The Reductive Desulfurization of Met and Cys Residues in Bovine RNase A Is Associated with trans Lipids Formation in a Mimetic Model of Biological Membranes

Reductive Stress of Sulfur-Containing Amino Acids within Proteins and Implication of Tandem Protein-Lipid Damage

Reductive radical stress represents the other side of the redox spectrum, less studied but equally important compared to oxidative stress. The reactivity of hydrogen atoms (H^•) and hydrated electrons (e^-_aq) connected with peptides/proteins is summarized, focusing on the chemical transformations of methionine (Met) and cystine (CysS-SCys) residues into α-aminobutyric acid and alanine, respectively. Chemical and mechanistic aspects of desulfurization processes with formation of diffusible sulfur-centered radicals, such as methanethiyl (CH₃S^•) and sulfhydryl (HS^•) radicals, are discussed. These findings are further applied to biomimetic radical chemistry, modeling the occurrence of tandem protein-lipid damages in proteo-liposomes and demonstrating that generation of sulfur-centered radicals from a variety of proteins is coupled with the cis-trans isomerization of unsaturated lipids in membranes. Recent applications to pharmaceutical and pharmacological contexts are described, evidencing novel perspectives in the stability of formulations and mode of action of drugs, respectively.

Effects of Simulated Space Radiations on the Tomato Root Proteome

Plant cultivation on spacecraft or planetary outposts is a promising and actual perspective both for food and bioactive molecules production. To this aim, plant response to ionizing radiations, as an important component of space radiation, must be assessed through on-ground experiments due to the potentially fatal effects on living systems. Hereby, we investigated the effects of X-rays and γ-rays exposure on tomato "hairy root" cultures (HRCs), which represent a solid platform for the production of pharmaceutically relevant molecules, including metabolites and recombinant proteins. In a space application perspective, we used an HRC system previously fortified through the accumulation of anthocyanins, which are known for their anti-oxidant properties. Roots were independently exposed to different photon radiations, namely X-rays (250 kV) and γ-rays (Co60, 1.25 MeV), both at the absorbed dose levels of 0.5, 5, and 10 Gy. Molecular changes induced in the proteome of HRCs were investigated by a comparative approach based on two-dimensional difference in-gel electrophoresis (2D-DIGE) technology, which allowed to highlight dynamic processes activated by these environmental stresses. Results revealed a comparable response to both photon treatments. In particular, the presence of differentially represented proteins were observed only when roots were exposed to 5 or 10 Gy of X-rays or γ-rays, while no variations were appreciated at 0.5 Gy of both radiations, when compared with unexposed control. Differentially represented proteins were identified by mass spectrometry procedures and their functional interactions were analyzed, revealing variations in the activation of stress response integrated mechanisms as well as in carbon/energy and protein metabolism. Specific results from above-mentioned procedures were validated by immunoblotting. Finally, a morphometric analysis verified the absence of significant alterations in the development of HRCs, allowing to ascribe the observed variations of protein expression to processes of acclimation to ionizing radiations. Overall results contribute to a meaningful risk evaluation for biological systems exposed to extra-terrestrial environments, in the perspective of manned interplanetary missions planned for the near future.

The Reaction of Thiyl Radical with Methyl Linoleate: Completing the Picture

Cis lipids can be converted by thiols and free radicals into trans lipids, which are therefore a valuable tell-tale for free radical activity in the cell's lipidome. Our previous studies have shown that polyunsaturated lipids are isomerized by alkanethiyl radicals (S^•) in a cycle propagated by reversible double-bond addition and terminated by radical H-abstraction from the lipid. A critical flaw in this picture has long been that the reported lipid abstraction rate from radiolysis studies is faster than addition-isomerization, implying that the "cycle" must be terminating faster than it is propagating! Herein, we resolved this longstanding puzzle by combining a detailed product analysis, with reinvestigation of the time-resolved kinetics, DFT calculations of the indicated pathways, and reformulation of the radical-stasis equations. We have determined thiol-coupled products in dilute solutions arise mainly from addition to the inside position of the bisallylic group, followed by rapid intramolecular H^• transfer, yielding allylic radicals (L_ZZ + S^• ⇄ SL^• → SL'^•) that are slowly reduced by thiol (SL'^• + SH → SL'H + S^•). The first-order grow-in rate of the L_-H^• signal (k_exp^280nm) may therefore be dominated by the addition-H-translocation rather than slower direct H^•-abstraction. Steady-state kinetic analysis of the new mechanism is consistent with products and the rates and trends for polyunsaturated fatty acids (PUFAs), monounsaturated fatty acids (MUFAs), and mixtures, with and without physiological [O₂]. Implications of this new paradigm for the thiol-ene reactivity fall in an interdisciplinary research area spanning from synthetic applications to metabolomics.

Sulfur Radical-Induced Redox Modifications in Proteins: Analysis and Mechanistic Aspects

SIGNIFICANCE

The sulfur-containing amino acids cysteine (Cys) and methionine (Met) are prominent protein targets of redox modification during conditions of oxidative stress. Here, two-electron pathways have received widespread attention, in part due to their role in signaling processes. However, Cys and Met are equally prone to one-electron pathways, generating intermediary radicals and/or radial ions. These radicals/radical ions can generate various reaction products that are not commonly monitored in redox proteomic studies, but they may be relevant for the fate of proteins during oxidative stress. Recent Advances: Time-resolved kinetic studies and product analysis have expanded our mechanistic understanding of radical reaction pathways of sulfur-containing amino acids. These reactions are now studied in some detail for Met and Cys in proteins, and homocysteine (Hcy) chemically linked to proteins, and the role of protein radical reactions in physiological processes is evolving.

CRITICAL ISSUES

Radical-derived products from Cys, Hcy, and Met can react with additional amino acids in proteins, leading to secondary protein modifications, which are potentially remote from initial points of radical attack. These products may contain intra- and intermolecular cross-links, which may lead to protein aggregation. Protein sequence and conformation will have a significant impact on the formation of such products, and a thorough understanding of reaction mechanisms and specifically how protein structure influences reaction pathways will be critical for identification and characterization of novel reaction products.

FUTURE DIRECTIONS

Future studies must evaluate the biological significance of novel reaction products that are derived from radical reactions of sulfur-containing amino acids. Antioxid. Redox Signal. 26, 388-405.

Radiation chemical studies of Gly-Met-Gly in aqueous solution

Important biological consequences are related to the reaction of HO^• radicals with methionine (Met). Several fundamental aspects remain to be defined when Met is an amino acid residue incorporated in the interior of peptides and proteins. The present study focuses on Gly-Met-Gly, the simplest peptide where Met is not a terminal residue. The reactions of HO^• with Gly-Met-Gly and its N-acetyl derivative were studied by pulse radiolysis technique. The transient absorption spectra were resolved into contributions from specific components of radical intermediates. Moreover, a detailed product analysis is provided for the first time for Met-containing peptides in radiolytic studies to support the mechanistic proposal. By parallel radiolytical and electrochemical reactions and consequent product identification, the formation of sulfoxide attributed to the direct HO^• radical attack on the sulfide functionality of the Met residue could be excluded, with the in situ generated hydrogen peroxide responsible for this oxidation. LC-MS and high resolution MS/MS were powerful analytical tools to envisage the structures of five products, thus allowing to complete the mechanistic picture of the overall Met-containing peptide reactivity.

A Promising Raman Spectroscopy Technique for the Investigation of trans and cis Cholesteryl Ester Isomers in Biological Samples

Lipid geometry is an important issue in biology and medicine. The cis-trans geometry conversion of double bonds in lipids is an endogenous process that can be mediated by sulfur-centered free radicals. Trans isomers of polyunsaturated fatty acids can be used as biological markers of free radical stress, and their presence in biological samples can be determined by synthesis and characterization of appropriate reference compounds. Fractions of plasma lipids, such as cholesteryl linoleate and arachidonate esters, are interesting targets because of their connection with membrane phospholipid turnover and their roles in cardiovascular health. In this context, Raman spectroscopy can provide a useful contribution, since Raman analysis can be performed directly on the lipid extracts without any derivatization reaction, is nondestructive, and can rapidly supply biochemical information. This study focused on the build up of Raman spectral libraries of different cis and trans isomers of cholesteryl esters to be used as references for the examination of complex biological samples and to facilitate isomer recognition. Unsaturated cholesteryl esters obtained by chemical synthesis and with different alkyl chain lengths, double bond numbers, or both, were analyzed. The potential of Raman analysis for trans isomer detection in biological samples was successfully tested on some cholesteryl ester lipid fractions from human serum. The data suggest promising applications of Raman spectroscopy in metabolomics and lipidomics.

Effects of ionizing radiation on biological molecules--mechanisms of damage and emerging methods of detection

SIGNIFICANCE

The detrimental effects of ionizing radiation (IR) involve a highly orchestrated series of events that are amplified by endogenous signaling and culminating in oxidative damage to DNA, lipids, proteins, and many metabolites. Despite the global impact of IR, the molecular mechanisms underlying tissue damage reveal that many biomolecules are chemoselectively modified by IR.

RECENT ADVANCES

The development of high-throughput "omics" technologies for mapping DNA and protein modifications have revolutionized the study of IR effects on biological systems. Studies in cells, tissues, and biological fluids are used to identify molecular features or biomarkers of IR exposure and response and the molecular mechanisms that regulate their expression or synthesis.

CRITICAL ISSUES

In this review, chemical mechanisms are described for IR-induced modifications of biomolecules along with methods for their detection. Included with the detection methods are crucial experimental considerations and caveats for their use. Additional factors critical to the cellular response to radiation, including alterations in protein expression, metabolomics, and epigenetic factors, are also discussed.

FUTURE DIRECTIONS

Throughout the review, the synergy of combined "omics" technologies such as genomics and epigenomics, proteomics, and metabolomics is highlighted. These are anticipated to lead to new hypotheses to understand IR effects on biological systems and improve IR-based therapies.

Non-enzymatic modifications in metallothioneins connected to lipid membrane damages: structural and biomimetic studies under reductive radical stress

Metallothioneins (MTs) are small cysteine-rich proteins with the ability to coordinate heavy metal atoms through metal-thiolate bonds, which are widely distributed among the animal and plant kingdoms. Multifunctional roles for MTs have been proposed, including their ability to scavenger various radicals and reactive oxygen species. In the present article we summarize available information of four MT polypeptides from different organisms, forming metal complexes with Zn(II), Cd(II) or Cu (I) ions. Non-enzymatic modifications of MTs under ionizing radiations and their consequences on the lipidic membrane compartment were studied by Raman spectroscopy and a biomimetic model, respectively. The latter is based on liposome technology and allows to measure the trans unsaturated fatty acid content as a result of reductive radical stress on MTs.

BIOLOGICAL SIGNIFICANCE

The effect of radical stress on the cell metabolism and functions is a very active field of research connecting various disciplines in life sciences. In this contest tandem radical damage has been the subject of recent investigations that pointed out its harmfulness in the general scenario of establishing the consequences of radical stress. By using biomimetic models of tandem damage we have for the first time tested the capability of metallothioneins (MTs), small metalloproteins rich of Cys residues, to damage another cell compartment like lipid membranes when they are undergone to reductive radical stress. The connection of MT reactivity with membrane lipid transformation can give a contribution to the puzzling context of radical stress occurring to biomolecules and the role as biological signaling. To this purpose, MT polypeptides from different organisms, exhibiting different sequence peculiarities, have been analyzed here. The spectroscopic analysis of these systems has allowed to identify modifications affecting metal-thiolate clusters, cystines, and Met residues, acting as efficient interceptors of reducing radical species. The chemical mechanism involving sulfur-containing moieties under reductive conditions discloses new scenarios that bring to the loss of sulfur-centered radicals by desulfurization reactions that change the natural sequences of MTs. Ala is a genetically coded amino acid, therefore the mutation of Cys to Ala occurring to a sequence by the radical process so far discussed, corresponds to a post-translational modification. Research on such mutation connected also to a free radical stress will be important to contribute for a complete picture of the degeneration associated to diseases and aging. Analogously, the Met to Aba mutation occurring after reductive stress transforms a natural amino acid into a natural, non-genetically-coded congener. Aba corresponds to a homologation of the alkyl chains normally present in genetically codified amino acids, such as methyl (in Ala) and isopropyl (in Leu), with an ethyl unit. Based on alkyl substitution, this modification can therefore be studied in order to understand its general consequences on the structure-activity relationships in proteins and, in particular, on molecular interactions. This article is part of a Special issue entitled: Posttranslational Protein modifications in biology and Medicine.

Combined Raman and IR spectroscopic study on the radical-based modifications of methionine

Among damages reported to occur on proteins, radical-based changes of methionine (Met) residues are one of the most important convalent post-translational modifications. The combined application of Raman and infrared (IR) spectroscopies for the characterisation of the radical-induced modifications of Met is described here. Gamma-irradiation was used to simulate the endogenous formation of reactive species such as hydrogen atoms (•H), hydroxyl radicals (•OH) and hydrogen peroxide (H(2)O(2)). These spectroscopic techniques coupled to mass experiments are suitable tools in detecting almost all the main radical-induced degradation products of Met that depend on the nature of the reactive species. In particular, Raman spectroscopy is useful in revealing the radical-induced modifications in the sulphur-containing moiety, whereas the IR spectra allow decarboxylation and deamination processes to be detected, as well as the formation of other degradation products. Thus, some band patterns useful for building a library of spectra-structure correlation for radical-based degradation of Met were identified. In particular, the bands due to the formation of methionine sulfoxide, the main oxidation product of Met, have been identified. All together, these results combine to produce a set of spectroscopic markers of the main processes occurring as a consequence of radical stress exposure, which can be used in a spectroscopic protocol for providing a first assessment of Met modifications in more complex systems such as peptides and proteins, and monitoring their impact on protein structure.

Use of Raman spectroscopy for the identification of radical-mediated damages in human serum albumin

Damages induced by free radicals on human serum albumin (HSA), the most prominent protein in plasma, were investigated by Raman spectroscopy. HSA underwent oxidative and reductive radical stress. Gamma-irradiation was used to simulate the endogenous formation of reactive radical species such as hydrogen atoms ((•)H), solvated electrons (e(aq)(-)) and hydroxyl radicals ((•)OH). Raman spectroscopy was shown to be a useful tool in identifying conformational changes of the protein structure and specific damages occurring at sensitive amino acid sites. In particular, the analysis of the S-S stretching region suggested the radical species caused modifications in the 17 disulphide bridges of HSA. The concomitant action of e(aq)(-) and (•)H atoms caused the formation of cyclic disulphide bridges, showing how cystine pairs act as efficient interceptors of reducing species, by direct scavenging and electron transfer reactions within the protein. This conclusion was further confirmed by the modifications visible in the Raman bands due to Phe and Tyr residues. As regards to protein folding, both oxidative and reductive radical stresses were able to cause a loss in α-helix content, although the latter remains the most abundant secondary structure component. β-turns motifs significantly increased as a consequence of the synergic action of e(aq)(-) and (•)H atoms, whereas a larger increase in the β-sheet content was found following the exposure to (•)OH and/or (•)H attack.

Radiation-induced reductive modifications of sulfur-containing amino acids within peptides and proteins

The complex scenario of radical stress reactions affecting peptides/proteins can be better elucidated through the design of biomimetic studies simulating the consequences of the different free radicals attacking amino acids. In this context, ionizing radiations allowed to examine the specific damages caused by H-atoms and electrons coupled with protons, thus establishing the molecular basis of reductive radical stress. This is an innovative concept that complements the well-known oxidative stress also in view of a complete understanding of the global consequences of radical species reactivities on living systems. This review summarizes the knowledge of the chemical changes present in sulfur-containing amino acids occurring in polypeptides under reductive radical conditions, in particular the transformation of Met and Cys residues into α-amino butyric acid and alanine, respectively. Reductive radical stress causing a desulfurization process, is therefore coupled with the formation of S-centered radicals, which in turn can diffuse apart and become responsible of the damage transfer from proteins to lipids. These reductive modifications assayed in different peptide/protein sequences constitute an integration of the molecular inventories that up to now take into account only oxidative transformations. They can be useful to achieve an integrated vision of the free radical reactivities in a multifunctional system and, overall, for wider applications in the redox proteomics field.

Hydrogen exchange equilibria in glutathione radicals: rate constants

The reduction of oxidized glutathione GSSG by hydrated electrons and hydrogen atoms to form GSSG^•− is quantitative. The radical anion dissociates into GS^• and GS⁻, and the S-centered radical subsequently abstracts a hydrogen intramolecularly. We observe sequential development of UV absorbance signatures that indicate the formation of both α- and β-carbon-centered radicals. From experiments performed at pH 2 and pH 11.8, we determined forward and reverse rate constants for the overall equilibrium between sulfur-centered and carbon-centered radicals: k_forward = 3·10⁵ s⁻¹, k_reverse = 7·10⁵ s⁻¹, and K = 0.4. Furthermore, on the basis of the differences between the kinetics traces at 240 and 280 nm, we estimate that α- and β-carbon-centered radicals are formed at a surprising ratio of 1:3. The ratios found at pH 2 also apply to pH 7, with the conclusion that the equilibrium ratio of S-centered:β-centered:α-centered radicals is, very approximately, 8:3:1. The formation of carbon-centered radicals could lead to irreversible damage in proteins via the formation of carbon−carbon bonds or backbone fragmentation.

Radiation chemical studies of methionine in aqueous solution: understanding the role of molecular oxygen

The oxidation of methionine is an important reaction in the biological milieu. Despite a few decades of intense studies, several fundamental aspects remain to be defined. We have investigated in detail the gamma-radiolysis of free methionine in the absence and presence of molecular oxygen followed by product characterization and quantification. The primary site of attack by HO(*) radicals and H(*) atoms is the sulfur atom of methionine. We have disclosed that HO(*) radicals do not oxidize methionine to the corresponding sulfoxide in either the presence or the absence of oxygen; the oxidizing species is H(2)O(2) derived either from the radiolysis of water or from the disproportionation of the byproduct O(2)(*-). 3-Methylthiopropionaldehyde is the major product of HO(*) radical attack in the presence of molecular oxygen. Together with the direct oxidation at sulfur as the major product, the potential of H(*) atoms is also proven to be highly specific for sulfur atom attack under anoxic and aerobic conditions. The major products derived from the H(*) atoms attack are found to be alpha-aminobutyric acid or homoserine, in the absence or presence of oxygen, respectively. All together, these results help clarify the fate of methionine related to a biological environment and offer a molecular basis for envisaging other possible pathways of in vivo degradation as well as other markers.

Membrane lipidomics and the geometry of unsaturated fatty acids from biomimetic models to biological consequences

In the last decades, free radical processes delineated an interdisciplinary field linking chemistry to biology and medicine. Free radical mechanisms became of importance as molecular basis of physiological and pathological conditions. Lipids, in particular, unsaturated fatty acids, are susceptible of free radical attack. The reactivity of the double bond toward free radicals is well known, in particular the reversible addition of radical species to this functionality determines the cis-trans double bond isomerization. Since the prevalent geometry displayed by unsaturated fatty acids in eukaryotes is cis, the occurrence of the cis-trans isomerization by free radicals corresponds to the loss of an important structural information linked to biological activity. The formation of trans isomers can have important meaning and consequences connected to radical stress. Free radical isomerization of membrane fatty acids has been the subject of research coupling the top-down approach by model studies, such as biomimetic chemistry in liposomes, with the bottom-up approach dealing with the examination of cell membrane lipidome in living systems under several physiopathological conditions. Methodologies and molecular libraries have been settled, for both liposome experiments and the examination of the radical stress in biological membranes. This chapter will give an overview of the current procedures used for liposome models and the cis-trans isomerization experiments, in order to build-up a library of trans geometrical fatty acid isomers.