the experimental results. In this work, we systematically evaluated the reduction step with commonly used reagents, i.e., dithiothreitol, 2-mercaptoethanol, tris(2-carboxyethyl)phosphine, or tris(3-hydroxypropyl)phosphine, and alkylation with iodoacetamide, acrylamide, N-ethylmaleimide, or 4-vinylpyridine. By using digested peptides from a yeast whole-cell lysate, the number of proteins and peptides identified were very similar using four different reducing reagents. The results from four alkylating reagents, however, were dramatically different with iodoacetamide giving the highest number of peptides with alkylated cysteine and the lowest number of peptides with incomplete cysteine alkylation and side reactions. Alkylation conditions with iodoacetamide were further optimized. To identify more peptides with cysteine, thiopropyl-sepharose 6B resins were used to enrich them, and the optimal conditions were employed for the reduction and alkylation. The enrichment resulted in over three times more cysteine-containing peptides than without enrichment. Systematic evaluation of the reduction and alkylation with different reagents can aid in a better design of bottom-up proteomic experiments.
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Affiliation(s)
- Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
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25
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Wang Q, Zhang C, Guo F, Li Z, Liu Y, Su Z. Novel Bioconjugation Strategy Using Elevated Hydrostatic Pressure: A Case Study for the Site-Specific Attachment of Polyethylene Glycol (PEGylation) of Recombinant Human Ciliary Neurotrophic Factor. Bioconjug Chem 2017; 28:2841-2848. [DOI: 10.1021/acs.bioconjchem.7b00531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Qi Wang
- State
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North Second Street, Zhong-Guan
Village, Beijing 100190, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chun Zhang
- State
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North Second Street, Zhong-Guan
Village, Beijing 100190, PR China
| | - Fangxia Guo
- State
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North Second Street, Zhong-Guan
Village, Beijing 100190, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zenglan Li
- State
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North Second Street, Zhong-Guan
Village, Beijing 100190, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yongdong Liu
- State
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North Second Street, Zhong-Guan
Village, Beijing 100190, PR China
| | - Zhiguo Su
- State
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North Second Street, Zhong-Guan
Village, Beijing 100190, PR China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, 210023, PR China
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26
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Nitric Oxide Modulates HCN Channels in Magnocellular Neurons of the Supraoptic Nucleus of Rats by an S-Nitrosylation-Dependent Mechanism. J Neurosci 2017; 36:11320-11330. [PMID: 27807172 DOI: 10.1523/jneurosci.1588-16.2016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/14/2016] [Indexed: 12/19/2022] Open
Abstract
The control of the excitability in magnocellular neurosecretory cells (MNCs) of the supraoptic nucleus has been attributed mainly to synaptic inputs from circunventricular organs. However, nitric oxide (NO), a gaseous messenger produced in this nucleus during isotonic and short-term hypertonic conditions, is an example of a modulator that can act directly on MNCs to modulate their firing rate. NO inhibits the electrical excitability of MNCs, leading to a decrease in the release of vasopressin and oxytocin. Although the effects of NO on MNCs are well established, the mechanism by which this gas produces its effect is, so far, unknown. Because NO acts independently of synaptic inputs, we hypothesized that ion channels present in MNCs are the targets of NO. To investigate this hypothesis, we used the patch-clamp technique in vitro and in situ to measure currents carried by hyperpolarization-activated and nucleotide-gated cation (HCN) channels and establish their role in determining the electrical excitability of MNCs in rats. Our results show that blockade of HCN channels by ZD7288 decreases MNC firing rate with significant consequences on the release of OT and VP, measured by radioimmunoassay. NO induced a significant reduction in HCN currents by binding to cysteine residues and forming S-nitrosothiol complexes. These findings shed new light on the mechanisms that control the electrical excitability of MNCs via the nitrergic system and strengthen the importance of HCN channels in the control of hydroelectrolyte homeostasis. SIGNIFICANCE STATEMENT Cells in our organism live in a liquid environment whose composition and osmolality are maintained within tight limits. Magnocellular neurons (MNCs) of the supra optic nucleus can sense osmolality and control the synthesis and secretion of vasopressin (VP) and oxytocin (OT) by the neurohypophysis. OT and VP act on the kidneys controlling the excretion of water and sodium to maintain homeostasis. Here we combined electrophysiology, molecular biology, and radioimmunoassay to show that the electrical activity of MNCs can be controlled by nitric oxide (NO), a gaseous messenger. NO reacts with cysteine residues (S-nitrosylation) on hyperpolarization-activated and nucleotide-gated cation channels decreasing the firing rate of MNCs and the consequent secretion of VP and OT.
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27
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Albumin-based drug delivery using cysteine 34 chemical conjugates – important considerations and requirements. Ther Deliv 2017; 8:511-519. [DOI: 10.4155/tde-2017-0038] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The long blood circulation time of albumin has been clinically utilized as a half-life extension technology for improved drug performance. The availability of one free thiol for site-selective chemical conjugation offers an alternative approach to current genetic fusion and association-based products. This special report highlights important factors for successful conjugation that allows the reader to design and evaluate next-generation albumin conjugates. Albumin type, available conjugation chemistries, linker length, animal models and influence of conjugation on albumin pharmacokinetics and drug activity are discussed.
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28
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Vandesquille M, Li T, Po C, Ganneau C, Lenormand P, Dudeffant C, Czech C, Grueninger F, Duyckaerts C, Delatour B, Dhenain M, Lafaye P, Bay S. Chemically-defined camelid antibody bioconjugate for the magnetic resonance imaging of Alzheimer's disease. MAbs 2017; 9:1016-1027. [PMID: 28657418 DOI: 10.1080/19420862.2017.1342914] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Today, molecular imaging of neurodegenerative diseases is mainly based on small molecule probes. Alternatively, antibodies are versatile tools that may be developed as new imaging agents. Indeed, they can be readily obtained to specifically target any antigen of interest and their scaffold can be functionalized. One of the critical issues involved in translating antibody-based probes to the clinic is the design and synthesis of perfectly-defined conjugates. Camelid single-domain antibody-fragments (VHHs) are very small and stable antibodies that are able to diffuse in tissues and potentially cross the blood brain barrier (BBB). Here, we selected a VHH (R3VQ) specifically targeting one of the main lesions of Alzheimer's disease (AD), namely the amyloid-beta (Aß) deposits. It was used as a scaffold for the design of imaging probes for magnetic resonance imaging (MRI) and labeled with the contrastophore gadolinium using either a random or site-specific approach. In contrast to the random strategy, the site-specific conjugation to a single reduced cysteine in the C-terminal part of the R3VQ generates a well-defined bioconjugate in a high yield process. This new imaging probe is able to cross the BBB and label Aß deposits after intravenous injection. Also, it displays improved r1 and r2 relaxivities, up to 30 times higher than a widely used clinical contrast agent, and it allows MRI detection of amyloid deposits in post mortem brain tissue of a mouse model of AD. The ability to produce chemically-defined VHH conjugates that cross the BBB opens the way for future development of tailored imaging probes targeting intracerebral antigens.
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Affiliation(s)
- Matthias Vandesquille
- a Institut Pasteur, Unité de Chimie des Biomolécules, Département Biologie Structurale et Chimie , Paris , France.,b CNRS UMR 3523, 75724 , France.,d French Alternative Energies and Atomic Energy Commission , Institute of Biomedical Imaging, Molecular Imaging Research Center , Fontenay-aux-Roses , France
| | - Tengfei Li
- c Institut Pasteur, CITECH, Plateforme d'Ingénierie des Anticorps , 75724 , Paris , France.,e Sorbonne Universités, UPMC Univ. Paris 06 UMR S 1127, and Inserm, U 1127, and CNRS UMR 7225, and ICM, 75013, Paris , France.,f Université Paris Diderot-Paris 7, Paris , France
| | - Chrystelle Po
- a Institut Pasteur, Unité de Chimie des Biomolécules, Département Biologie Structurale et Chimie , Paris , France.,b CNRS UMR 3523, 75724 , France.,d French Alternative Energies and Atomic Energy Commission , Institute of Biomedical Imaging, Molecular Imaging Research Center , Fontenay-aux-Roses , France
| | - Christelle Ganneau
- a Institut Pasteur, Unité de Chimie des Biomolécules, Département Biologie Structurale et Chimie , Paris , France.,b CNRS UMR 3523, 75724 , France
| | - Pascal Lenormand
- c Institut Pasteur, CITECH, Plateforme d'Ingénierie des Anticorps , 75724 , Paris , France
| | - Clémence Dudeffant
- e Sorbonne Universités, UPMC Univ. Paris 06 UMR S 1127, and Inserm, U 1127, and CNRS UMR 7225, and ICM, 75013, Paris , France
| | - Christian Czech
- g F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development, NORD DTA, Roche Innovation Center Basel , Basel , Switzerland
| | - Fiona Grueninger
- g F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development, NORD DTA, Roche Innovation Center Basel , Basel , Switzerland
| | - Charles Duyckaerts
- e Sorbonne Universités, UPMC Univ. Paris 06 UMR S 1127, and Inserm, U 1127, and CNRS UMR 7225, and ICM, 75013, Paris , France
| | - Benoît Delatour
- e Sorbonne Universités, UPMC Univ. Paris 06 UMR S 1127, and Inserm, U 1127, and CNRS UMR 7225, and ICM, 75013, Paris , France
| | - Marc Dhenain
- d French Alternative Energies and Atomic Energy Commission , Institute of Biomedical Imaging, Molecular Imaging Research Center , Fontenay-aux-Roses , France
| | - Pierre Lafaye
- c Institut Pasteur, CITECH, Plateforme d'Ingénierie des Anticorps , 75724 , Paris , France
| | - Sylvie Bay
- a Institut Pasteur, Unité de Chimie des Biomolécules, Département Biologie Structurale et Chimie , Paris , France.,b CNRS UMR 3523, 75724 , France
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29
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Müller T, Winter D. Systematic Evaluation of Protein Reduction and Alkylation Reveals Massive Unspecific Side Effects by Iodine-containing Reagents. Mol Cell Proteomics 2017; 16:1173-1187. [PMID: 28539326 DOI: 10.1074/mcp.m116.064048] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 05/23/2017] [Indexed: 12/27/2022] Open
Abstract
Reduction and alkylation of cysteine residues is part of virtually any proteomics workflow. Despite its frequent use, up to date no systematic investigation of the impact of different conditions on the outcome of proteomics studies has been performed. In this study, we compared common reduction reagents (dithiothreitol, tris-(2-carboxyethyl)-phosphine, and β-mercaptoethanol) and alkylation reagents (iodoacetamide, iodoacetic acid, acrylamide, and chloroacetamide). Using in-gel digests as well as SAX fractionated in-solution digests of cytosolic fractions of HeLa cells, we evaluated 13 different reduction and alkylation conditions resulting in considerably varying identification rates. We observed strong differences in offsite alkylation reactions at 7 amino acids as well as at the peptide N terminus, identifying single and double adducts of all reagents. Using dimethyl labeling, mass tolerant searches, and synthetic peptide experiments, we identified alkylation of methionine residues by iodine-containing alkylation reagents as one of the major factors for the differences. We observed differences of more than 9-fold in numbers of identified methionine-containing peptide spectral matches for in-gel digested samples between iodine- and noniodine-containing alkylation reagents. This was because of formation of carbamidomethylated and carboxymethylated methionine side chains and a resulting prominent neutral loss during ESI ionization or in MS/MS fragmentation, strongly decreasing identification rates of methionine-containing peptides. We achieved best results with acrylamide as alkylation reagent, whereas the highest numbers of peptide spectral matches were obtained when reducing with dithiothreitol and β-mercaptoethanol for the in-solution and the in-gel digested samples, respectively.
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Affiliation(s)
- Torsten Müller
- From the ‡Institute for Biochemistry and Molecular Biology, University of Bonn, Germany
| | - Dominic Winter
- From the ‡Institute for Biochemistry and Molecular Biology, University of Bonn, Germany
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30
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Boyatzis AE, Bringans SD, Piggott MJ, Duong MN, Lipscombe RJ, Arthur PG. Limiting the Hydrolysis and Oxidation of Maleimide–Peptide Adducts Improves Detection of Protein Thiol Oxidation. J Proteome Res 2017; 16:2004-2015. [DOI: 10.1021/acs.jproteome.6b01060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Amber E. Boyatzis
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - Matthew J. Piggott
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Marisa N. Duong
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - Peter G. Arthur
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
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31
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Kellermann G, Dingli F, Masson V, Dauzonne D, Ségal-Bendirdjian E, Teulade-Fichou MP, Loew D, Bombard S. Exploring the mechanism of inhibition of human telomerase by cysteine-reactive compounds. FEBS Lett 2017; 591:863-874. [DOI: 10.1002/1873-3468.12589] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 01/30/2017] [Accepted: 02/04/2017] [Indexed: 11/05/2022]
Affiliation(s)
| | - Florent Dingli
- Laboratoire de Spectrometrie de Masse Protéomique; Institut Curie; University PSL; Paris France
| | - Vanessa Masson
- Laboratoire de Spectrometrie de Masse Protéomique; Institut Curie; University PSL; Paris France
| | - Daniel Dauzonne
- Département Recherche; CNRS UMR3666/INSERM U1143; Institut Curie; Paris Cedex 05 France
| | | | | | - Damarys Loew
- Laboratoire de Spectrometrie de Masse Protéomique; Institut Curie; University PSL; Paris France
| | - Sophie Bombard
- INSERM UMR-S 1007; Université Paris Descartes; France
- CNRS UMR9187/INSERM U1196; Institut Curie; Centre Universitaire; University Paris Sud; Orsay France
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32
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Han J, Weisbrod RM, Shao D, Watanabe Y, Yin X, Bachschmid MM, Seta F, Janssen-Heininger YMW, Matsui R, Zang M, Hamburg NM, Cohen RA. The redox mechanism for vascular barrier dysfunction associated with metabolic disorders: Glutathionylation of Rac1 in endothelial cells. Redox Biol 2016; 9:306-319. [PMID: 27693992 PMCID: PMC5045950 DOI: 10.1016/j.redox.2016.09.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Oxidative stress is implicated in increased vascular permeability associated with metabolic disorders, but the underlying redox mechanism is poorly defined. S-glutathionylation, a stable adduct of glutathione with protein sulfhydryl, is a reversible oxidative modification of protein and is emerging as an important redox signaling paradigm in cardiovascular physiopathology. The present study determines the role of protein S-glutathionylation in metabolic stress-induced endothelial cell permeability. METHODS AND RESULTS In endothelial cells isolated from patients with type-2 diabetes mellitus, protein S-glutathionylation level was increased. This change was also observed in aortic endothelium in ApoE deficient (ApoE-/-) mice fed on Western diet. Metabolic stress-induced protein S-glutathionylation in human aortic endothelial cells (HAEC) was positively correlated with elevated endothelial cell permeability, as reflected by disassembly of cell-cell adherens junctions and cortical actin structures. These impairments were reversed by adenoviral overexpression of a specific de-glutathionylation enzyme, glutaredoxin-1 in cultured HAECs. Consistently, transgenic overexpression of human Glrx-1 in ApoE-/- mice fed the Western diet attenuated endothelial protein S-glutathionylation, actin cytoskeletal disorganization, and vascular permeability in the aorta. Mechanistically, glutathionylation and inactivation of Rac1, a small RhoGPase, were associated with endothelial hyperpermeability caused by metabolic stress. Glutathionylation of Rac1 on cysteine 81 and 157 located adjacent to guanine nucleotide binding site was required for the metabolic stress to inhibit Rac1 activity and promote endothelial hyperpermeability. CONCLUSIONS Glutathionylation and inactivation of Rac1 in endothelial cells represent a novel redox mechanism of vascular barrier dysfunction associated with metabolic disorders.
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Affiliation(s)
- Jingyan Han
- Vascular Biology Section, Evans Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA.
| | - Robert M Weisbrod
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Di Shao
- Vascular Biology Section, Evans Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Yosuke Watanabe
- Vascular Biology Section, Evans Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Xiaoyan Yin
- Framingham Heart Study, Boston University School of Medicine, Boston, MA, USA
| | - Markus M Bachschmid
- Vascular Biology Section, Evans Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Francesca Seta
- Vascular Biology Section, Evans Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | | | - Reiko Matsui
- Vascular Biology Section, Evans Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Mengwei Zang
- Department of Molecular Medicine, Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, South Texas Veterans Health Care System, San Antonio, TX, USA
| | - Naomi M Hamburg
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Richard A Cohen
- Vascular Biology Section, Evans Department of Medicine, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
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Yang J, Carroll KS, Liebler DC. The Expanding Landscape of the Thiol Redox Proteome. Mol Cell Proteomics 2015; 15:1-11. [PMID: 26518762 DOI: 10.1074/mcp.o115.056051] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 12/18/2022] Open
Abstract
Cysteine occupies a unique place in protein chemistry. The nucleophilic thiol group allows cysteine to undergo a broad range of redox modifications beyond classical thiol-disulfide redox equilibria, including S-sulfenylation (-SOH), S-sulfinylation (-SO(2)H), S-sulfonylation (-SO(3)H), S-nitrosylation (-SNO), S-sulfhydration (-SSH), S-glutathionylation (-SSG), and others. Emerging evidence suggests that these post-translational modifications (PTM) are important in cellular redox regulation and protection against oxidative damage. Identification of protein targets of thiol redox modifications is crucial to understanding their roles in biology and disease. However, analysis of these highly labile and dynamic modifications poses challenges. Recent advances in the design of probes for thiol redox forms, together with innovative mass spectrometry based chemoproteomics methods make it possible to perform global, site-specific, and quantitative analyses of thiol redox modifications in complex proteomes. Here, we review chemical proteomic strategies used to expand the landscape of thiol redox modifications.
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Affiliation(s)
- Jing Yang
- From the ‡National Center for Protein Sciences · Beijing, Beijing, 102206, China; §State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, 102206, China;
| | - Kate S Carroll
- ¶Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458
| | - Daniel C Liebler
- ‖Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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34
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Nadler W, Berg R, Walch P, Hanke S, Baalmann M, Kerner A, Trumpp A, Roesli C. Ion source-dependent performance of 4-vinylpyridine, iodoacetamide, and N-maleoyl derivatives for the detection of cysteine-containing peptides in complex proteomics. Anal Bioanal Chem 2015; 408:2055-67. [DOI: 10.1007/s00216-015-9113-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 10/05/2015] [Accepted: 10/09/2015] [Indexed: 01/03/2023]
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35
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Jiang J, Wang K, Nice EC, Zhang T, Huang C. High-throughput screening of cellular redox sensors using modern redox proteomics approaches. Expert Rev Proteomics 2015; 12:543-55. [PMID: 26184698 DOI: 10.1586/14789450.2015.1069189] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cancer cells are characterized by higher levels of intracellular reactive oxygen species (ROS) due to metabolic aberrations. ROS are widely accepted as second messengers triggering pivotal signaling pathways involved in the process of cell metabolism, cell cycle, apoptosis, and autophagy. However, the underlying cellular mechanisms remain largely unknown. Recently, accumulating evidence has demonstrated that ROS initiate redox signaling through direct oxidative modification of the cysteines of key redox-sensitive proteins (termed redox sensors). Uncovering the functional changes underlying redox regulation of redox sensors is urgently required, and the role of different redox sensors in distinct disease states still remains to be identified. To assist this, redox proteomics has been developed for the high-throughput screening of redox sensors, which will benefit the development of novel therapeutic strategies for cancer treatment. Highlighted here are recent advances in redox proteomics approaches and their applications in identifying redox sensors involved in tumor development.
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Affiliation(s)
- Jingwen Jiang
- a 1 State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China.,b 2 Hainan Medical University, Haikou, 571199, PR China
| | - Kui Wang
- a 1 State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- c 3 Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Tao Zhang
- d 4 School of Biomedical Sciences, Chengdu Medical College, Chengdu 610500, PR China
| | - Canhua Huang
- a 1 State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China.,b 2 Hainan Medical University, Haikou, 571199, PR China
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36
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Slade WO, Werth EG, McConnell EW, Alvarez S, Hicks LM. Quantifying reversible oxidation of protein thiols in photosynthetic organisms. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:631-640. [PMID: 25698223 DOI: 10.1007/s13361-014-1073-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 06/04/2023]
Abstract
Photosynthetic organisms use dynamic post-translational modifications to survive and adapt, which include reversible oxidative modifications of protein thiols that regulate protein structure, function, and activity. Efforts to quantify thiol modifications on a global scale have relied upon peptide derivatization, typically using isobaric tags such as TMT, ICAT, or iTRAQ that are more expensive, less accurate, and provide less proteome coverage than label-free approaches--suggesting the need for improved experimental designs for studies requiring maximal coverage and precision. Herein, we present the coverage and precision of resin-assisted thiol enrichment coupled to label-free quantitation for the characterization of reversible oxidative modifications on protein thiols. Using C. reinhardtii and Arabidopsis as model systems for algae and plants, we quantified 3662 and 1641 unique cysteinyl peptides, respectively, with median coefficient of variation (CV) of 13% and 16%. Further, our method is extendable for the detection of protein abundance changes and stoichiometries of cysteine oxidation. Finally, we demonstrate proof-of-principle for our method, and reveal that exogenous hydrogen peroxide treatment regulates the C. reinhardtii redox proteome by increasing or decreasing the level of oxidation of 501 or 67 peptides, respectively. As protein activity and function is controlled by oxidative modifications on protein thiols, resin-assisted thiol enrichment coupled to label-free quantitation can reveal how intracellular and environmental stimuli affect plant survival and fitness through oxidative stress.
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Affiliation(s)
- William O Slade
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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37
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Paulech J, Liddy KA, Engholm-Keller K, White MY, Cordwell SJ. Global analysis of myocardial peptides containing cysteines with irreversible sulfinic and sulfonic acid post-translational modifications. Mol Cell Proteomics 2015; 14:609-20. [PMID: 25561502 DOI: 10.1074/mcp.m114.044347] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cysteine (Cys) oxidation is a crucial post-translational modification (PTM) associated with redox signaling and oxidative stress. As Cys is highly reactive to oxidants it forms a range of post-translational modifications, some that are biologically reversible (e.g. disulfides, Cys sulfenic acid) and others (Cys sulfinic [Cys-SO2H] and sulfonic [Cys-SO3H] acids) that are considered "irreversible." We developed an enrichment method to isolate Cys-SO2H/SO3H-containing peptides from complex tissue lysates that is compatible with tandem mass spectrometry (MS/MS). The acidity of these post-translational modification (pKa Cys-SO3H < 0) creates a unique charge distribution when localized on tryptic peptides at acidic pH that can be utilized for their purification. The method is based on electrostatic repulsion of Cys-SO2H/SO3H-containing peptides from cationic resins (i.e. "negative" selection) followed by "positive" selection using hydrophilic interaction liquid chromatography. Modification of strong cation exchange protocols decreased the complexity of initial flowthrough fractions by allowing for hydrophobic retention of neutral peptides. Coupling of strong cation exchange and hydrophilic interaction liquid chromatography allowed for increased enrichment of Cys-SO2H/SO3H (up to 80%) from other modified peptides. We identified 181 Cys-SO2H/SO3H sites from rat myocardial tissue subjected to physiologically relevant concentrations of H2O2 (<100 μm) or to ischemia/reperfusion (I/R) injury via Langendorff perfusion. I/R significantly increased Cys-SO2H/SO3H-modified peptides from proteins involved in energy utilization and contractility, as well as those involved in oxidative damage and repair.
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Affiliation(s)
- Jana Paulech
- From the ‡School of Molecular Bioscience, The University of Sydney, Australia 2006
| | - Kiersten A Liddy
- From the ‡School of Molecular Bioscience, The University of Sydney, Australia 2006; §Charles Perkins Centre, The University of Sydney, Australia 2006
| | - Kasper Engholm-Keller
- ¶Children's Medical Research Institute, Westmead, Australia 2145; ‖Centre for Clinical Proteomics, Odense University Hospital, Odense C, Denmark DK-5000; **Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark DK-5230
| | - Melanie Y White
- From the ‡School of Molecular Bioscience, The University of Sydney, Australia 2006; §Charles Perkins Centre, The University of Sydney, Australia 2006; ‡‡Discipline of Pathology, School of Medical Sciences, The University of Sydney, Australia 2006
| | - Stuart J Cordwell
- From the ‡School of Molecular Bioscience, The University of Sydney, Australia 2006; §Charles Perkins Centre, The University of Sydney, Australia 2006; ‡‡Discipline of Pathology, School of Medical Sciences, The University of Sydney, Australia 2006
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Guo M, Weng G, Yin D, Hu X, Han J, Du Y, Liu Y, Tang D, Pan Y. Identification of the over alkylation sites of a protein by IAM in MALDI-TOF/TOF tandem mass spectrometry. RSC Adv 2015. [DOI: 10.1039/c5ra18595e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Overalkylation often appears during the proteolytic digestion process when using iodoacetamide (IAM) to protect the produced side chain thiol of Cys from disulfide bonds.
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Affiliation(s)
- Mengzhe Guo
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
- Key Laboratory of New Drug Research and Clinical Pharmacy
| | - Guofeng Weng
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
| | - Dengyang Yin
- Key Laboratory of New Drug Research and Clinical Pharmacy
- Xuzhou Medical College
- Xuzhou
- China
- Department of Pharmaceutical Analysis
| | - Xunxiu Hu
- Key Laboratory of New Drug Research and Clinical Pharmacy
- Xuzhou Medical College
- Xuzhou
- China
- Department of Pharmaceutical Analysis
| | - Jie Han
- Key Laboratory of New Drug Research and Clinical Pharmacy
- Xuzhou Medical College
- Xuzhou
- China
- Department of Pharmaceutical Analysis
| | - Yan Du
- Key Laboratory of New Drug Research and Clinical Pharmacy
- Xuzhou Medical College
- Xuzhou
- China
- Department of Pharmaceutical Analysis
| | - Yaqin Liu
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
| | - Daoquan Tang
- Key Laboratory of New Drug Research and Clinical Pharmacy
- Xuzhou Medical College
- Xuzhou
- China
- Department of Pharmaceutical Analysis
| | - Yuanjiang Pan
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
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Silva-Jiménez H, Ortega Á, García-Fontana C, Ramos JL, Krell T. Multiple signals modulate the activity of the complex sensor kinase TodS. Microb Biotechnol 2014; 8:103-15. [PMID: 24986263 PMCID: PMC4321377 DOI: 10.1111/1751-7915.12142] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/22/2014] [Accepted: 06/07/2014] [Indexed: 11/28/2022] Open
Abstract
The reason for the existence of complex sensor kinases is little understood but thought to lie in the capacity to respond to multiple signals. The complex, seven-domain sensor kinase TodS controls in concert with the TodT response regulator the expression of the toluene dioxygenase pathway in Pseudomonas putida F1 and DOT-T1E. We have previously shown that some aromatic hydrocarbons stimulate TodS activity whereas others behave as antagonists. We show here that TodS responds in addition to the oxidative agent menadione. Menadione but no other oxidative agent tested inhibited TodS activity in vitro and reduced PtodX expression in vivo. The menadione signal is incorporated by a cysteine-dependent mechanism. The mutation of the sole conserved cysteine of TodS (C320) rendered the protein insensitive to menadione. We evaluated the mutual opposing effects of toluene and menadione on TodS autophosphorylation. In the presence of toluene, menadione reduced TodS activity whereas toluene did not stimulate activity in the presence of menadione. It was shown by others that menadione increases expression of glucose metabolism genes. The opposing effects of menadione on glucose and toluene metabolism may be partially responsible for the interwoven regulation of both catabolic pathways. This work provides mechanistic detail on how complex sensor kinases integrate different types of signal molecules.
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Affiliation(s)
- Hortencia Silva-Jiménez
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, C/ Prof. Albareda 1, Granada, 18008, Spain
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40
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Buchowiecka AK. Puzzling over protein cysteine phosphorylation – assessment of proteomic tools for S-phosphorylation profiling. Analyst 2014; 139:4118-23. [DOI: 10.1039/c4an00724g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The article provides useful information necessary for designing experiments in the emerging cysteine phosphoproteomics.
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Affiliation(s)
- A. K. Buchowiecka
- Institute of Technical Biochemistry
- Lodz University of Technology
- 90-924 Lodz, Poland
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41
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Vento M, Hummler H, Dawson J, Escobar J, Kuligowski J. Use of Oxygen in the Resuscitation of Neonates. OXIDATIVE STRESS IN APPLIED BASIC RESEARCH AND CLINICAL PRACTICE 2014. [DOI: 10.1007/978-1-4939-1405-0_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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42
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Reisz JA, Bechtold E, King SB, Poole LB, Furdui CM. Thiol-blocking electrophiles interfere with labeling and detection of protein sulfenic acids. FEBS J 2013; 280:6150-61. [PMID: 24103186 DOI: 10.1111/febs.12535] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/03/2013] [Accepted: 09/12/2013] [Indexed: 01/07/2023]
Abstract
Cellular exposure to reactive oxygen species induces rapid oxidation of DNA, proteins, lipids and other biomolecules. At the proteome level, cysteine thiol oxidation is a prominent post-translational process that is implicated in normal physiology and numerous pathologies. Methods for investigating protein oxidation include direct labeling with selective chemical probes and indirect tag-switch techniques. Common to both approaches is chemical blocking of free thiols using reactive electrophiles to prevent post-lysis oxidation or other thiol-mediated cross-reactions. These reagents are used in large excess, and their reactivity with cysteine sulfenic acid, a critical oxoform in numerous proteins, has not been investigated. Here we report the reactivity of three thiol-blocking electrophiles, iodoacetamide, N-ethylmaleimide and methyl methanethiosulfonate, with protein sulfenic acid and dimedone, the structural core of many sulfenic acid probes. We demonstrate that covalent cysteine -SOR (product) species are partially or fully susceptible to reduction by dithiothreitol, tris(2-carboxyethyl)phosphine and ascorbate, regenerating protein thiols, or, in the case of ascorbate, more highly oxidized species. The implications of this reactivity on detection methods for protein sulfenic acids and S-nitrosothiols are discussed.
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Affiliation(s)
- Julie A Reisz
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
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43
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Yang H, Wan D, Song F, Liu Z, Liu S. α-Cyano-4-hydroxycinnamic acid, sinapinic acid, and ferulic acid as matrices and alkylating agents for matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of cysteine-containing peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1410-1412. [PMID: 23681820 DOI: 10.1002/rcm.6587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/30/2013] [Accepted: 04/01/2013] [Indexed: 06/02/2023]
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44
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Echterbille J, Quinton L, Gilles N, De Pauw E. Ion Mobility Mass Spectrometry as a Potential Tool To Assign Disulfide Bonds Arrangements in Peptides with Multiple Disulfide Bridges. Anal Chem 2013; 85:4405-13. [DOI: 10.1021/ac303686w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Julien Echterbille
- Laboratory of Mass Spectrometry,
GIGA-R, Department of Chemistry, University of Liege, Liege, Belgium
| | - Loïc Quinton
- Laboratory of Mass Spectrometry,
GIGA-R, Department of Chemistry, University of Liege, Liege, Belgium
| | - Nicolas Gilles
- iBiTec-S,
SIMOPRO, Commissariat à l’Energie Atomique, Gif-sur-Yvette,
France
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry,
GIGA-R, Department of Chemistry, University of Liege, Liege, Belgium
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45
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Paulech J, Solis N, Edwards AV, Puckeridge M, White MY, Cordwell SJ. Large-Scale Capture of Peptides Containing Reversibly Oxidized Cysteines by Thiol-Disulfide Exchange Applied to the Myocardial Redox Proteome. Anal Chem 2013; 85:3774-80. [DOI: 10.1021/ac400166e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jana Paulech
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Nestor Solis
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Alistair V.G. Edwards
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Max Puckeridge
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Melanie Y. White
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Stuart J. Cordwell
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
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46
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Rombouts I, Lagrain B, Brunnbauer M, Delcour JA, Koehler P. Improved identification of wheat gluten proteins through alkylation of cysteine residues and peptide-based mass spectrometry. Sci Rep 2013; 3:2279. [PMID: 23880742 PMCID: PMC3721084 DOI: 10.1038/srep02279] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/09/2013] [Indexed: 11/22/2022] Open
Abstract
The concentration and composition of wheat gluten proteins and the presence, concentration and location of cysteine residues therein are important for wheat flour quality. However, it is difficult to identify gluten proteins, as they are an extremely polymorphic mixture of prolamins. We here present methods for cysteine labeling of wheat prolamins with 4-vinylpyridine (4-VP) and iodoacetamide (IDAM) which, as compared to label-free analysis, substantially improve identification of cysteine-containing peptides in enzymic prolamin digests by electrospray ionization--tandem mass spectrometry. Both chymotrypsin and thermolysin yielded cysteine-containing peptides from different gluten proteins, but more proteins could be identified after chymotryptic digestion. In addition, to the best of our knowledge, we were the first to label prolamins with isotope coded affinity tags (ICAT), which are commonly used for quantitative proteomics. However, more peptides were detected after labeling gluten proteins with 4-VP and IDAM than with ICAT.
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Affiliation(s)
- Ine Rombouts
- German Research Center for Food Chemistry, Leibniz Institute, Lise-Meitner-Strasse 34, D-85354 Freising, Germany.
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