Chantal Houée-Levin

Evidence for the formation of disulfide radicals in protein crystals upon X-ray irradiation

Irradiation of proteins with intense X-ray radiation produced by third-generation synchrotron sources generates specific structural and chemical alterations, including breakage of disulfide bonds and decarboxylation. In this paper, disulfide bond lengths in irradiated crystals of the enzyme Torpedo californica acetylcholinesterase are examined based on quantum simulations and on experimental data published previously. The experimental data suggest that one disulfide bond elongates by approximately 0.7 A upon X-ray irradiation as seen in a series of nine data sets collected on a single crystal. Simulation of the same bond suggests elongation by a similar value if a disulfide-radical anion is formed by trapping an electron. The absorption spectrum of a crystal irradiated under similar conditions shows a peak at approximately 400 nm, which in aqueous solution has been attributed to disulfide radicals. The results suggest that the formation of disulfide radicals in protein crystals owing to X-ray irradiation can be observed experimentally, both by structural means and by absorption spectroscopy.

ANTIOXIDANT ACTION OF SODIUM DIETHYLDITHIOCARBAMATE : REACTION WITH HYDROGEN PEROXIDE AND SUPEROXIDE RADICAL

The oxidation of sodium diethyldithiocarbamate (DDC) by hydrogen peroxide or superoxide radicals has been investigated. Hydrogen peroxide oxidizes DDC, leading to the formation of a hydrated form of disulfiram, a dimer of DDC having a disulfide group. In equimolar conditions, the overall process appears as a first-order reaction (k = 0.025 +/- 0.005 s-1), the first step being a second-order reaction (k = 5.0 +/- 0.1 mol-1.1.s-1). No radical intermediate was observed in this process. In the presence of an excess of any of the reagents, the hydrated form of disulfiram transforms into different products corresponding to the fixation of oxygen by sulfur atoms or replacement of C = S group by ketone function, in the presence of an excess of hydrogen peroxide. Superoxide anions (produced by steady-state 60Co gamma-radiolysis) oxidize DDC, yielding similar products to those obtained with hydrogen peroxide with a maximum oxidation G-value of 0.3 mumol.J-1. The rate constant k(O2.- + DDC) is equal to 900 mol-1.1.s-1.

Radiation chemistry of proteins

Publisher Summary This chapter reviews most recent data on radiation chemistry of proteins and provides an overview of the unknown aspects in protein radiation chemistry as well as in some of the expected biological consequences of protein radiolytic modifications. Under irradiation, proteins are affected by direct and indirect effects of ionizing radiations. When these macromolecules are in liquid solution, the indirect effects are predominant and the direct effects can be neglected. On the contrary, in a solid state, proteins are ionized mainly by direct interaction. Proteins in a solid state can be found in different forms, lyophilized or in frozen aqueous solution. Under irradiation, lyophilized proteins mostly aggregate. On the contrary, irradiation of frozen protein solutions gives rise to fragmentation. In an aqueous solution, the first step is the reaction of free radicals. This reaction proceeds with a rate constant that varies with the nature of the free radical but very little with the protein. The chemical nature of the resulting odd-electron site(s) can be hypothesized, but prediction of its location is still difficult. The reactivity of residues depends on many factors, including accessibility, neighboring residues, and electrostatic guidance.

Exploring oxidative modifications of tyrosine: An update on mechanisms of formation, advances in analysis and biological consequences

Abstract Protein oxidation is increasingly recognised as an important modulator of biochemical pathways controlling both physiological and pathological processes. While much attention has focused on cysteine modifications in reversible redox signalling, there is increasing evidence that other protein residues are oxidised in vivo with impact on cellular homeostasis and redox signalling pathways. A notable example is tyrosine, which can undergo a number of oxidative post-translational modifications to form 3-hydroxy-tyrosine, tyrosine crosslinks, 3-nitrotyrosine and halogenated tyrosine, with different effects on cellular functions. Tyrosine oxidation has been studied extensively in vitro, and this has generated detailed information about the molecular mechanisms that may occur in vivo. An important aspect of studying tyrosine oxidation both in vitro and in biological systems is the ability to monitor the formation of oxidised derivatives, which depends on a variety of analytical techniques. While antibody-dependent techniques such as ELISAs are commonly used, these have limitations, and more specific assays based on spectroscopic or spectrometric techniques are required to provide information on the exact residues modified and the nature of the modification. These approaches have helped understanding of the consequences of tyrosine oxidation in biological systems, especially its effects on cell signalling and cell dysfunction, linking to roles in disease. There is mounting evidence that tyrosine oxidation processes are important in vivo and can contribute to cellular pathology.

The One-Electron Reduction Potential of Methionine-Containing Peptides Depends on the Sequence

The protein residue methionine (Met) is one of the main targets of oxidizing free radicals produced in oxidative stress. Despite its biological importance, the mechanism of the oxidation of this residue is still partly unknown. In particular the one-electron redox potentials of the couple Met(•+)/Met have not been measured. In this work, two approaches, experimental as well as theoretical, were applied for three dipeptides L-Met L-Gly, L-Gly L-Met and L-Met L-Met. Measurements by electrochemistry indicated differences in the ease of oxidation. Two DFT methods (BH&HLYP and PBE0) with two basis sets (6-31G(d) and 6-311+G(2d,2p)) were used to determine the redox potentials of Met in these peptides present in different conformations. In agreement with experimental results, we show that they vary with the sequence and the spatial structure of the peptide, most of the values being higher than 1 V (up to 2 V) vs NHE.

Pulse radiolysis studies on superoxide reductase from Treponema pallidum.

Superoxide reductases (SORs) are small metalloenzymes, which catalyze reduction of O2 − to H2O2. The reaction of the enzyme from Treponema pallidum with superoxide was studied by pulse radiolysis methods. The first step is an extremely fast bi‐molecular reaction of the ferrous center with O2 −, with a rate constant of 6×108 M−1 s−1. A first intermediate is formed which is converted to a second one with a slower rate constant of 4800 s−1. This latter value is 10 times higher than the corresponding one previously reported in the case of SOR from Desulfoarculus baarsii. The reconstituted spectra for the two intermediates are consistent with formation of transient iron‐peroxide species.

Ab Initio and QM/MM Study of Electron Addition on the Disulfide Bond in Thioredoxin

Thioredoxin controls the intracellular redox potential through a disulfide/dithiol couple. Under conditions of oxidative stress, this protein functions via one-electron exchange, in which formation of the disulfide radical anion occurs. Combined quantum mechanical (QM) and molecular mechanical (MM) calculations using two- and three-level ONIOM schemes were performed on the thioredoxin (Trx) protein of Chlamydomonas reinhardtii in its oxidized-disulfide and one-electron-reduced forms. In both cases, the active site disulfide moiety was described at the MP2(fc)/6-31+G(d) level, and larger regions of varying sizes around the active site were described at the B3LYP/6-31+G(d) level. The remainder of the 112 residues and 33 water molecules of the crystal structure (PDB entry 1EP7) were described by the AMBER force field. Adiabatic electron affinities were calculated for the disulfide bond in all systems. Separate QM or QM/QM calculations were performed on the QM regions to establish the role of the remainder of the protein on the active site properties. The radical anion species becomes more stable as the number of amide groups in the vicinity increases. One-electron reduction potentials were calculated for the small molecule models, and approximated for the protein for which the values are similar to the experimental one (approximately 0 V). This high reduction potential is due to interaction with the charged end of Lys40, as indicated by mutation in silico to norleucine. The inclusion of the protonated Asp30 side chain and a water molecule in the QM region leads to an increase in the electron affinity. Proton transfer from the Asp30 side chain to the Cys39 sulfur in the radical anion species is strongly disfavored. The radical anion is more stable than the protonated form, which is consistent with experimental results.

The use of the methods of radiolysis to explore the mechanisms of free radical modifications in proteins.

The method of radiolysis is based upon the interaction of ionising radiation with the solvent (water). One can form the same free radicals as in conditions of oxidative stress ((•)OH, O2(•)(-), NO2(•)…). Moreover, the quantity of reactive oxygen (ROS) or nitrogen (RNS) species formed in the irradiated medium can be calculated knowing the dose and the radiation chemical yield, G, thus this method is quantitative. The use of the method of radiolysis has provided a wealth of data, especially about the kinetics of the oxidation by various free radicals and their mechanisms, the identification of transients formed, their lifetimes and the possibility to repair them by the so-called antioxidants. In this review we have collected the most recent data about protein oxidation that might be useful to a proteomic approach. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.

Methionine Residue Acts as a Prooxidant in the •OH-Induced Oxidation of Enkephalins

Enkephalins are bioactive pentapeptides (Tyr-Gly-Gly-Phe-Leu (Leu-enk) and Tyr-Gly-Gly-Phe-Met (Met-enk)) produced while an organism is under mental and/or physical stress. In the course of their biological action they are exposed to reactive oxygen and nitrogen species. We have reinvestigated the reactions of (•)OH radicals toward these peptides in order to elucidate the oxidation mechanisms and the final products. Nanosecond pulse radiolysis was used to obtain the spectra of the reaction intermediates and their kinetics. Additional insight into details of the oxidation mechanism was gained by identification of main final products by means of UV-vis spectrophotometry, HPLC coupled with fluorescence spectroscopy, and mass spectrometry. The key processes are different in both peptides. In Leu-enk, the first step is an (•)OH radical addition to the aromatic rings of Tyr and Phe residues that leads to hydroxylated residues, dihydroxyphenylalanine (DOPA) from Tyr and tyrosine isomers from Phe, respectively. In Met-enk, these processes are less important, an additional target being the sulfur atom of the methionine residue. Depending on pH either an OH-adduct (hydroxysulfuranyl radical) or a sulfur radical cation undergo intramolecular electron transfer with Tyr residue resulting in a repair of Met and oxidation of Tyr to tyrosyl radicals and a final formation of dityrosine. At low pH, the OH-adducts to Tyr residue are precursors of tyrosyl radicals and dityrosine. Thus, the final products coming from oxidation of the Tyr residue depend strongly on the neighboring residues and the pH.

Assessing the Role of the Active-site Cysteine Ligand in the Superoxide Reductase from Desulfoarculus baarsii

Superoxide reductase is a novel class of non-heme iron proteins that catalyzes the one-electron reduction of \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{O}_{2}^{{\bar{.}}}\) \end{document} to H2O2, providing an antioxidant defense in some bacteria. Its active site consists of an unusual non-heme Fe2+ center in a [His4 Cys1] square pyramidal pentacoordination. In this class of enzyme, the cysteine axial ligand has been hypothesized to be an essential feature in the reactivity of the enzyme. Previous Fourier transform infrared spectroscopy studies on the enzyme from Desulfoarculus baarsii revealed that a protonated carboxylate group, proposed to be the side chain of Glu114, is in interaction with the cysteine ligand. In this work, using pulse radiolysis, Fourier transform infrared, and resonance Raman spectroscopies, we have investigated to what extent the presence of this Glu114 carboxylic lateral chain affects the strength of the S—Fe bond and the reaction of the iron active site with superoxide. The E114A mutant shows significantly modified pulse radiolysis kinetics for the protonation process of the first reaction intermediate. Resonance Raman spectroscopy demonstrates that the E114A mutation results in both a strengthening of the S—Fe bond and an increase in the extent of freeze-trapping of a Fe-peroxo species after treatment with H2O2 by a specific strengthening of the Fe—O bond. A fine tuning of the strength of the S—Fe bond by the presence of Glu114 appears to be an essential factor for both the strength of the Fe—O bond and the pKa value of the Fe3+-peroxo intermediate species to form the reaction product H2O2.