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Mayasich SA, Goldsmith MR, Mattingly KZ, LaLone CA. Combining In Vitro and In Silico New Approach Methods to Investigate Type 3 Iodothyronine Deiodinase Chemical Inhibition Across Species. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1032-1048. [PMID: 36825751 PMCID: PMC10895443 DOI: 10.1002/etc.5591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
New approach methodologies (NAMs) are being developed to reduce and replace vertebrate animal testing in support of ecotoxicology and risk assessment. The US Environmental Protection Agency's Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) bioinformatic tool was used to evaluate amino acid sequence conservation of the type 3 iodothyronine deiodinase (DIO3) enzyme across species to demonstrate NAM applications for understanding effects of chemical interactions with a specific protein target. Existing literature was used to identify critical amino acids for thyroid hormone binding and interaction with a reducing cofactor. The SeqAPASS tool identifies whether known critical amino acids involved in ligand binding are exact, partial, or not matches across species compared with a template species based on molecular weight and side chain classification. This evaluation guided the design of variant proteins representing critical amino acid substitutions found in various species. Site-directed mutagenesis of the wild-type (WT) human DIO3 gene sequence was used to create six variant proteins expressed in cell culture, which were then tested in vitro for chemical inhibition. Significant differences in in vitro median inhibitory concentration results were observed among variants for potential competitive inhibitors. A molecular model representing the WT human DIO3 was constructed using Molecular Operating Environment (MOE) software and mutated in silico to create the six variants. The MOE Site Finder tool identified the proposed catalytic and cofactor sites and potential alternative binding sites. Virtual docking did not provide affinity scores with sufficient resolution to rank the potency of the chemical inhibitors. Chemical characteristics, function and location of substituted amino acids, and complexities of the protein target are important considerations in developing NAMs to evaluate chemical susceptibility across species. Environ Toxicol Chem 2023;42:1032-1048. © 2023 University of Wisconsin-Madison. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Sally A. Mayasich
- Aquatic Sciences Center, University of Wisconsin‐Madison, Madison, Wisconsin, USA
- Office of Research and Development, Center for Computational Toxicology and Ecology, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota
| | - Michael R. Goldsmith
- Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, North Carolina
- Congruence Therapeutics, Montreal, Quebec, Canada
| | | | - Carlie A. LaLone
- Office of Research and Development, Center for Computational Toxicology and Ecology, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota
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Jobson J, Tsegay PS, Beltran MT, Taher EA, Rein SR, Liu Y, Rein KS. Brevetoxin induces a shift in the redox state of the proteome and unfolded protein response in human lymphoblast cells that can be alleviated with the acrolein scavenger MESNA. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 100:104137. [PMID: 37127110 DOI: 10.1016/j.etap.2023.104137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/24/2023] [Accepted: 04/29/2023] [Indexed: 05/03/2023]
Abstract
Human lymphoblast cells were treated with the marine algal toxin, brevetoxin-2 (PbTx-2), and its effects on the proteome were assessed by redox proteomics using cysteine reactive tandem mass tags (TMT). Additionally, cells were simultaneously treated with PbTx-2 and the antioxidant and acrolein scavenger sodium 2-mercaptoethylsulfonate (MESNA) to determine if MESNA could prevent the proteomic effects of brevetoxin-2. A massive shift in the redox state of the proteome of brevetoxin-2 treated cells was observed. The main pathway affected was genetic information processing. Significantly oxidized proteins included Trx-1, peroxyredoxins (Prxs), ribosomal proteins, and the eukaryotic initiation factor 2 β subunit (eIF2β). Proteins that were overexpressed in brevetoxin-treated cells included four folding chaperones. These effects were diminished in the presence of MESNA indicating that MESNA may act through its antioxidant properties or as a brevetoxin scavenger. These studies provide novel insights into new prophylactics for brevetoxicosis in humans and wildlife.
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Affiliation(s)
- Jordan Jobson
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Pawlos S Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
| | - Mayra Tabares Beltran
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Eman A Taher
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Samuel R Rein
- The School District of Philadelphia, Philadelphia, PA 19130, USA
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Kathleen S Rein
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; Current address: The Water School, Department of Marine and Earth Science and Department of Chemistry and Physics, Florida Gulf Coast University, Fort Myers, FL 33965.
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Alapa M, Cui C, Shu P, Li H, Kholodovych V, Beuve A. Selective cysteines oxidation in soluble guanylyl cyclase catalytic domain is involved in NO activation. Free Radic Biol Med 2021; 162:450-460. [PMID: 33161042 PMCID: PMC7889651 DOI: 10.1016/j.freeradbiomed.2020.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/30/2020] [Accepted: 11/01/2020] [Indexed: 12/18/2022]
Abstract
Nitric oxide (NO) binds to soluble guanylyl cyclase (GC1) and stimulates its catalytic activity to produce cGMP. Despite the key role of the NO-cGMP signaling in cardiovascular physiology, the mechanisms of GC1 activation remain ill-defined. It is believed that conserved cysteines (Cys) in GC1 modulate the enzyme's activity through thiol-redox modifications. We previously showed that GC1 activity is modulated via mixed-disulfide bond by protein disulfide isomerase and thioredoxin 1. Herein we investigated the novel concept that NO-stimulated GC1 activity is mediated by thiol/disulfide switches and aimed to map the specific Cys that are involved. First, we showed that the dithiol reducing agent Tris (2-carboxyethyl)-phosphine reduces GC1 response to NO, indicating the significance of Cys oxidation in NO activation. Second, using dibromobimane, which fluoresces when crosslinking two vicinal Cys thiols, we demonstrated decreased fluorescence in NO-stimulated GC1 compared to unstimulated conditions. This suggested that NO-stimulated GC1 contained more bound Cys, potentially disulfide bonds. Third, to identify NO-regulated Cys oxidation using mass spectrometry, we compared the redox status of all Cys identified in tryptic peptides, among which, ten were oxidized and two were reduced in NO-stimulated GC1. Fourth, we resorted to computational modeling to narrow down the Cys candidates potentially involved in disulfide bond and identified Cys489 and Cys571. Fifth, our mutational studies showed that Cys489 and Cys571 were involved in GC1'response to NO, potentially as a thiol/disulfide switch. These findings imply that specific GC1 Cys sensitivity to redox environment is critical for NO signaling in cardiovascular physiology.
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Affiliation(s)
- Maryam Alapa
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School-Rutgers, Newark, NJ, 07103, USA
| | - Chuanlong Cui
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School-Rutgers, Newark, NJ, 07103, USA; Center for Advanced Proteomics Research- New Jersey Medical School- Rutgers, Newark, NJ, 07103, USA
| | - Ping Shu
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School-Rutgers, Newark, NJ, 07103, USA
| | - Hong Li
- Center for Advanced Proteomics Research- New Jersey Medical School- Rutgers, Newark, NJ, 07103, USA
| | - Vlad Kholodovych
- Office of Advanced Research Computing, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Annie Beuve
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School-Rutgers, Newark, NJ, 07103, USA.
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Lim HM, Park SH, Nam MJ. Induction of apoptosis in indole-3-carbinol-treated lung cancer H1299 cells via ROS level elevation. Hum Exp Toxicol 2020; 40:812-825. [DOI: 10.1177/0960327120969968] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This study was focused on investigating the anticancer potential of indole-3-carbinol (I3C) against lung cancer H1299 cells via an increase in ROS levels. To investigate the induction of growth arrest and/or cell death in H1299 cells, a cell cycle arrest assay, terminal deoxynucleotidyl transferase (TdT)-mediated dUTP-biotin nick-end labeling (TUNEL) assay, and reactive oxygen species (ROS) detection assay were performed. Through the TUNEL assay, we detected I3C-induced DNA fragmentation. Fluorescence-activated cell sorting (FACS) analysis showed that I3C induced an increase in ROS levels and apoptotic rate in a dose- and time-dependent manner in H1299 cells. Western blotting demonstrated that activated forms of caspase-3, caspase-7, caspase-9, and poly (ADP-ribose) polymerase (PARP) were increased in I3C-treated H1299 cells following treatment with I3C. Furthermore, protein expression levels of FOXO3, bim, bax, and phosphorylated ERK and JNK were increased, while those of pAkt, Bcl-xL, and Bcl-2 were decreased by I3C treatment of H1299 cells. To confirm the relationship between cell apoptosis and ROS generation, H1299 cells were treated with I3C simultaneously with N-acetylcysteine (NAC), and it was shown that ROS levels decreased and viability increased. Moreover, in western blot analysis, expression of anti-apoptotic proteins (thioredoxin1, peroxiredoxin-1, Bcl-2, and Bcl-xL) in I3C-treated cells was evidently downregulated and pro-apoptotic proteins (active ASK1 and cleaved PARP) were upregulated compared to cells co-treated with NAC. The study showed that I3C induced downregulation of ROS regulator proteins and elevation of ROS, thus activating apoptotic signaling cascades in human lung cancer H1299 cells.
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Affiliation(s)
- Heui Min Lim
- Department of Biological Science, Gachon University, Gyeonggi-do, Republic of Korea
| | - See-Hyoung Park
- Department of Bio and Chemical Engineering, Hongik University, Sejong-si, Republic of Korea
| | - Myeong Jin Nam
- Department of Biological Science, Gachon University, Gyeonggi-do, Republic of Korea
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Reina S, Pittalà MGG, Guarino F, Messina A, De Pinto V, Foti S, Saletti R. Cysteine Oxidations in Mitochondrial Membrane Proteins: The Case of VDAC Isoforms in Mammals. Front Cell Dev Biol 2020; 8:397. [PMID: 32582695 PMCID: PMC7287182 DOI: 10.3389/fcell.2020.00397] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022] Open
Abstract
Cysteine residues are reactive amino acids that can undergo several modifications driven by redox reagents. Mitochondria are the source of an abundant production of radical species, and it is surprising that such a large availability of highly reactive chemicals is compatible with viable and active organelles, needed for the cell functions. In this work, we review the results highlighting the modifications of cysteines in the most abundant proteins of the outer mitochondrial membrane (OMM), that is, the voltage-dependent anion selective channel (VDAC) isoforms. This interesting protein family carries several cysteines exposed to the oxidative intermembrane space (IMS). Through mass spectrometry (MS) analysis, cysteine posttranslational modifications (PTMs) were precisely determined, and it was discovered that such cysteines can be subject to several oxidization degrees, ranging from the disulfide bridge to the most oxidized, the sulfonic acid, one. The large spectra of VDAC cysteine oxidations, which is unique for OMM proteins, indicate that they have both a regulative function and a buffering capacity able to counteract excess of mitochondrial reactive oxygen species (ROS) load. The consequence of these peculiar cysteine PTMs is discussed.
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Affiliation(s)
- Simona Reina
- Section of Molecular Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Maria Gaetana Giovanna Pittalà
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Francesca Guarino
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Angela Messina
- Section of Molecular Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Vito De Pinto
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Salvatore Foti
- Organic Mass Spectrometry Laboratory, Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Rosaria Saletti
- Organic Mass Spectrometry Laboratory, Department of Chemical Sciences, University of Catania, Catania, Italy
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Domingos RM, Teixeira RD, Zeida A, Agudelo WA, Alegria TGP, da Silva Neto JF, Vieira PS, Murakami MT, Farah CS, Estrin DA, Netto LES. Substrate and Product-Assisted Catalysis: Molecular Aspects behind Structural Switches along Organic Hydroperoxide Resistance Protein Catalytic Cycle. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Renato M. Domingos
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - Raphael D. Teixeira
- Departamento de Biociências, Instituto de Quı́mica, Universidade de São Paulo, 05508-000 Sao Paulo, Brazil
| | - Ari Zeida
- Departamento de Quı́mica Inorgánica Analı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - William A. Agudelo
- Departamento de Quı́mica Inorgánica Analı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Thiago G. P. Alegria
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - José F. da Silva Neto
- Departamento de Biologia Celular e Molecular e Bioagentes Biociências, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900 São Paulo, Brazil
| | - Plínio S. Vieira
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970, Brazil
| | - Mario T. Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970, Brazil
| | - Chuck S. Farah
- Departamento de Biociências, Instituto de Quı́mica, Universidade de São Paulo, 05508-000 Sao Paulo, Brazil
| | - Dario A. Estrin
- Departamento de Quı́mica Inorgánica Analı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Luis E. S. Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
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Abstract
Introduction: Protein thiols are susceptible to oxidation in health and disease. Redox proteomics methods facilitate the identification, quantification, and rationalization of oxidation processes including those involving protein thiols. These residues are crucial to understanding redox homeostasis underpinning normal cell functioning and regulation as well as novel biomarkers of pathology and promising novel drug targets.Areas covered: This article reviews redox proteomic approaches to study of protein thiols in some important human pathologies and assesses the clinical potential of individual Cys residues as novel biomarkers for disease detection and as targets for novel treatments.Expert commentary: Although protein thiols are not as routinely used as redox biomarkers as some other lesions such as carbonylation, there has been growing recent interest in their potential. Driven largely by developments in high-resolution mass spectrometry it is possible now to identify proteins that are redox modified at thiol groups or that interact with regulatory oxidoreductases. Thiols that are specifically susceptible to modification by reactive oxygen species can be routinely identified now and quantitative MS can be used to quantify the proportion of a protein that is redox modified.
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Affiliation(s)
- David Sheehan
- Department of Chemistry, Khalifa University, Abu Dhabi, United Arab Emirates.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Brian McDonagh
- Department of Physiology, School of Medicine, National University of Ireland, Galway, Ireland
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Vajrychova M, Salovska B, Pimkova K, Fabrik I, Tambor V, Kondelova A, Bartek J, Hodny Z. Quantification of cellular protein and redox imbalance using SILAC-iodoTMT methodology. Redox Biol 2019; 24:101227. [PMID: 31154163 PMCID: PMC6545335 DOI: 10.1016/j.redox.2019.101227] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/06/2019] [Accepted: 05/19/2019] [Indexed: 12/17/2022] Open
Abstract
Under normal conditions, the cellular redox status is maintained in a steady state by reduction and oxidation processes. These redox alterations in the cell are mainly sensed by protein thiol residues of cysteines thus regulating protein function. The imbalance in redox homeostasis may therefore regulate protein turnover either directly by redox modulating of transcription factors or indirectly by the degradation of damaged proteins due to oxidation. A new analytical method capable of simultaneously assessing cellular protein expression and cysteine oxidation would provide a valuable tool for the field of cysteine-targeted biology. Here, we show a workflow based on protein quantification using metabolic labeling and determination of cysteine oxidation using reporter ion quantification. We applied this approach to determine protein and redox changes in cells after 5-min, 60-min and 32-h exposure to H2O2, respectively. Based on the functional analysis of our data, we confirmed a biological relevance of this approach and its applicability for parallel mapping of cellular proteomes and redoxomes under diverse conditions. In addition, we revealed a specific pattern of redox changes in peroxiredoxins in a short time-interval cell exposure to H2O2. Overall, our present study offers an innovative, versatile experimental approach to the multifaceted assessment of cellular proteome and its redox status, with broad implications for biomedical research towards a better understanding of organismal physiology and diverse disease conditions.
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Affiliation(s)
- Marie Vajrychova
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec Kralove, Czech Republic
| | - Barbora Salovska
- Department of Genome Integrity, Institute of Molecular Genetics of the ASCR, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Kristyna Pimkova
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec Kralove, Czech Republic
| | - Ivo Fabrik
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec Kralove, Czech Republic
| | - Vojtech Tambor
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec Kralove, Czech Republic
| | - Alexandra Kondelova
- Department of Genome Integrity, Institute of Molecular Genetics of the ASCR, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Jiri Bartek
- Department of Genome Integrity, Institute of Molecular Genetics of the ASCR, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic; Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark; Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Karolinska Institute, Tomtebodavägen 23A, 171 65, Stockholm, Sweden.
| | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics of the ASCR, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic.
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