Molecular basis of intramolecular electron transfer in proteins during radical-mediated oxidations: Computer simulation studies in model tyrosine–cysteine peptides in solution

Petruk, Ariel Alcides; Bartesaghi, Silvina; Trujillo, Madia; Estrin, Darı́o A.; Murgida, Daniel H.; Kalyanaraman, Balaraman; Marti, Marcelo Adrian; Radí, Rafael

doi:10.1016/j.abb.2012.05.012

Cited by 30 publications

(31 citation statements)

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“…The versatile physico-chemical properties of tyrosine allows it to play a central role in conformation and molecular recognition 5 ; moreover, tyrosine has special roles by virtue of the phenol functionality: 1) it can receive phosphate groups in target proteins by way of protein tyrosine kinases and 2) it participates in electron transfer processes with the intermediate formation of a tyrosyl radical (Tyr • )( E o’ = +0.94 V) 7 .…”

Section: Biochemical Properties Of Tyrosine and Nitrotyrosinementioning

confidence: 99%

Protein Tyrosine Nitration: Biochemical Mechanisms and Structural Basis of Functional Effects

2012

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CONSPECTUS The nitration of protein tyrosine residues to 3-nitrotyrosine represents an oxidative postranslational modification that unveils the disruption of nitric oxide (•NO) signaling and metabolism towards pro-oxidant processes. Indeed, excess levels of reactive oxygen species in the presence of •NO or •NO-derived metabolites lead to the formation of nitrating species such as peroxynitrite. Thus, protein 3-nitrotyrosine has been established as a biomarker of cell, tissue and systemic “nitroxidative stress”. Moreover, tyrosine nitration modifies key properties of the amino acid (i.e. phenol group pKa, redox potential, hydrophobicity and volume). Thus, the incorporation of a nitro group (−NO2) to protein tyrosines can lead to profound structural and functional changes, some of which contribute to altered cell and tissue homeostasis. In this Account, I describe our current efforts to define 1) biologically-relevant mechanisms of protein tyrosine nitration and 2) how this modification can cause changes in protein structure and function at the molecular level. First, the relevance of protein tyrosine nitration via free radical-mediated reactions (in both peroxynitrite-dependent or independent pathways) involving the intermediacy of tyrosyl radical (Tyr•) will be underscored. This feature of the nitration process becomes critical as Tyr• can take variable fates, including the formation of 3-nitrotyrosine. Fast kinetic techniques, electron paramagnetic resonance (EPR) studies, bioanalytical methods and kinetic simulations have altogether assisted to characterize and fingerprint the reactions of tyrosine with peroxynitrite and one-electron oxidants and its further evolution to 3-nitrotyrosine. Recent findings show that nitration of tyrosines in proteins associated to biomembranes is linked to the lipid peroxidation process via a connecting reaction that involves the one-electron oxidation of tyrosine by lipid peroxyl radicals (LOO•). Second, immunochemical and proteomic-based studies indicate that protein tyrosine nitration is a selective process in vitro and in vivo, preferentially directed to a subset of proteins, and within those proteins, typically one or two tyrosine residues are site-specifically modified. The nature and site(s) of formation of the proximal oxidizing/nitrating species, the physico-chemical characteristics of the local microenvironment and also structural features of the protein account for part of this selectivity. Then, how this relatively subtle chemical modification in one tyrosine residue can sometimes cause dramatic changes in protein activity has remained elusive. Herein, I will analyze recent structural biology data of two pure and homogenously nitrated mitochondrial proteins (i.e. cytochrome c and MnSOD) to illustrate regio-selectivity and structural effects of tyrosine nitration, and subsequent impact in protein loss- or even gain-of-function.

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Section: Biochemical Properties Of Tyrosine and Nitrotyrosinementioning

confidence: 99%

Protein Tyrosine Nitration: Biochemical Mechanisms and Structural Basis of Functional Effects

2012

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“…glutathione readily consumes • NO 2 ), the action of several enzymes which attenuate oxidant formation ( i.e. peroxiredoxins and SOD) or by the repair of • Tyr, either by reductants such as glutathione or ascorbic acid, or by intramolecular electron transfer processes [122,123] (Figure 3). In spite of these considerations, some proteins are preferentially nitrated.…”

Section: Peroxynitrite Footprintsmentioning

confidence: 99%

Kinetic and mechanistic considerations to assess the biological fate of peroxynitrite

Carballal

Bartesaghi

Radí

2014

Biochimica et Biophysica Acta (BBA) - General Subjects

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137

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Background Peroxynitrite, the product of the reaction between superoxide radicals and nitric oxide, is an elusive oxidant of short half-life and low steady-state concentration in biological systems; it promotes nitroxidative damage. Scope of Review We will consider kinetic and mechanistic aspects that allow rationalizing the biological fate of peroxynitrite from data obtained by a combination of methods that include fast kinetic techniques, electron paramagnetic resonance and kinetic simulations. In addition, we provide a quantitative analysis of peroxynitrite production rates and conceivable state-state levels in living systems. Major Conclusions The preferential reactions of peroxynitrite in vivo include those with carbon dioxide, thiols and metalloproteins; its homolysis represents only < 1 % of its fate. To note, carbon dioxide accounts for a significant fraction of peroxynitrite consumption leading to the formation of strong one-electron oxidants, carbonate radicals and nitrogen dioxide. On the other hand, peroxynitrite is rapidly reduced by peroxiredoxins, which represent efficient thiol-based peroxynitrite detoxification systems. Glutathione, present at mM concentration in cells and frequently considered a direct scavenger of peroxynitrite, does not react sufficiently fast with it in vivo; glutathione mainly inhibits peroxynitrite-dependent processes by reactions with secondary radicals. The detection of protein 3-nitrotyrosine, a molecular footprint, can demonstrate peroxynitrite formation in vivo. Basal peroxynitrite formation rates in cells can be estimated in the order of 0.1 to 0.5 μM s−1 and its steady-state concentration ~ 1 nM. General Significance The analysis provides a handle to predict the preferential fate and steady-state levels of peroxynitrite in living systems. This is useful to understand pathophysiological aspects and pharmacological prospects connected to peroxynitrite.

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“…The probability of ET toward the ferryl-oxoheme group was calculated using the pathways algorithm (56,57). This method looks for the best possible path connecting the electron donor and the acceptor, and it was successfully used by our group previously (58)(59)(60)(61)(62). Briefly, according to the Marcus theory (63), the ET rate constant (k ET ) depends on the reaction standard free energy (ΔG°), the reorganization energy (λ), and the electronic coupling matrix (T DA ), described in the following equation:…”

Section: Methodsmentioning

confidence: 99%

Kinetics, subcellular localization, and contribution to parasite virulence of a Trypanosoma cruzi hybrid type A heme peroxidase ( Tc APx-CcP)

Hugo

Martínez

Trujillo

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The Trypanosoma cruzi ascorbate peroxidase is, by sequence analysis, a hybrid type A member of class I heme peroxidases [TcAPx-cytochrome c peroxidase (CcP)], suggesting both ascorbate (Asc) and cytochrome c (Cc) peroxidase activity. Here, we show that the enzyme reacts fast with H 2 O 2 (k = 2.9 × 10 7 M −1 ·s −1 ) and catalytically decomposes H 2 O 2 using Cc as the reducing substrate with higher efficiency than Asc (k cat /K m = 2.1 × 10 5 versus 3.5 × 10 4 M −1 ·s −1 , respectively). Visible-absorption spectra of purified recombinant TcAPx-CcP after H 2 O 2 reaction denote the formation of a compound I-like product, characteristic of the generation of a tryptophanyl radical-cation (Trp 233•+ ). Mutation of Trp 233 to phenylalanine (W233F) completely abolishes the Cc-dependent peroxidase activity. In addition to Trp 233•+ , a Cys 222 -derived radical was identified by electron paramagnetic resonance spin trapping, immunospin trapping, and MS analysis after equimolar H 2 O 2 addition, supporting an alternative electron transfer (ET) pathway from the heme. Molecular dynamics studies revealed that ET between Trp 233 and Cys 222 is possible and likely to participate in the catalytic cycle. Recognizing the ability of TcAPx-CcP to use alternative reducing substrates, we searched for its subcellular localization in the infective parasite stages (intracellular amastigotes and extracellular trypomastigotes). TcAPx-CcP was found closely associated with mitochondrial membranes and, most interestingly, with the outer leaflet of the plasma membrane, suggesting a role at the host-parasite interface. TcAPx-CcP overexpressers were significantly more infective to macrophages and cardiomyocytes, as well as in the mouse model of Chagas disease, supporting the involvement of TcAPx-CcP in pathogen virulence as part of the parasite antioxidant armamentarium.Trypanosoma cruzi | heme peroxidase | oxidants | virulence | kinetics

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Molecular basis of intramolecular electron transfer in proteins during radical-mediated oxidations: Computer simulation studies in model tyrosine–cysteine peptides in solution

Cited by 30 publications

References 58 publications

Protein Tyrosine Nitration: Biochemical Mechanisms and Structural Basis of Functional Effects

Protein Tyrosine Nitration: Biochemical Mechanisms and Structural Basis of Functional Effects

Kinetic and mechanistic considerations to assess the biological fate of peroxynitrite

Kinetics, subcellular localization, and contribution to parasite virulence of a Trypanosoma cruzi hybrid type A heme peroxidase ( Tc APx-CcP)

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