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Ghasemi F, Nili-Ahmadabadi A, Omidifar N, Nili-Ahmadabadi M. Protective potential of thymoquinone against cadmium, arsenic, and lead toxicity: A short review with emphasis on oxidative pathways. J Appl Toxicol 2023; 43:1764-1777. [PMID: 36872630 DOI: 10.1002/jat.4459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 02/13/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023]
Abstract
Heavy metals are among the most important environmental pollutions used in various industries. Their extensive use has increased human susceptibility to different chronic diseases. Toxic metal exposure, especially cadmium, arsenic, and lead, causes oxidative damages, mitochondrial dysfunction, and genetic and epigenetic modifications. Meanwhile, thymoquinone (TQ) is an effective component of Nigella sativa oil that plays an important role in preventing the destructive effects of heavy metals. The present review discusses how TQ can protect various tissues against oxidative damage of heavy metals. This review is based on the research reported about the protective effects of TQ in the toxicity of heavy metals, approximately the last 10 years (2010-2021). Scientific databases, including Scopus, Web of Science, and PubMed, were searched using the following keywords either alone or in combination: cadmium, arsenic, lead, TQ, and oxidative stress. TQ, as a potent antioxidant, can distribute to cellular compartments and prevent oxidative damage of toxic metals. However, depending on the type of toxic metal and the carrier system used to release TQ in biological systems, its therapeutic dosage range may be varied.
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Affiliation(s)
- Farzad Ghasemi
- Faculty of Pharmacy, Eastern Mediterranean University, Famagusta, North Cyprus, Turkey
| | - Amir Nili-Ahmadabadi
- Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
- Department of Pharmacology and Toxicology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Navid Omidifar
- Medical Education Research Center, Department of Pathology, Medical School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Nili-Ahmadabadi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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2
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Garrido Ruiz D, Sandoval-Perez A, Rangarajan AV, Gunderson EL, Jacobson MP. Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation. Biochemistry 2022; 61:2165-2176. [PMID: 36161872 PMCID: PMC9583617 DOI: 10.1021/acs.biochem.2c00349] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cysteine side chains
can exist in distinct oxidation
states depending
on the pH and redox potential of the environment, and cysteine oxidation
plays important yet complex regulatory roles. Compared with the effects
of post-translational modifications such as phosphorylation, the effects
of oxidation of cysteine to sulfenic, sulfinic, and sulfonic acid
on protein structure and function remain relatively poorly characterized.
We present an analysis of the role of cysteine reactivity as a regulatory
factor in proteins, emphasizing the interplay between electrostatics
and redox potential as key determinants of the resulting oxidation
state. A review of current computational approaches suggests underdeveloped
areas of research for studying cysteine reactivity through molecular
simulations.
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Affiliation(s)
- Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Angelica Sandoval-Perez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Amith Vikram Rangarajan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Emma L Gunderson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
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3
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Benchoam D, Semelak JA, Cuevasanta E, Mastrogiovanni M, Grassano JS, Ferrer-Sueta G, Zeida A, Trujillo M, Möller MN, Estrin DA, Alvarez B. Acidity and nucleophilic reactivity of glutathione persulfide. J Biol Chem 2020; 295:15466-15481. [PMID: 32873707 DOI: 10.1074/jbc.ra120.014728] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
Persulfides (RSSH/RSS-) participate in sulfur trafficking and metabolic processes, and are proposed to mediate the signaling effects of hydrogen sulfide (H2S). Despite their growing relevance, their chemical properties are poorly understood. Herein, we studied experimentally and computationally the formation, acidity, and nucleophilicity of glutathione persulfide (GSSH/GSS-), the derivative of the abundant cellular thiol glutathione (GSH). We characterized the kinetics and equilibrium of GSSH formation from glutathione disulfide and H2S. A pKa of 5.45 for GSSH was determined, which is 3.49 units below that of GSH. The reactions of GSSH with the physiologically relevant electrophiles peroxynitrite and hydrogen peroxide, and with the probe monobromobimane, were studied and compared with those of thiols. These reactions occurred through SN2 mechanisms. At neutral pH, GSSH reacted faster than GSH because of increased availability of the anion and, depending on the electrophile, increased reactivity. In addition, GSS- presented higher nucleophilicity with respect to a thiolate with similar basicity. This can be interpreted in terms of the so-called α effect, i.e. the increased reactivity of a nucleophile when the atom adjacent to the nucleophilic atom has high electron density. The magnitude of the α effect correlated with the Brønsted nucleophilic factor, βnuc, for the reactions with thiolates and with the ability of the leaving group. Our study constitutes the first determination of the pKa of a biological persulfide and the first examination of the α effect in sulfur nucleophiles, and sheds light on the chemical basis of the biological properties of persulfides.
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Affiliation(s)
- Dayana Benchoam
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Jonathan A Semelak
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Argentina
| | - Ernesto Cuevasanta
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Unidad de Bioquímica Analítica, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Mauricio Mastrogiovanni
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Juan S Grassano
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Argentina
| | - Gerardo Ferrer-Sueta
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Matías N Möller
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Argentina.
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.
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Yamaguchi R, Haraguchi M, Yamaguchi R, Sakamoto A, Narahara S, Sugiuchi H, Yamaguchi Y. TRIM28/TIF1β and Fli-1 negatively regulate peroxynitrite generation via DUOX2 to decrease the shedding of membrane-bound fractalkine in human macrophages after exposure to substance P. Cytokine 2020; 134:155180. [PMID: 32673994 DOI: 10.1016/j.cyto.2020.155180] [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: 04/01/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 11/25/2022]
Abstract
The chemokine fractalkine is synthesized as a membrane-bound protein, but studies have shown that serum levels of soluble fractalkine are elevated in inflammatory and autoimmune diseases. Patients with autoimmune diseases also have increased serum levels of neuropeptide substance P (SP). The shedding activity of the ADAM family is induced by peroxynitrite, but that of SP is unclear. Treatment of human macrophages with SP upregulated levels of membrane-bound fractalkine. Interestingly, small interfering RNA (siRNA) for DUOX2 further increased membrane-bound fractalkine but decreased soluble fractalkine compared with cells treated with SP alone. SP induced nitric oxide 2/inducible nitric oxide synthase (NOS2/iNOS) mRNA and increased levels of nitrotyrosine, a biomarker of peroxynitrite, whereas transfection with DUOX2 siRNA blunted upregulation of nitrotyrosine. Most importantly, N(ω)-nitro-L-arginine methyl ester (L-NAME, a nitric oxide synthase inhibitor) decreased protein levels of nitrotyrosine and concomitantly increased expression of membrane-bound fractalkine after exposure to SP. As for the signaling pathway of TGFβ1 (an inhibitor of iNOS mRNA expression), silencing of RNA for TAK-1 upregulated membrane-bound fractalkine, but silencing of RNA for the Smad family did not. Interfering RNA of transcription factor specificity protein 1 (Sp1) upregulated protein levels of TGFβ1/LAP. Most importantly, double transfection with siRNA for Sp1 and TRIM28/TIF1βor Fli-1 led to a significant increase in TGFβ1/LAP levels and a corresponding reduction of NOS2/iNOS, which inhibited the shedding of membrane-bound fractalkine. In conclusion, TRIM28/TIF1β and Fli-1 negatively regulate TGFβ1 expression to upregulate the generation of peroxynitrite, leading to increased shedding of membrane-bound fractalkine induced by SP.
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Affiliation(s)
- Rui Yamaguchi
- Graduate School of Medical Science, Kumamoto Health Science University, Kitaku Izumi-machi 325 Kumamoto 861-5598, Japan
| | - Misa Haraguchi
- Graduate School of Medical Science, Kumamoto Health Science University, Kitaku Izumi-machi 325 Kumamoto 861-5598, Japan
| | - Reona Yamaguchi
- Department of Neuroscience, Graduate School of Medicine and Faculty of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Arisa Sakamoto
- Graduate School of Medical Science, Kumamoto Health Science University, Kitaku Izumi-machi 325 Kumamoto 861-5598, Japan
| | - Shinji Narahara
- Graduate School of Medical Science, Kumamoto Health Science University, Kitaku Izumi-machi 325 Kumamoto 861-5598, Japan
| | - Hiroyuki Sugiuchi
- Graduate School of Medical Science, Kumamoto Health Science University, Kitaku Izumi-machi 325 Kumamoto 861-5598, Japan
| | - Yasuo Yamaguchi
- Graduate School of Medical Science, Kumamoto Health Science University, Kitaku Izumi-machi 325 Kumamoto 861-5598, Japan.
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Semelak JA, Battistini F, Radi R, Trujillo M, Zeida A, Estrin DA. Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide. J Chem Inf Model 2019; 60:843-853. [PMID: 31718175 DOI: 10.1021/acs.jcim.9b00817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this work, we employ a multiscale quantum-classical mechanics (QM/MM) scheme to investigate the chemical reactivity of sulfenic acids toward hydrogen peroxide, both in aqueous solution and in the protein environment of the peroxiredoxin alkyl hydroperoxide reductase E from Mycobacterium tuberculosis (MtAhpE). The reaction of oxidation of cysteine with hydrogen peroxides, catalyzed by peroxiredoxins, is usually accelerated several orders of magnitude in comparison with the analogous reaction in solution. The resulting cysteine sulfenic acid is then reduced in other steps of the catalytic cycle, recovering the original thiol. However, under some conditions, the sulfenic acid can react with another equivalent of oxidant to form a sulfinic acid. This process is called overoxidation and has been associated with redox signaling. Herein, we employed a multiscale scheme based on density function theory calculations coupled to the classical AMBER force field, developed in our group, to establish the molecular basis of thiol overoxidation by hydrogen peroxide. Our results suggest that residues that play key catalytic roles in the oxidation of MtAhpE are not relevant in the overoxidation process. Indeed, the calculations propose that the process is unfavored by this particular enzyme microenvironment.
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Affiliation(s)
- J A Semelak
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET , Facultad de Ciencias Exactas y Naturales , Ciudad Universitaria, Pab. 2 , CP 1428 , Buenos Aires , Argentina
| | - F Battistini
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , 08028 Barcelona , Spain
| | - R Radi
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - M Trujillo
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - A Zeida
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - D A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET , Facultad de Ciencias Exactas y Naturales , Ciudad Universitaria, Pab. 2 , CP 1428 , Buenos Aires , Argentina
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6
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Zeida A, Trujillo M, Ferrer-Sueta G, Denicola A, Estrin DA, Radi R. Catalysis of Peroxide Reduction by Fast Reacting Protein Thiols. Chem Rev 2019; 119:10829-10855. [PMID: 31498605 DOI: 10.1021/acs.chemrev.9b00371] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Life on Earth evolved in the presence of hydrogen peroxide, and other peroxides also emerged before and with the rise of aerobic metabolism. They were considered only as toxic byproducts for many years. Nowadays, peroxides are also regarded as metabolic products that play essential physiological cellular roles. Organisms have developed efficient mechanisms to metabolize peroxides, mostly based on two kinds of redox chemistry, catalases/peroxidases that depend on the heme prosthetic group to afford peroxide reduction and thiol-based peroxidases that support their redox activities on specialized fast reacting cysteine/selenocysteine (Cys/Sec) residues. Among the last group, glutathione peroxidases (GPxs) and peroxiredoxins (Prxs) are the most widespread and abundant families, and they are the leitmotif of this review. After presenting the properties and roles of different peroxides in biology, we discuss the chemical mechanisms of peroxide reduction by low molecular weight thiols, Prxs, GPxs, and other thiol-based peroxidases. Special attention is paid to the catalytic properties of Prxs and also to the importance and comparative outlook of the properties of Sec and its role in GPxs. To finish, we describe and discuss the current views on the activities of thiol-based peroxidases in peroxide-mediated redox signaling processes.
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Affiliation(s)
| | | | | | | | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET , Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , 2160 Buenos Aires , Argentina
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7
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Zaffagnini M, Fermani S, Marchand CH, Costa A, Sparla F, Rouhier N, Geigenberger P, Lemaire SD, Trost P. Redox Homeostasis in Photosynthetic Organisms: Novel and Established Thiol-Based Molecular Mechanisms. Antioxid Redox Signal 2019; 31:155-210. [PMID: 30499304 DOI: 10.1089/ars.2018.7617] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Significance: Redox homeostasis consists of an intricate network of reactions in which reactive molecular species, redox modifications, and redox proteins act in concert to allow both physiological responses and adaptation to stress conditions. Recent Advances: This review highlights established and novel thiol-based regulatory pathways underlying the functional facets and significance of redox biology in photosynthetic organisms. In the last decades, the field of redox regulation has largely expanded and this work is aimed at giving the right credit to the importance of thiol-based regulatory and signaling mechanisms in plants. Critical Issues: This cannot be all-encompassing, but is intended to provide a comprehensive overview on the structural/molecular mechanisms governing the most relevant thiol switching modifications with emphasis on the large genetic and functional diversity of redox controllers (i.e., redoxins). We also summarize the different proteomic-based approaches aimed at investigating the dynamics of redox modifications and the recent evidence that extends the possibility to monitor the cellular redox state in vivo. The physiological relevance of redox transitions is discussed based on reverse genetic studies confirming the importance of redox homeostasis in plant growth, development, and stress responses. Future Directions: In conclusion, we can firmly assume that redox biology has acquired an established significance that virtually infiltrates all aspects of plant physiology.
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Affiliation(s)
- Mirko Zaffagnini
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | - Simona Fermani
- 2 Department of Chemistry Giacomo Ciamician, University of Bologna, Bologna, Italy
| | - Christophe H Marchand
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Alex Costa
- 4 Department of Biosciences, University of Milan, Milan, Italy
| | - Francesca Sparla
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | | | - Peter Geigenberger
- 6 Department Biologie I, Ludwig-Maximilians-Universität München, LMU Biozentrum, Martinsried, Germany
| | - Stéphane D Lemaire
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Paolo Trost
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
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Radi R. The origins of nitric oxide and peroxynitrite research in Uruguay: 25 years of contributions to the biochemical and biomedical sciences. Nitric Oxide 2019; 87:83-89. [DOI: 10.1016/j.niox.2019.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 12/12/2022]
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Shu N, Lorentzen LG, Davies MJ. Reaction of quinones with proteins: Kinetics of adduct formation, effects on enzymatic activity and protein structure, and potential reversibility of modifications. Free Radic Biol Med 2019; 137:169-180. [PMID: 31026584 DOI: 10.1016/j.freeradbiomed.2019.04.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/22/2019] [Accepted: 04/22/2019] [Indexed: 01/08/2023]
Abstract
Quinones are a common motif in many biological compounds, and have been linked to tissue damage as they can undergo redox cycling to generate radicals, and/or act as Michael acceptors with nucleophiles, such as protein Cys residues, with consequent adduct formation. The kinetics and consequences of these Michael reactions are poorly characterized. In this study we hypothesized that adduction of protein Cys residues with quinones would be rapid, structure-dependent, quantitatively-significant, and result in altered protein structure and function. Multiple quinones were incubated with glyceraldehyde-3-phosphate dehydrogenase (GAPDH), creatine kinase (CK), papain, bovine (BSA) and human (HSA) serum albumins, with the kinetics of adduction and effects on protein structure and activity determined. Adduction rate constants at Cys residues, which were dependent on the quinone and protein structure, and thiol pKa, are in the range 102-105 M-1 s-1. p-Benzoquinone (BQ) induced dimerization of GAPDH and CK (but not BSA, HSA, or papain) in a dose- and time-dependent manner. Incubation of purified proteins, or cell lysates, with quinones resulted in a rapid loss of GAPDH and CK activity; this loss correlated well with the rate constant for Cys adduction. Glutathione (GSH) reacts competitively with quinones, and could reverse the loss of activity and dimerization of GAPDH and CK. Mass spectrometry peptide mass mapping provided evidence for BQ adduction to GAPDH to specific Cys residues (Cys149, Cys244), whereas all Cys residues in CK were modified. These data suggested that quinones can induce biological effects by rapid and selective formation of adducts with Cys residues in proteins.
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Affiliation(s)
- Nan Shu
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
| | - Lasse G Lorentzen
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark.
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Lackmann JW, Bruno G, Jablonowski H, Kogelheide F, Offerhaus B, Held J, Schulz-von der Gathen V, Stapelmann K, von Woedtke T, Wende K. Nitrosylation vs. oxidation - How to modulate cold physical plasmas for biological applications. PLoS One 2019; 14:e0216606. [PMID: 31067274 PMCID: PMC6505927 DOI: 10.1371/journal.pone.0216606] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
Thiol moieties are major targets for cold plasma-derived nitrogen and oxygen species, making CAPs convenient tools to modulate redox-signaling pathways in cells and tissues. The underlying biochemical pathways are currently under investigation but especially the role of CAP derived RNS is barely understood. Their potential role in protein thiol nitrosylation would be relevant in inflammatory processes such as wound healing and improving their specific production by CAP would allow for enhanced treatment options beyond the current application. The impact of a modified kINPen 09 argon plasma jet with nitrogen shielding on cysteine as a thiol-carrying model substance was investigated by FTIR spectroscopy and high-resolution mass spectrometry. The deposition of short-lived radical species was measured by electron paramagnetic resonance spectroscopy, long-lived species were quantified by ion chromatography (NO2-, NO3-) and xylenol orange assay (H2O2). Product profiles were compared to samples treated with the so-called COST jet, being introduced by a European COST initiative as a reference device, using both reference conditions as well as conditions adjusted to kINPen gas mixtures. While thiol oxidation was dominant under all tested conditions, an Ar + N2/O2 gas compositions combined with a nitrogen curtain fostered nitric oxide deposition and the desired generation of S-nitrosocysteine. Interestingly, the COST-jet revealed significant differences in its chemical properties in comparison to the kINPen by showing a more stable production of RNS with different gas admixtures, indicating a different •NO production pathway. Taken together, results indicate various chemical properties of kINPen and COST-jet as well as highlight the potential of plasma tuning not only by gas admixtures alone but by adjusting the surrounding atmosphere as well.
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Affiliation(s)
- Jan-Wilm Lackmann
- ZIK plasmatis at Leibniz Institute for Plasma Science and Technology (INP Greifswald e.V.), Greifswald, Germany
- * E-mail: (JWL); (KW)
| | - Giuliana Bruno
- ZIK plasmatis at Leibniz Institute for Plasma Science and Technology (INP Greifswald e.V.), Greifswald, Germany
| | - Helena Jablonowski
- ZIK plasmatis at Leibniz Institute for Plasma Science and Technology (INP Greifswald e.V.), Greifswald, Germany
| | - Friederike Kogelheide
- Institute for Electrical Engineering and Plasma Technology, Ruhr University Bochum, Bochum, Germany
| | - Björn Offerhaus
- Institute for Electrical Engineering and Plasma Technology, Ruhr University Bochum, Bochum, Germany
| | - Julian Held
- Experimental Physics II, Ruhr University Bochum, Bochum, Germany
| | | | - Katharina Stapelmann
- Institute for Electrical Engineering and Plasma Technology, Ruhr University Bochum, Bochum, Germany
- Plasma for Life Sciences, Department of Nuclear Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Thomas von Woedtke
- ZIK plasmatis at Leibniz Institute for Plasma Science and Technology (INP Greifswald e.V.), Greifswald, Germany
| | - Kristian Wende
- ZIK plasmatis at Leibniz Institute for Plasma Science and Technology (INP Greifswald e.V.), Greifswald, Germany
- * E-mail: (JWL); (KW)
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11
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Chronic Exposure to Sodium Fluoride Triggers Oxidative Biochemistry Misbalance in Mice: Effects on Peripheral Blood Circulation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:8379123. [PMID: 30224946 PMCID: PMC6129794 DOI: 10.1155/2018/8379123] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/30/2018] [Accepted: 06/07/2018] [Indexed: 12/25/2022]
Abstract
The excessive fluoride (F) exposure is associated with damage to cellular processes of different tissue types, due to changes in enzymatic metabolism and breakdown of redox balance. However, few studies evaluate doses of F compatible with human consumption. Thus, this study evaluated the effects of chronic exposure to sodium fluoride (NaF) on peripheral blood of mice from the evaluation of biochemical parameters. The animals were divided into three groups (n = 10) and received three concentrations of NaF in the drinking water for 60 days: 0 mg/L F, 10 mg/L F, and 50 mg/L F. The blood was then collected for trolox equivalent antioxidant capacity (TEAC), thiobarbituric acid reactive substances (TBARS), concentrations of nitric oxide (NO), superoxide dismutase (SOD), catalase (CAT), and reduced glutathione (GSH). The results showed that doses of 10 mg/L F and 50 mg/L F were able to increase TBARS concentration and decrease NO levels and CAT activity in the blood, but there was no statistical difference for SOD levels. The 50 mg/L F group showed an increase in TEAC levels and a decrease in the GSH content when compared to the control group. In this way, oxidative changes in blood from chronic exposure to F, especially at the highest dose, indicate that F may be a toxic agent and, therefore, the long-term exposure to excessive doses should be avoided.
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12
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Marcolongo JP, Zeida A, Semelak JA, Foglia NO, Morzan UN, Estrin DA, González Lebrero MC, Scherlis DA. Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code. Front Chem 2018; 6:70. [PMID: 29619365 PMCID: PMC5871697 DOI: 10.3389/fchem.2018.00070] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/05/2018] [Indexed: 12/13/2022] Open
Abstract
In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.
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Affiliation(s)
- Juan P Marcolongo
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ari Zeida
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Jonathan A Semelak
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nicolás O Foglia
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Uriel N Morzan
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dario A Estrin
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariano C González Lebrero
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Damián A Scherlis
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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13
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Ferrer-Sueta G, Campolo N, Trujillo M, Bartesaghi S, Carballal S, Romero N, Alvarez B, Radi R. Biochemistry of Peroxynitrite and Protein Tyrosine Nitration. Chem Rev 2018; 118:1338-1408. [DOI: 10.1021/acs.chemrev.7b00568] [Citation(s) in RCA: 292] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Gerardo Ferrer-Sueta
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Nicolás Campolo
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Silvina Bartesaghi
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sebastián Carballal
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Romero
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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14
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Li J, Liu Y, Kim E, March JC, Bentley WE, Payne GF. Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology. Free Radic Biol Med 2017; 105:110-131. [PMID: 28040473 DOI: 10.1016/j.freeradbiomed.2016.12.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/06/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022]
Abstract
The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H2O2) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this electrochemical tool for in vitro redox-probing.
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Affiliation(s)
- Jinyang Li
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - Yi Liu
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - Eunkyoung Kim
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - John C March
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - Gregory F Payne
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA.
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15
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Marcolongo JP, Morzan UN, Zeida A, Scherlis DA, Olabe JA. Nitrosodisulfide [S 2NO] - (perthionitrite) is a true intermediate during the "cross-talk" of nitrosyl and sulfide. Phys Chem Chem Phys 2016; 18:30047-30052. [PMID: 27774554 DOI: 10.1039/c6cp06314d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nitrosodisulfide S2NO- is a controversial intermediate in the reactions of S-nitrosothiols with HS- that produce NO and HNO. QM-MM molecular dynamics simulations combined with TD-DFT analysis contribute to a clear identification of S2NO- in water, acetone and acetonitrile, accounting for the UV-Vis signatures and broadening the mechanistic picture of N/S signaling in biochemistry.
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Affiliation(s)
- Juan P Marcolongo
- Departamento de Química Inorgánica, Analítica y Química Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina.
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16
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Degendorfer G, Chuang CY, Kawasaki H, Hammer A, Malle E, Yamakura F, Davies MJ. Peroxynitrite-mediated oxidation of plasma fibronectin. Free Radic Biol Med 2016; 97:602-615. [PMID: 27396946 DOI: 10.1016/j.freeradbiomed.2016.06.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/13/2016] [Accepted: 06/16/2016] [Indexed: 01/10/2023]
Abstract
Fibronectin is a large dimeric glycoprotein present in both human plasma and in basement membranes. The latter are specialized extracellular matrices underlying endothelial cells in the artery wall. Peroxynitrous acid (ONOOH) a potent oxidizing and nitrating agent, is formed in vivo from superoxide and nitric oxide radicals by stimulated macrophages and other cells. Considerable evidence supports ONOOH involvement in human atherosclerotic lesion development and rupture, possibly via extracellular matrix damage. Here we demonstrate that Tyr and Trp residues on human plasma fibronectin are highly sensitive to ONOOH with this resulting in the formation of 3-nitrotyrosine, 6-nitrotryptophan and dityrosine as well as protein aggregation and fragmentation. This occurs with equimolar or greater levels of oxidant, and in a dose-dependent manner. Modification of Tyr was quantitatively more significant than Trp (9.1% versus 1.5% conversion with 500μM ONOOH) after accounting for parent amino acid abundance, but only accounts for a small percentage of the total oxidant added. LC-MS studies identified 28 nitration sites (24 Tyr, 4 Trp) with many of these present within domains critical to protein function, including the cell-binding and anastellin domains. Human coronary artery endothelial cells showed decreased adherence and cell-spreading on ONOOH-modified fibronectin compared to control, consistent with cellular dysfunction induced by the modified matrix. Studies on human atherosclerotic lesions have provided evidence for co-localization of 3-nitrotyrosine and fibronectin. ONOOH-mediated fibronectin modification and compromised cell-matrix interactions, may contribute to endothelial cell dysfunction, a weakening of the fibrous cap of atherosclerotic lesions, and an increased propensity to rupture.
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Affiliation(s)
- Georg Degendorfer
- The Heart Research Institute, Newtown, NSW, Australia; Faculty of Medicine, The University of Sydney, NSW, Australia
| | - Christine Y Chuang
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
| | - Hiroaki Kawasaki
- Department of Chemistry, Juntendo University School of Health Care and Nursing, 1-1 Hiragagakuendai, Inzai, Chiba 270-1606, Japan
| | - Astrid Hammer
- Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Ernst Malle
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Fumiyuki Yamakura
- Department of Chemistry, Juntendo University School of Health Care and Nursing, 1-1 Hiragagakuendai, Inzai, Chiba 270-1606, Japan
| | - Michael J Davies
- The Heart Research Institute, Newtown, NSW, Australia; Faculty of Medicine, The University of Sydney, NSW, Australia; Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark.
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17
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Carballal S, Cuevasanta E, Yadav PK, Gherasim C, Ballou DP, Alvarez B, Banerjee R. Kinetics of Nitrite Reduction and Peroxynitrite Formation by Ferrous Heme in Human Cystathionine β-Synthase. J Biol Chem 2016; 291:8004-13. [PMID: 26867575 DOI: 10.1074/jbc.m116.718734] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 01/01/2023] Open
Abstract
Cystathionine β-synthase (CBS) is a pyridoxal phosphate-dependent enzyme that catalyzes the condensation of homocysteine with serine or with cysteine to form cystathionine and either water or hydrogen sulfide, respectively. Human CBS possesses a noncatalytic heme cofactor with cysteine and histidine as ligands, which in its oxidized state is relatively unreactive. Ferric CBS (Fe(III)-CBS) can be reduced by strong chemical and biochemical reductants to Fe(II)-CBS, which can bind carbon monoxide (CO) or nitric oxide (NO(•)), leading to inactive enzyme. Alternatively, Fe(II)-CBS can be reoxidized by O2to Fe(III)-CBS, forming superoxide radical anion (O2 (̇̄)). In this study, we describe the kinetics of nitrite (NO2 (-)) reduction by Fe(II)-CBS to form Fe(II)NO(•)-CBS. The second order rate constant for the reaction of Fe(II)-CBS with nitrite was obtained at low dithionite concentrations. Reoxidation of Fe(II)NO(•)-CBS by O2showed complex kinetic behavior and led to peroxynitrite (ONOO(-)) formation, which was detected using the fluorescent probe, coumarin boronic acid. Thus, in addition to being a potential source of superoxide radical, CBS constitutes a previously unrecognized source of NO(•)and peroxynitrite.
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Affiliation(s)
- Sebastián Carballal
- From the Departamento de Bioquímica, Facultad de Medicina, Center for Free Radical and Biomedical Research, and
| | - Ernesto Cuevasanta
- Center for Free Radical and Biomedical Research, and Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo 11800, Uruguay and
| | - Pramod K Yadav
- the Department of Biological Chemistry, Medical Center, University of Michigan, Ann Arbor, Michigan 48109-0600
| | - Carmen Gherasim
- the Department of Biological Chemistry, Medical Center, University of Michigan, Ann Arbor, Michigan 48109-0600
| | - David P Ballou
- the Department of Biological Chemistry, Medical Center, University of Michigan, Ann Arbor, Michigan 48109-0600
| | - Beatriz Alvarez
- Center for Free Radical and Biomedical Research, and Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo 11800, Uruguay and
| | - Ruma Banerjee
- the Department of Biological Chemistry, Medical Center, University of Michigan, Ann Arbor, Michigan 48109-0600
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18
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Kovacs I, Holzmeister C, Wirtz M, Geerlof A, Fröhlich T, Römling G, Kuruthukulangarakoola GT, Linster E, Hell R, Arnold GJ, Durner J, Lindermayr C. ROS-Mediated Inhibition of S-nitrosoglutathione Reductase Contributes to the Activation of Anti-oxidative Mechanisms. FRONTIERS IN PLANT SCIENCE 2016; 7:1669. [PMID: 27891135 PMCID: PMC5102900 DOI: 10.3389/fpls.2016.01669] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/24/2016] [Indexed: 05/18/2023]
Abstract
Nitric oxide (NO) has emerged as a signaling molecule in plants being involved in diverse physiological processes like germination, root growth, stomata closing and response to biotic and abiotic stress. S-nitrosoglutathione (GSNO) as a biological NO donor has a very important function in NO signaling since it can transfer its NO moiety to other proteins (trans-nitrosylation). Such trans-nitrosylation reactions are equilibrium reactions and depend on GSNO level. The breakdown of GSNO and thus the level of S-nitrosylated proteins are regulated by GSNO-reductase (GSNOR). In this way, this enzyme controls S-nitrosothiol levels and regulates NO signaling. Here we report that Arabidopsis thaliana GSNOR activity is reversibly inhibited by H2O2in vitro and by paraquat-induced oxidative stress in vivo. Light scattering analyses of reduced and oxidized recombinant GSNOR demonstrated that GSNOR proteins form dimers under both reducing and oxidizing conditions. Moreover, mass spectrometric analyses revealed that H2O2-treatment increased the amount of oxidative modifications on Zn2+-coordinating Cys47 and Cys177. Inhibition of GSNOR results in enhanced levels of S-nitrosothiols followed by accumulation of glutathione. Moreover, transcript levels of redox-regulated genes and activities of glutathione-dependent enzymes are increased in gsnor-ko plants, which may contribute to the enhanced resistance against oxidative stress. In sum, our results demonstrate that reactive oxygen species (ROS)-dependent inhibition of GSNOR is playing an important role in activation of anti-oxidative mechanisms to damping oxidative damage and imply a direct crosstalk between ROS- and NO-signaling.
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Affiliation(s)
- Izabella Kovacs
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München – German Research Center for Environmental HealthNeuherberg, Germany
| | - Christian Holzmeister
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München – German Research Center for Environmental HealthNeuherberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Ruprecht-Karls-Universität HeidelbergHeidelberg, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München – German Research Center for Environmental HealthNeuherberg, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Gaby Römling
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München – German Research Center for Environmental HealthNeuherberg, Germany
| | - Gitto T. Kuruthukulangarakoola
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München – German Research Center for Environmental HealthNeuherberg, Germany
| | - Eric Linster
- Centre for Organismal Studies Heidelberg, Ruprecht-Karls-Universität HeidelbergHeidelberg, Germany
| | - Rüdiger Hell
- Centre for Organismal Studies Heidelberg, Ruprecht-Karls-Universität HeidelbergHeidelberg, Germany
| | - Georg J. Arnold
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München – German Research Center for Environmental HealthNeuherberg, Germany
- Lehrstuhl für Biochemische Pflanzenpathologie, Technische Universität MünchenFreising, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München – German Research Center for Environmental HealthNeuherberg, Germany
- *Correspondence: Christian Lindermayr,
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19
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Storkey C, Pattison DI, Ignasiak MT, Schiesser CH, Davies MJ. Kinetics of reaction of peroxynitrite with selenium- and sulfur-containing compounds: Absolute rate constants and assessment of biological significance. Free Radic Biol Med 2015; 89:1049-56. [PMID: 26524402 DOI: 10.1016/j.freeradbiomed.2015.10.424] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/22/2022]
Abstract
Peroxynitrite (the physiological mixture of ONOOH and its anion, ONOO(-)) is a powerful biologically-relevant oxidant capable of oxidizing and damaging a range of important targets including sulfides, thiols, lipids, proteins, carbohydrates and nucleic acids. Excessive production of peroxynitrite is associated with several human pathologies including cardiovascular disease, ischemic-reperfusion injury, circulatory shock, inflammation and neurodegeneration. This study demonstrates that low-molecular-mass selenols (RSeH), selenides (RSeR') and to a lesser extent diselenides (RSeSeR') react with peroxynitrite with high rate constants. Low molecular mass selenols react particularly rapidly with peroxynitrite, with second order rate constants k2 in the range 5.1 × 10(5)-1.9 × 10(6)M(-1)s(-1), and 250-830 fold faster than the corresponding thiols (RSH) and many other endogenous biological targets. Reactions of peroxynitrite with selenides, including selenosugars are approximately 15-fold faster than their sulfur homologs with k2 approximately 2.5 × 10(3)M(-1)s(-1). The rate constants for diselenides and sulfides were slower with k2 0.72-1.3 × 10(3)M(-1)s(-1) and approximately 2.1 × 10(2)M(-1)s(-1) respectively. These studies demonstrate that both endogenous and exogenous selenium-containing compounds may modulate peroxynitrite-mediated damage at sites of acute and chronic inflammation, with this being of particular relevance at extracellular sites where the thiol pool is limited.
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Affiliation(s)
- Corin Storkey
- The Heart Research Institute, 7 Eliza Street, Newtown, NSW 2042, Australia; Faculty of Medicine, University of Sydney, Sydney, NSW 2006, Australia
| | - David I Pattison
- The Heart Research Institute, 7 Eliza Street, Newtown, NSW 2042, Australia; Faculty of Medicine, University of Sydney, Sydney, NSW 2006, Australia
| | - Marta T Ignasiak
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Belgdamsvej 3, Copenhagen 2200, Denmark
| | - Carl H Schiesser
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Michael J Davies
- The Heart Research Institute, 7 Eliza Street, Newtown, NSW 2042, Australia; Faculty of Medicine, University of Sydney, Sydney, NSW 2006, Australia; Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Belgdamsvej 3, Copenhagen 2200, Denmark.
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20
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Zeida A, Reyes AM, Lichtig P, Hugo M, Vazquez DS, Santos J, González Flecha FL, Radi R, Estrin DA, Trujillo M. Molecular Basis of Hydroperoxide Specificity in Peroxiredoxins: The Case of AhpE from Mycobacterium tuberculosis. Biochemistry 2015; 54:7237-47. [DOI: 10.1021/acs.biochem.5b00758] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
| | - Aníbal M. Reyes
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | - Martín Hugo
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | | | | | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | - Madia Trujillo
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
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21
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Trujillo M, Alvarez B, Radi R. One- and two-electron oxidation of thiols: mechanisms, kinetics and biological fates. Free Radic Res 2015; 50:150-71. [PMID: 26329537 DOI: 10.3109/10715762.2015.1089988] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The oxidation of biothiols participates not only in the defense against oxidative damage but also in enzymatic catalytic mechanisms and signal transduction processes. Thiols are versatile reductants that react with oxidizing species by one- and two-electron mechanisms, leading to thiyl radicals and sulfenic acids, respectively. These intermediates, depending on the conditions, participate in further reactions that converge on different stable products. Through this review, we will describe the biologically relevant species that are able to perform these oxidations and we will analyze the mechanisms and kinetics of the one- and two-electron reactions. The processes undergone by typical low-molecular-weight thiols as well as the particularities of specific thiol proteins will be described, including the molecular determinants proposed to account for the extraordinary reactivities of peroxidatic thiols. Finally, the main fates of the thiyl radical and sulfenic acid intermediates will be summarized.
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Affiliation(s)
- Madia Trujillo
- a Departamento de Bioquímica , Facultad de Medicina, Universidad de la República , Montevideo , Uruguay .,b Center for Free Radical and Biomedical Research , Universidad de la República , Montevideo , Uruguay , and
| | - Beatriz Alvarez
- b Center for Free Radical and Biomedical Research , Universidad de la República , Montevideo , Uruguay , and.,c Laboratorio de Enzimología, Facultad de Ciencias , Universidad de la República , Montevideo , Uruguay
| | - Rafael Radi
- a Departamento de Bioquímica , Facultad de Medicina, Universidad de la República , Montevideo , Uruguay .,b Center for Free Radical and Biomedical Research , Universidad de la República , Montevideo , Uruguay , and
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22
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Defelipe LA, Lanzarotti E, Gauto D, Marti MA, Turjanski AG. Protein topology determines cysteine oxidation fate: the case of sulfenyl amide formation among protein families. PLoS Comput Biol 2015; 11:e1004051. [PMID: 25741692 PMCID: PMC4351059 DOI: 10.1371/journal.pcbi.1004051] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 11/17/2014] [Indexed: 02/07/2023] Open
Abstract
Cysteine residues have a rich chemistry and play a critical role in the catalytic activity of a plethora of enzymes. However, cysteines are susceptible to oxidation by Reactive Oxygen and Nitrogen Species, leading to a loss of their catalytic function. Therefore, cysteine oxidation is emerging as a relevant physiological regulatory mechanism. Formation of a cyclic sulfenyl amide residue at the active site of redox-regulated proteins has been proposed as a protection mechanism against irreversible oxidation as the sulfenyl amide intermediate has been identified in several proteins. However, how and why only some specific cysteine residues in particular proteins react to form this intermediate is still unknown. In the present work using in-silico based tools, we have identified a constrained conformation that accelerates sulfenyl amide formation. By means of combined MD and QM/MM calculation we show that this conformation positions the NH backbone towards the sulfenic acid and promotes the reaction to yield the sulfenyl amide intermediate, in one step with the concomitant release of a water molecule. Moreover, in a large subset of the proteins we found a conserved beta sheet-loop-helix motif, which is present across different protein folds, that is key for sulfenyl amide production as it promotes the previous formation of sulfenic acid. For catalytic activity, in several cases, proteins need the Cysteine to be in the cysteinate form, i.e. a low pKa Cys. We found that the conserved motif stabilizes the cysteinate by hydrogen bonding to several NH backbone moieties. As cysteinate is also more reactive toward ROS we propose that the sheet-loop-helix motif and the constraint conformation have been selected by evolution for proteins that need a reactive Cys protected from irreversible oxidation. Our results also highlight how fold conservation can be correlated to redox chemistry regulation of protein function. Cysteine oxidation is emerging as a relevant regulatory mechanism of enzymatic function in the cell. Many proteins are protected from over oxidation by reactive oxygen species by the formation of a cyclic sulfenyl amide. Understanding how cyclic sulfenyl amide is formed and its dependence on protein structure is not only a basic question but necessary to predict which proteins may auto protect from over oxidation We describe a structural motif, which includes cysteine residues with a constrained conformation in a “forbidden” region of the Ramachandran plot plus a Beta-Cys-loop-helix motif, which has a reactive low pKa Cysteine and also enables to form the cyclic sulfenyl amide with a low activation barrier. Our QM/MM computations show that the cyclization reaction only occurs if the “forbidden” conformation is acquired by the Cysteine residue. This structural motif was identified at least in 7 PFAM families and 145 proteins with solved structure, showing that a large number of proteins could have the ability to go through such cyclic product preventing irreversible oxidation.
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Affiliation(s)
- Lucas A. Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- INQUIMAE/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Buenos Aires, Argentina
| | - Esteban Lanzarotti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Diego Gauto
- INQUIMAE/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Buenos Aires, Argentina
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- INQUIMAE/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Buenos Aires, Argentina
- * E-mail: (MAM); (AGT)
| | - Adrián G. Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- INQUIMAE/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Buenos Aires, Argentina
- * E-mail: (MAM); (AGT)
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23
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Cuevasanta E, Zeida A, Carballal S, Wedmann R, Morzan UN, Trujillo M, Radi R, Estrin DA, Filipovic MR, Alvarez B. Insights into the mechanism of the reaction between hydrogen sulfide and peroxynitrite. Free Radic Biol Med 2015; 80:93-100. [PMID: 25555671 DOI: 10.1016/j.freeradbiomed.2014.12.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 12/20/2022]
Abstract
Hydrogen sulfide and peroxynitrite are endogenously generated molecules that participate in biologically relevant pathways. A revision of the kinetic features of the reaction between peroxynitrite and hydrogen sulfide revealed a complex process. The rate constant of peroxynitrite decay, (6.65 ± 0.08) × 10(3) M(-1) s(-1) in 0.05 M sodium phosphate buffer (pH 7.4, 37°C), was affected by the concentration of buffer. Theoretical modeling suggested that, as in the case of thiols, the reaction is initiated by the nucleophilic attack of HS(-) on the peroxide group of ONOOH by a typical bimolecular nucleophilic substitution, yielding HSOH and NO2(-). In contrast to thiols, the reaction then proceeds to the formation of distinct products that absorb near 408 nm. Experiments in the presence of scavengers and carbon dioxide showed that free radicals are unlikely to be involved in the formation of these products. The results are consistent with product formation involving the reactive intermediate HSSH and its fast reaction with a second peroxynitrite molecule. Mass spectrometry and UV-Vis absorption spectra predictions suggest that at least one of the products is HSNO2 or its isomer HSONO.
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Affiliation(s)
- Ernesto Cuevasanta
- Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, 11800 Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Química Inorgánica, Analítica, y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina
| | - Sebastián Carballal
- Center for Free Radical and Biomedical Research, Universidad de la República, 11800 Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
| | - Rudolf Wedmann
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Uriel N Morzan
- Departamento de Química Inorgánica, Analítica, y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina
| | - Madia Trujillo
- Center for Free Radical and Biomedical Research, Universidad de la República, 11800 Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
| | - Rafael Radi
- Center for Free Radical and Biomedical Research, Universidad de la República, 11800 Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica, y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina
| | - Milos R Filipovic
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, 91058 Erlangen, Germany.
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, 11800 Montevideo, Uruguay.
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24
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Beck KF, Euler J, Eisel F, Beck M, Köhler Y, Sha LK, von Knethen A, Longen S, Pfeilschifter J. Cytokines induce protein kinase A-mediated signalling by a redox-dependent mechanism in rat renal mesangial cells. Biochem Pharmacol 2014; 93:362-9. [PMID: 25437456 DOI: 10.1016/j.bcp.2014.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 01/10/2023]
Abstract
Glomerular mesangial cells are smooth muscle cell-like pericytes and are regarded as key players in kidney diseases. In an inflammatory setting, these cells produce high amounts of inflammatory cytokines, chemokines and redox mediators such as reactive oxygen species or nitric oxide (NO). The temporal production of ROS, NO and other redox mediators markedly contributes to the final outcome of inflammatory diseases. Recently, we reported that platelet-derived growth factor forced mesangial cells to activate the regulatory subunit of protein kinase A (PKA RI) by a redox-dependent mechanism but independent from changes in cyclic AMP. This prompted us to further analyze the dimerization of PKA RI and activation of PKA-driven signalling in an inflammatory context. Stimulation of rat mesangial cells with interleukin-1β and tumour necrosis factor-α [2 nM] induced the formation of PKA RI heterodimers in a time-dependent manner. PKA RI dimerization was accompanied with the formation of ROS, NO and peroxynitrite as well as a depletion of reduced glutathione. Furthermore, dimerization of PKA RI was paralleled by enhanced activity of PKA as shown by the phosphorylation of vasodilator-stimulated phosphoprotein (VASP) at serine 157 that was independent of the formation of cyclic AMP. Remarkably, exogenously administered peroxynitrite potently induced dimerization of PKA RI, whereas pharmacologic inhibition of inducible NO synthase (iNOS) and scavenging of peroxynitrite reduced PKA RI dimerization and VASP phosphorylation to control levels thus clearly indicating a causal role for endogenously formed peroxynitrite on PKA signalling. Consequently, the treatment of inflammatory diseases with anti-oxidants or NOS inhibitors may alter PKA activity.
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Affiliation(s)
- Karl-Friedrich Beck
- Pharmazentrum Frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany.
| | - Johannes Euler
- Pharmazentrum Frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
| | - Florian Eisel
- Pharmazentrum Frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
| | - Martina Beck
- Pharmazentrum Frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
| | - Yvette Köhler
- Pharmazentrum Frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
| | - Lisa Katharina Sha
- Institut für Biochemie, Pathobiochemie, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
| | - Andreas von Knethen
- Institut für Biochemie, Pathobiochemie, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
| | - Sebastian Longen
- Pharmazentrum Frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
| | - Josef Pfeilschifter
- Pharmazentrum Frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
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25
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Zeida A, Reyes AM, Lebrero MCG, Radi R, Trujillo M, Estrina DA. The extraordinary catalytic ability of peroxiredoxins: a combined experimental and QM/MM study on the fast thiol oxidation step. Chem Commun (Camb) 2014; 50:10070-3. [PMID: 25045760 PMCID: PMC4336542 DOI: 10.1039/c4cc02899f] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peroxiredoxins (Prxs) catalyze the reduction of peroxides, a process of key relevance in a variety of cellular processes. The first step in the catalytic cycle of all Prxs is the oxidation of a cysteine residue to sulfenic acid, which occurs 10(3)-10(7) times faster than in free cysteine. We present an experimental kinetics and hybrid QM/MM investigation to explore the reaction of Prxs with H2O2 using alkyl hydroperoxide reductase E from Mycobacterium tuberculosis as a Prx model. We report for the first time the thermodynamic activation parameters of H2O2 reduction using Prx, which show that protein significantly lowers the activation enthalpy, with an unfavourable entropic effect, compared to the uncatalyzed reaction. The QM/MM simulations show that the remarkable catalytic effects responsible for the fast H2O2 reduction in Prxs are mainly due to an active-site arrangement, which establishes a complex hydrogen bond network activating both reactive species.
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Affiliation(s)
- Ari Zeida
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina
| | - Anibal M. Reyes
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Mariano C. G. Lebrero
- IQUIFIB-Dpto. Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
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26
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Zeida A, Guardia CM, Lichtig P, Perissinotti LL, Defelipe LA, Turjanski A, Radi R, Trujillo M, Estrin DA. Thiol redox biochemistry: insights from computer simulations. Biophys Rev 2014; 6:27-46. [PMID: 28509962 PMCID: PMC5427810 DOI: 10.1007/s12551-013-0127-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/03/2013] [Indexed: 12/13/2022] Open
Abstract
Thiol redox chemical reactions play a key role in a variety of physiological processes, mainly due to the presence of low-molecular-weight thiols and cysteine residues in proteins involved in catalysis and regulation. Specifically, the subtle sensitivity of thiol reactivity to the environment makes the use of simulation techniques extremely valuable for obtaining microscopic insights. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of selected relevant issues in thiol redox biochemistry, such as investigations on (1) the protonation state of cysteine in protein, (2) two-electron oxidation of thiols by hydroperoxides, chloramines, and hypochlorous acid, (3) mechanistic and kinetics aspects of the de novo formation of disulfide bonds and thiol-disulfide exchange, (4) formation of sulfenamides, (5) formation of nitrosothiols and transnitrosation reactions, and (6) one-electron oxidation pathways.
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Affiliation(s)
- Ari Zeida
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Carlos M Guardia
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Pablo Lichtig
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Laura L Perissinotti
- Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB, Canada, T2N 2N4
| | - Lucas A Defelipe
- Departamento de Química Biológica and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Adrián Turjanski
- Departamento de Química Biológica and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina.
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27
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Nitsche MA, Ferreria M, Mocskos EE, González Lebrero MC. GPU Accelerated Implementation of Density Functional Theory for Hybrid QM/MM Simulations. J Chem Theory Comput 2014; 10:959-67. [DOI: 10.1021/ct400308n] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Matías A. Nitsche
- Departamento
de Computación, FCEN, UBA, Buenos Aires C1428EGA, Argentina
| | - Manuel Ferreria
- Centro de Simulación
Computacional para Aplicaciones Tecnológicas, CSC, CONICET, Buenos Aires C1425FQD, Argentina
| | - Esteban E. Mocskos
- Departamento
de Computación, FCEN, UBA, Buenos Aires C1428EGA, Argentina
- Centro de Simulación
Computacional para Aplicaciones Tecnológicas, CSC, CONICET, Buenos Aires C1425FQD, Argentina
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28
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Morikawa M, Ando Y, Kita A, Sugita M, Matsumura S, Terashima M. Comprehensive Evaluation of the Antioxidant Activity of Miso by the Myoglobin Method. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2014. [DOI: 10.3136/fstr.20.1221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Yu Ando
- Department of Biosphere Sciences, Kobe College
| | - Asami Kita
- Department of Biosphere Sciences, Kobe College
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