Protein Oxidation and Aging E-Book

Tilman Grune

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Serie: Wiley Series in Protein and Peptide Science
• Sprache: Englisch

Seitenzahl: 1104

Veröffentlichungsjahr: 2012

Beschreibung

Reviews our current understanding of the role of protein oxidation in aging and age-related diseases Protein oxidation is at the core of the aging process. Setting forth a variety of new methods and approaches, this book helps researchers conveniently by exploring the aging process and developing more effective therapies to prevent or treat age-related diseases. There have been many studies dedicated to the relationship between protein oxidation and age-related pathology; now it is possible for researchers and readers to learn new techniques as utilizing protein oxidation products as biomarkers for aging. Protein Oxidation and Aging begins with a description of the tremendous variety of protein oxidation products. Furthermore, it covers: * Major aspects of the protein oxidation process * Cellular mechanisms for managing oxidized proteins * Role of protein oxidation in aging * Influence of genetic and environmental factors on protein oxidation * Measuring protein oxidation in the aging process * Protein oxidation in age-related diseases References at the end of each chapter serve as a gateway to the growing body of original research studies and reviews in the field.

Leseprobe

Table of Contents

COVER

WILEY SERIES ON PROTEIN AND PEPTIDE SCIENCE

TITLE PAGE

COPYRIGHT PAGE

INTRODUCTION TO THE WILEY SERIES ON PROTEIN AND PEPTIDE SCIENCE

PREFACE

1 OXIDATIVE STRESS AND PROTEIN OXIDATION

1.1 THE LARGE VARIETY OF PROTEIN OXIDATION PRODUCTS

1.2 REVERSIBLE OXIDATIVE MODIFICATIONS

1.3 IRREVERSIBLE OXIDATION PRODUCTS

1.4 THE OXIDATION OF EXTRACELLULAR MATRIX, MEMBRANE AND CYTOSKELETAL PROTEINS

1.5 MECHANISM AND FACTORS INFLUENCING THE FORMATION OF PROTEIN OXIDATION PRODUCTS

1.6 PROTEIN AGGREGATES: FORMATION AND SPECIFIC METABOLIC EFFECTS

1.7 METHODS TO MEASURE PROTEIN OXIDATION PRODUCTS IN RESEARCH LABORATORIES

2 REMOVAL OF OXIDIZED PROTEINS

2.1 THE LIMITED REPAIR OF SOME OXIDIZED PROTEINS

2.2 PROTEOLYSIS

2.3 THE ROLE OF OTHER PROTEASES IN THE FATE OF OXIDIZED PROTEINS

2.4 ROLE OF HEAT SHOCK PROTEINS IN PROTEIN DEGRADATION

2.5 CONCLUSION

3 PROTEIN OXIDATION AND AGING: DIFFERENT MODEL SYSTEMS AND AFFECTING FACTORS

3.1 PROTEIN OXIDATION DURING AGING: LOWER ORGANISMS AND CELLULAR MODEL SYSTEMS

3.2 NONMAMMALIAN MODEL SYSTEMS AND THE ACCUMULATION OF OXIDIZED PROTEINS DURING AGING

3.3 AGE-RELATED PROTEIN OXIDATION IN HUMANS AND MAMMALS

3.4 INHERITED FACTORS INFLUENCING PROTEIN OXIDATION DURING AGING

3.5 AGE-RELATED PROTEIN AGGREGATE FORMATION IN MODEL SYSTEMS

3.6 ENVIRONMENTAL FACTORS AFFECTING HEALTHY AGING

3.7 REPAIR AND DEGRADATION OF OXIDIZED PROTEINS DURING AGING

4 PROTEIN OXIDATION IN SOME AGE-RELATED DISEASES

4.1 PROTEIN OXIDATION DURING NEURODEGENERATION AND NEUROLOGICAL DISEASES

4.2 PROTEIN OXIDATION IN CARDIAC DISEASES

4.3 PROTEIN OXIDATION IN DIABETES

4.4 PROTEIN OXIDATION IN DEGENERATIVE ARTHRITIS

4.5 PROTEIN OXIDATION IN MUSCLE WASTING AND SARCOPENIA

4.6 PROTEIN OXIDATION IN DESTRUCTIVE EYE DISEASES

4.7 PROTEIN OXIDATION IN OSTEOPOROSIS

4.8 PROTEIN OXIDATION IN CANCER

4.9 OTHER DISEASES

ABBREVIATIONS

INDEX

Copyright © 2013 by John Wiley & Sons, Inc. All rights reserved

Published by John Wiley & Sons, Inc., Hoboken, New Jersey

Published simultaneously in Canada

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Library of Congress Cataloging-in-Publication Data:

Grune, Tilman.

Protein oxidation and aging / by Tilman Grune, Betul Catalgol, Tobias Jung.

p. ; cm. – (Wiley series on protein and peptide science)

 Includes bibliographical references and index.

 ISBN 978-0-470-87828-6 (cloth : alk. paper)

 I. Catalgol, Betul. II. Jung, Tobias (Research associate) III. Title. IV. Series: Wiley series in protein and peptide science.

 [DNLM: 1. Proteins–metabolism. 2. Aging–physiology. 3. Neurodegenerative Diseases–etiology. 4. Oxidative Stress–physiology. 5. Proteins–physiology. QU 55]

 612.3'98–dc23

2012040264

INTRODUCTION TO THE WILEY SERIES ON PROTEIN AND PEPTIDE SCIENCE

Proteins and peptides are the major functional components of the living cell. They are involved in all aspects of the maintenance of life. Their structural and functional repertoires are endless. They may act alone or in conjunction with other proteins, peptides, nucleic acids, membranes, small molecules, and ions during various stages of life. Dysfunction of proteins and peptides may result in the development of various pathological conditions and diseases. Therefore, the protein/peptide structure–function relationship is a key scientific problem lying at the junction point of modern biochemistry, biophysics, genetics, physiology, molecular and cellular biology, proteomics, and medicine.

The Wiley Series on Protein and Peptide Science is designed to supply a complementary perspective from current publications by focusing each volume on a specific protein- or peptide-associated question and endowing it with the broadest possible context and outlook. The volumes in this series should be considered required reading for biochemists, biophysicists, molecular biologists, geneticists, cell biologists, and physiologists as well as those specialists in drug design and development, proteomics, and molecular medicine with an interest in proteins and peptides. I hope that each reader will find in the volumes within this book series interesting and useful information.

First and foremost I would like to acknowledge the assistance of Anita Lekhwani of John Wiley & Sons, Inc., throughout this project. She has guided me through countless difficulties in the preparation of this book series and her enthusiasm, input, suggestions, and efforts were indispensable in bringing the Wiley Series on Protein and Peptide Science into existence. I would like to take this opportunity to thank everybody whose contribution in one way or another has helped and supported this project. Finally, special thank you goes to my wife, sons, and mother for their constant support, invaluable assistance, and continuous encouragement.

VLADIMIR N. UVERSKYSeptember 2008

PREFACE

Protein oxidation is one of the intensively investigated areas in modern cell biology. With increasing knowledge about protein-damaging agents, including reactive oxygen and nitrogen species, reducing sugars, and others, the involvement of protein oxidation in numerous diseases and the aging process itself becomes more obvious.

Interestingly, the chemical processes of protein and amino acid oxidation were already studied a long time ago. At the very beginning of modern biochemistry, for example, in one of the first issues of the Journal of Biological Chemistry, the chemical oxidation of amino acids was already tested, as in the article of H.D. Dakin, “The oxidation of leucin, α-amido-isovaleric acid and of α-amido-n-valeric acid with hydrogen peroxide” (J. Biol. Chem. 4: 63–76, 1908). Later that year, the same author described in more detail the formation of aldehydic oxidation products of amino acids in an article called “Note on the oxidation of glutamic and aspartic acids by means of hydrogen peroxide” (J. Biol. Chem. 5: 409–411, 1908). Until today, the formation of such protein carbonyls is still considered to be one of the most important highlights of protein oxidation. Although protein oxidation was investigated for a long time in chemical models in biology, it was somehow neglected, whereas the processes of lipid peroxidation were studied intensively.

Today, it is well accepted that proteins are among the main targets for oxidants. This is due to their abundance in biological systems and the high rate constants for several reactions of proteins with some oxidants. Since protein oxidation impairs the functionality of enzymes, receptors, antibodies, transport, and structural proteins, it is of immense importance for cell biology. However, most oxidized proteins are degraded by various intracellular proteolytic pathways, but some oxidized proteins appear to be poorly degraded and, therefore, accumulate within cells. This accumulation was one of the first discovered highlights of biochemical changes during the aging process, already described in the nineteenth century by A. Hannover (Kgl. Danske Vidensk. Kabernes Selkobs Naturv. Math. Afh. Copenhagen 10: 1–112, 1842) and J. H. Koneff (Beiträge zur Kenntnis der Nervenzellen der peripheren Ganglien. Mitt. Naturforsch. Gesellsch. Bern. 44: 13–14, 1886). Today, it is well accepted that protein oxidation and the accumulation of oxidized proteins contributes to the aging process, especially in postmitotic tissues. Furthermore, oxidized and modified proteins accumulate in a range of human pathologies.

This monograph will focus on the major aspects of the protein oxidation process (Chapter 1) and the main mechanisms that show how cells deal with proteins once they are oxidized (Chapter 2). The role of protein oxidation during aging, as well as the investigation of various aging models, the roles of genetic and environmental factors, and the ways of measuring protein oxidation in the aging process, are described in Chapter 3. In the last chapter (Chapter 4), a short overview on protein oxidation in a number of age-related diseases is described; however, in view of the abundance of literature on the modification and aggregation of proteins in some of the mentioned diseases, this is just a short excurse into this field.

Since I was busy with several projects, I first declined the invitation of the publisher John Wiley & Sons, Inc., to prepare a monograph on protein oxidation and aging, and it was only by Dr. Betul Catalgol and Dr. Tobias Jung offering their help that persuaded me to write this book. I want to take this opportunity to thank both of my coworkers for their extensive support. Dr. Betul Catalgol did the search and viewing of several thousand literature sources and is responsible for drafting Chapters 1, 3, and 4. Dr. Tobias Jung is responsible for Chapter 2 and the diagrams in this volume.

I cordially wish to thank my collaborators for their contribution and hope that the scope and the details of this monograph will be a useful source for basic scientists working in the field of protein oxidation and biology of aging.

TILMAN GRUNEVolume EditorMarch 2012

1

OXIDATIVE STRESS AND PROTEIN OXIDATION

Oxygen is a fundamental component of aerobic life. Molecular oxygen offers the opportunity for respiration, which is energetically more efficient than fermentation. However, the switch to an oxidative atmosphere was a source of massive environmental stress on existing life, forcing all organisms to adapt (1).

Biological systems are frequently exposed to reactive oxygen species (ROS) and reactive nitrogen species (RNS) which are generated exogenously as pollutants in the atmosphere (photochemical smog, ozone, pesticides, xenobiotics), during exposure to ultraviolet (UV) irradiation, X- or γ-rays, and endogenously as by-products of mitochondria-catalyzed electron transport reactions; products of oxidase-catalyzed reactions such as cytochrome P450 (CYP450) detoxification reactions; generated by metal-catalyzed reactions; products of arginine metabolism; and produced by neutrophils and macrophages during inflammatory conditions such as phagocytic oxidative bursts and peroxisomal leakage (2–4). In addition, these species play a role in a series of pathological situations, including atherosclerosis, rheumatoid arthritis, and other chronic inflammatory diseases; cancer, cataract, diabetes, and diabetic retinopathy; or neurodegenerative disorders such as Parkinson’s disease (PD) and Alzheimer’s disease (AD), as well as aging (5, 6).

Oxidative stress causes damage reactions which are mediated by a small fraction of the total oxygen consumed. This small percentage of the consumed oxygen is transformed to activated oxygen by-products, which might cause oxidative damage to biological molecules. However, a system of antioxidant defenses acts protectively to oppose the oxidative damage and is aimed to quench some reactive intermediates. Oxidative damage and antioxidant defense are normally in a more or less dynamic equilibrium. Often in the oxidative damage to biological molecules, trace elements such as iron or copper are involved (7).

The defense against ROS-mediated oxidative damage in all organisms is catalyzed by a large variety of different antioxidant defense systems which can either prevent the formation of these ROS/RNS or convert the most reactive metabolites into less active ones or inactivate these derivatives totally. These systems include a number of enzymes as major components, such as the superoxide dismutases (SODs), catalases (CAT), glutathione peroxidases (GPxs), reductases, and glutathione-S-transferases (GST); and a number of other thiol-specific enzymes, methionine sulfoxide reductases (MSR), and thioredoxin (Trx) reductases. Several metal-binding proteins such as ceruloplasmin, ferritin, and transferrin are also considered to be involved in the antioxidative defense, along with a number metabolites and cofactors (NADP+/nicotinamide adenine dinucleotide phosphate [NADPH], NAD+/nicotinamide adenine dinu­cleotide [NADH], lipoic acid, uric acid [UA], bilirubin, etc.), and some dietary components (vitamins C and E), and some trace metals as Mg2+, Mn2+, or Zn2+ (8). Interestingly, it seems to be established that the ability to cope with ROS decreases with age in most cells, tissues, or organisms. Moreover, it seems to be established that a continuous low-level exposure of some, if not all, of these ROS may be involved in the regulation, induction, and maintenance of a number of biological functions (9) by regulating diverse cell signaling events (10, 11). However, overwhelmingly high concentrations of ROS can oxidize nucleic acids, lipids, and proteins. Much of the damage can be repaired; however, if unrepaired, oxidized DNA and RNA can lead to transcription/translation errors, and consequently lead to the synthesis of abnormal proteins, which in turn might not be only nonfunctional, but can also be more sensitive to oxidation by ROS (12, 13). The ability to counteract oxidative stress situations is declining with age, thereby causing higher vulnerability of older cells, tissues, and organisms to oxidative damage (14). ROS are potentially able to attack all cellular structures; however, the reactivity of the substrates might differ in dependence of the ROS and the target molecule generated, but in principle, macromolecules such as lipids, DNA, and proteins are major targets (15).

The interaction of ROS with lipids is generally known as a process called lipid peroxidation (LPO). This process might lead to the loss of membrane integrity and hence compromise several cellular functions, including signaling events such as the activation of the phospholipases A2 mediated by changes in the membrane structure and composition. Activation of the phospholipase, in turn, leads to an increase in an influx of Ca2+ ions and activation of further downstream molecules, including lipoxygenases (LOXs). Interestingly, LOX transforms polyunsaturated fatty acids (PUFAs) into lipid hydroperoxides (LOOHs). These reactions are generally catalyzed by these enzymes in a highly selective and specific manner. Additionally, LOOHs are also formed by nonenzymatic LPO processes. Furthermore, intermediate products of LPO are formed by the decomposition of the hydroperoxides, resulting in some LPO products such as epoxides and highly unsaturated aldehydic compounds, which are of high chemical reactivity and difficult to detect (16).

LPO seems to be involved in a gradual cell damage occurring in some chronic diseases, for example in diabetes, rheumatism, atherosclerosis, and in the aging process itself. Importantly, dying cells in injured tissue also release enzymes able to facilitate the nonenzymatic LPO process. Some scenarios include the cleavage of membranes by esterases, the release of free unsaturated fatty acids, which are prone to enzymatic and nonenzymatic LPO, and the formation of LOOHs. In a series of nonenzymatic steps involving iron ions, these LOOHs decompose (17). For example, Das et al. demonstrated high LPO levels in the tissues of different-aged pigs with high concentrations of PUFAs in phospholipids of the membranes (18).

Besides LPO, one of the most significant consequences of oxidative stress is proposed to be oxidative DNA damage. However, due to the efficient DNA repair mechanisms, only a minor part of this DNA damage becomes permanent, forming mutations and/or genetic instability. Many different DNA base changes have been seen following some form of oxidative stress, and these lesions are widely considered as a first step in the development of cancer and are also implicated in the process of aging. The DNA repair mechanisms involved in the removal of oxidative DNA lesions are complex. For example, in Cockayne syndrome, characterized by premature aging, there appears to be deficiencies in the repair of oxidative DNA damage in the nuclear DNA, and this may be the major underlying cause of the disease (19). Oxidative damage to DNA causes not only strand breaks, but also the formation of specific base adducts, such as 8-hydroxy-2′-deoxyguanosine (7).

Accumulation of DNA lesions with age may be the underlying cause for age-associated diseases including cancer. ROS cause many types of DNA damage, including the abundant formation of 8-oxoguanine (8-oxoG) and thymine glycol (TG). 8-OxoG adopts a syn conformation and pairs with adenine, leading to transversion mutations, which may play a role in the development of cancer and the process of aging. In contrast, TG strongly blocks DNA replication and transcription and must be efficiently removed and repaired to maintain genetic stability. Base excision repair (BER) is the main excision repair system that removes 8-oxoG and TG. Persistent DNA damage can cause cell cycle arrest or induction of transcription, induction of signal transduction pathways, replication errors, and genomic instability (20).

Oxidative DNA damage accumulates with age in mitochondrial DNA rather than nuclear DNA. The mitochondrial theory of aging postulates that DNA damage and mutations accumulate in the mitochondrial genome, lead­ing to mitochondrial dysfunction and cell death. Experimental data from several laboratories suggest that the amount of DNA damage such as 8-oxoG increases in the mitochondrial genome with age, and it is reported that mtDNA from 23-month-old rat liver mitochondria has four times higher 8-oxoG than mtDNA from 6-month-old animals. In contrast, no significant change in the level of 8-oxoG was found in nuclear DNA from the same animals. In the same study, it has also been proposed that DNA repair capacity declines with age (21).

DNA repair is obviously a crucial function necessary to maintain genomic stability and function, so there is a need to understand whether and how mtDNA undergoes repair. Interestingly, the DNA repair activity appears to increase with age in the mitochondria, whereas it declines in the nucleus. Even with this increased DNA repair, there is still an increase in oxidative DNA base lesions observed in the mitochondria with age. This suggests that the oxidative DNA damage in mitochondria is dramatically increased during aging, which cannot be overcome by repair enzymes, although with higher activities.

BER is the major mechanism for the correction of damaged nucleobases resulting from alkylation and oxidation of DNA (22). Mitochondria have an efficient BER repair capacity, but cannot repair most bulky lesions normally repaired by nucleotide excision repair (NER) (21). The first step in the BER pathway consists of excision of the abnormal base by several specific DNA-N-glycosylases. A decrease in BER activity was found to be related to an increased risk of carcinogenesis and aging. To investigate BER activities in more detail, a new technique was developed to analyze DNA repair based on surface plasmon resonance imag­ing (SPRi) (22).

Base damage is often caused by ROS, for example, hydroxyl radical (HO), superoxide radical (O2), and hydrogen peroxide (H2O2). Besides the repair mechanisms previously mentioned, another line of defense is the repair of oxidative damage in DNA by the intricate network of DNA repair mechanisms. Transcription-coupled repair (TCR), global genome repair (GGR), mismatch repair (MMR), translesion synthesis (TLS), homologous recombination (HR), and nonhomologous end-joining (NHEJ) also contribute somehow to the repair of oxidative DNA damage. TCR and MMR are also important backup pathways for the repair of transcribed strands and newly replicated strands, respectively (23).

Besides lipids and DNA, proteins are also prevalent targets for ROS-mediated oxidative damage. Many years ago, proteins have been recognized as major targets of oxidative modification, and the accumulation of oxidized proteins is a characteristic feature of aging cells. Moreover, in particular, proteins show age-dependent changes in their steady-state levels, considered as a part of developmental biology (24). The age-related accumulation of oxidized proteins is dependent on the balance between the generation of oxidatively modified proteins and their elimination by protein degradation and repair systems. During the last years of research, an increase in the amount of oxidized proteins has been described in many experimental aging models, often measured by the accumulation of protein carbonyls, tyrosine oxidation products, or by the accumulation of protein-containing pigments such as lipofuscin (15).

Many factors influence the level of protein damage induced by ROS. It is worth noting that this includes, of course, the nature and concentration of the ROS, the availability of the target protein, and the presence and functionality of antioxidant enzymes and compounds (25).

Oxidative protein damage plays a crucial role in cellular functionality since the oxidized proteins lose their catalytic functions. Therefore, the oxidative damage to a specific protein, might lead to more or less a pronounced loss of a particular biochemical function. It is required to mention here that such an oxidative protein damage might be mediated directly by ROS/RNS, but also by the secondary reactions via other by-products of oxidative stress. Examples of such secondary modification include carbohydrates and lipids modified by oxidative stress (including LPO products). Often studied examples of such reactive intermediate metabolites are the LPO products malondialdehyde (MDA) or 4-hydroxynonenal (HNE). A number of studies demonstrated the cross-linking and inactivation effects of these molecules on proteins (26). Besides the “classical” oxidation of proteins by ROS/RNS, the reaction with reducing sugars is also modifying proteins readily. This nonenzymatic glycation/glycoxidation process is also called the Maillard reaction or nonenzymatic glycosylation. In this nonenzymatic reaction, reducing sugars interact with proteins, often first by a reaction leading to the formation of Schiff base, that is, an imine double bond between the aldehyde group of the sugar and the amino group in the protein, often the epsilon amino group of lysine residues. Such an imine is quickly rearranged to form a ketoamine, forming a so-called Amadori product. Further reactions of the Amadori products lead to the irreversible formation of advanced glycation end products (AGEs) (2). Many of the reactions are site specific and influenced by reduction–oxidation (redox) cycling metals, mainly iron or copper. Generally, the classification of the oxidative modifications is done by separating the reactions into those which oxidize and cleave the peptide bond and those which modify side chains. Oxidative protein modifications are also divided into specific and global ones. In the specific modifications such as dityrosine formation, less residues or proteins are affected, while in the global ones such as carbonyl formation, a more or less substantial fraction of proteins might be affected in the sample (24).

Several types of ROS-induced protein modifications have been demonstrated, including the loss of sulfhydryl (-SH) groups, formation of carbonyls, disulfide cross-links, dityrosine cross-links, nitrotyrosine, and glyoxidation and LPO adducts, among others (27). Some modifications listed here are: the oxidation of leucine resulting in the formation of various hydroxyleucines; tryptophan oxidation to form N-formylkynurenine, kynurenine, and further downstream products; histidine oxidation to form aspartate or asparagine; phenylalanine oxidation to ortho- and metatyrosine; tyrosine oxidation to form 3,4-dihydroxyphenylalanine (DOPA), dityrosine, 3-chlorotyrosine, and 3-nitrotyrosine (3-NY); and methionine (Met) oxidation to form methionine sulfoxide (MetSO). Some of the most commonly measured protein oxidation products of Val, Leu, Ile, Lys, Glu, Arg, and Pro are alcohols and carbonyl groups (28). Protein carbonyl groups have the advantage of being abundantly formed on a (theoretically) low background of carbonyl groups in nonoxidized proteins, resulting from the few carbonyl-bearing enzymatically introduced posttranslational modifications. However, protein carbonyls have the disadvantage of being nonspecific oxidation markers. In addition to the modification of amino acid side chains, oxidation reactions can also lead to a fragmentation of polypeptide chains, or to the formation of protein aggregates by intermolecular cross-linking of peptides and proteins (29). Other nonenzymatic processes can also contribute to protein modification: as Nε-carboxymethyllysine (Nε-CML), pentosidine, and a range of compounds called AGEs, as already mentioned (28).

It was long assumed that oxidation of many proteins is a random process, however certain proteins or protein domains seem to be oxidized preferentially or accumulate in the oxidized form more easily. Recently, the existence of site-specific oxidation processes is discussed more and more. This is supported by selective findings that some enzymes have been observed due to accumulating in an oxidized form during aging (30, 31), for example, glutamine synthetase (GS) (32, 33), mitochondrial aconitase (34), adenine nucleotide translocase (35) and calcineurin (36), glucose-6-phosphate dehydrogenase (G6PDH) (14), tyrosine hydroxylase (37), and some enzymes of the antioxidant defense system (38, 39). Interestingly, the elongation factor 2 (EF-2) was found to be oxidized during aging, a process that is proposed to lead partially to the decline of protein synthesis during aging (40).

Accumulation of oxidized proteins is a complex process dependent on the formation rates of different ROS species, the levels of numerous antioxidative systems, and the rates of degradation of oxidized proteins by a multiplicity of proteases that have been shown to decline during aging. Because the cellular levels of oxidized proteins are dependent upon so many variables, the mechanisms responsible for the accumulation of oxidatively modified proteins in one individual may be very different from those involved in another individual (29). Interestingly, certain oxidation processes of cysteine (Cys) and Met are reversible due to the existence of specific enzymatic systems, which can bring these modifications back to the reduced form. Irreversible oxidation products of other amino acids are most frequently hydroxylated and carbonylated amino acid derivatives. Oxidized proteins are generally less active, less thermostable, and have exposed hydrophobic amino acids at their surface (41). In order to be removed from the cellular protein pool, proteins harboring such irreversible amino acid modifications have to be degraded.

However, aging is accompanied by a loss of the cellular proteolytic activity and hence a further increase in the accumulation of damaged proteins and more thermolabile and catalytically inactive enzymes.

Therefore, whereas oxidative damage to nucleic acids is subject to an efficient repair by highly efficient mechanisms, the repair of damage to proteins appears to be limited to the reduction of oxidized derivatives of the sulfur-containing amino acid residues, as already mentioned. The reason for that is the plethora of possible oxidation products of the 20 amino acids, obviously exceeding in their numbers the range of an efficient repair. Therefore, the repair of other than sulfur-containing amino acids after protein oxidation has not been demonstrated. Hence, these damaged proteins are target for degradation by various intracellular proteases, including cathepsins, calpains, and especially the 20S proteasome (42, 43).

However, certain oxidized proteins are poorly handled by cells, and together with possible alterations in the rate of production of oxidized proteins, this may contribute to the observed accumulation and damaging actions of oxidized proteins during aging and in pathologies such as diabetes, atherosclerosis, and neurodegenerative diseases. Protein oxidation may also sometimes play controlling roles in cellular remodeling and cell growth. Proteins are also key targets in defensive cytolysis and in inflammatory self-damage (44).

1.1 THE LARGE VARIETY OF PROTEIN OXIDATION PRODUCTS

1.1.1 Primary Protein Oxidation Products

As previously mentioned, free radical and oxidant flux, as by-products of metabolic and energy transfer processes, are an inevitable hallmark of oxidative life. It is suggested that the formed reactive species react with cellular components, including proteins. Protein molecules containing such modified moieties may diffuse or be transported to other parts of the cell different from their origin, thus damaging more components due to secondary reactions (45).

Radicals react in a variety of reactions, including electron transfer (oxidation or reduction of the substrate), hydrogen abstraction, fragmentation and rearrangement, dimerization, disproportionation, and substitution (concerted addition and elimination) with amino acids, peptides, and proteins. The result of an interaction of a radical with a peptide is the formation of a peptide radical. The properties of the radicals formed on peptides and proteins depend on the nature and reactivity of the attacking radical. Thus, electrophilic radicals (e.g., HO, alkoxyl radicals) preferentially oxidize electron-rich sites, whereas nucleophilic species (such as phenyl and many other carbon-centered radicals) attack electron-deficient sites (46). While the positional selectivity and rates of radical attack on free amino acids are relatively well characterized, the situation with peptides and proteins is less clear. There is a wide variation in the magnitude of the rate constants for attack by species such as HO on free amino acids, and this can be readily accounted for a preferential attack at sites remote from the deactivating (powerfully electron-withdrawing) protonated amine group at the α-carbon of free amino acids, and the presence of radical stabilizing groups on some side chains. Furthermore, the deactivating effect of the protonated amino group is exerted over long distances, so that the attack on hydrocarbon side chains (e.g., Val, Leu, Ile) skewed toward the most remote sites (47–49). Thus, the ratio of an attack at potential sites is different from that expected on the basis of the greater stability of tertiary > secondary > primary carbon-centered radicals arising from the increased number of electron-releasing (stabilizing) alkyl groups.

The selectivity of an attack on side chains is also markedly affected by the presence of a functional group which can stabilize the resulting radicals. Thus, hydrogen atom abstraction occurs preferentially at positions adjacent to electron-stabilizing groups such as hydroxy groups (in Ser and Thr), carboxyl and amide functions (in Asp, Glu, Asn, Gln), and the guanidine residue in Arg (46). In contrast, the protonated amine function on the Lys side chain has a similar effect as the protonated amine group on the α-carbon. This results in hydrogen abstraction at sites remote from both groups, and hence products arising mainly from the C4 and C5 positions on Lys (50, 51). Addition reactions are usually faster than hydrogen atom abstraction reactions, as there is no bond breaking involved in the transition state. Hence, addition to the aromatic rings of Phe, Tyr, Trp, and His, and the sulfur atoms of Met and Cys predominates over abstraction from the methylene (-CH2-) groups. The adduct species formed with the aromatic rings are stabilized by delocalization on to neighboring double bonds. The only major exception occurs with Cys, where hydrogen abstraction from the thiol (-SH) group is particularly fast (52).

The conversion of the deactivating amine group on the α-carbon into an (electron delocalizing) amide function through the formation of a peptide bond increases both the extent and rate constant for attack of radicals such as HO at the α-carbon, thereby resulting in significant levels of backbone oxidation (49, 53). The range of rate constants for HO attack on amino acid derivatives (e.g., N-acetylated species) or simple two amino acid peptides (e.g., the Gly-X series) is much smaller than that observed with the free amino acids (46).

The α-carbon radical formed as a result of hydrogen atom abstraction from the backbone is particularly stable as a result of electron delocalization on both the neighboring amide group (on the N-terminal side) and the carbonyl function (on the C-terminal side) (54). This has important consequences for radical transfer reactions. Not all α-carbon radicals are of equal stability, however, and there is evidence for preferential formation at Gly residues in peptides (55). This has been postulated to arise because of steric interactions between the side chain and backbone groups, which prevents the α-carbon radical from achieving planarity (and hence effective electron delocalization) for those residues with bulky side chains (56). This results in the secondary α-carbon radical formed from Gly being more stable than the tertiary α-carbon radical formed from other amino acids in peptides.

Secondary and tertiary structures may play a significant role in blocking access of radicals present to backbone sites as a result of the outward protuberance of the side chains. This would suggest that side chain reactions may play a more important role in the chemistry of intact globular or sheet proteins than in the chemistry of disordered structures or small random coil peptides (57).

ROS-mediated oxidation of amino acid side chains leads to the formation of 2-oxohistidine from histidine (58), but also to the unstable amino acids asparagine and aspartic acid (59); tryptophan residues oxidation leads to kynurenine or N-formylkynurenine (60); tyrosine residues lead to dihydroxy derivatives (61); Met residues lead to MetSO or methionine sulfone derivatives (62); leucine and valine residues lead to hydroxy derivatives; and Cys residues lead to disulfide derivatives (63). Of particular significance is the fact that oxidation of many of the proteinogenic amino acids (lysine, arginine, and proline residues) lead to the formation of carbonyl derivatives (64). Other products of ROS attack on proteins include hydroperoxides and alcohols. Particularly reactive is the hydroxyl radical, which can introduce hydroxyl groups into phenylalanine and tyrosine residues, and cleave the ring structure of tryptophan. A peptide bond cleavage may also occur (59).

Amino acid composition results from mutation–selection balance caused by the antagonism between mutational biases and the selective pressure to maintain protein function and structural stability (1). Toxicity of oxidized proteins is related to oxidative cleavage of the polypeptide chain, modification of amino acid side chains, generation of protein–protein cross-linkage, and formation of derivatives sensitive to proteolytic degradation (29).

The amino acids most susceptible to oxidation (histidine, tryptophan, methionine, tyrosine, and Cys) (65) would be avoided in highly oxidizing environments. This effect should be more prominent on amino acids subject to irreversible oxidation (histidine, tryptophan, and tyrosine) than on amino acids capable of reversible oxidation (Met and Cys) (1). Because oxygen diffuses through the membranes to enter the cell, membrane proteins are expected to show signs of adaptation to high oxygen concentrations.

HO was shown to be the most effective oxidant, whereas other species are more selective (but less efficiently in inactivation), such as (SCN)2−,Br2−,Cl2−, and I2−. For example, (SCN)2− was found to react with a key tryptophan residue in pepsin and so inactivates the enzyme, although damage could be reversed by the same radical (44). Inactivation by hydrated electrons has also been reported (66), but its significance, and that of the previously mentioned selective radicals, for biological systems may be limited. In studies on D-amino acid oxidase, it was found that removal of the coenzyme FAD enhanced radical damage and inactivation, illustrating that conformation and ligands can affect the extent of inactivation (44).

However, proteins may differ strongly in their susceptibility to oxidative damage. The redox-sensitive amino acids of bovine serum albumin (BSA), for example, were shown to be oxidized about twice as fast as those of GS (67), and intact proteins are less sensitive to oxidation than misfolded proteins (12).

1.1.1.1 Carbon-Centered Radicals 

These radicals may be produced at either side chains or α-carbon sites, following the reaction of radicals with large peptides and proteins. Carbon-centered radicals are generally formed via radical addition to an aromatic ring, hydrogen abstraction from C-H bonds (side chain or α-carbon), or secondary reactions of alkoxyl-, peroxyl- (68), or nitrogen-centered radicals (69). Carbon-centered radicals formed on proteins dimerize in the absence of O2, or can form peroxyl radicals in its presence (70) (Fig. 1.1). Peroxyl radical formation predominates against dimerization in the presence of O2, because for dimerization two radicals are necessary and this might be sterically hindered. Peroxyl radicals can also be generated, in the absence of O2, from metal ion-catalyzed decomposition of hydroperoxides (71, 72). In contrast, in the absence of O2, some of the substituted carbon-centered radicals undergo slow unimolecular elimination reactions. Thus, α-hydroxyalkyl radicals with L-amino groups (e.g., those formed from Ser and Thr) can release NH3. This process may occur with some side chain-derived radicals, for example those formed at C5 of 5-hydroxylysine.

FIG. 1.1 α-Substituted heteroatom containing peroxyl radicals may undergo a quick elimination of HOO or O2− as shown in reaction 1. A carbon-centered radical as found in C6 of lysine side chains can react very fast with O2, releasing peroxyl radicals (HOO) and NH3+ (reaction 2), forming an α-aminoadipate-δ-semialdehyde. Carbon-centered radicals of aromatic ring structure also form peroxyl radicals (reaction 3)

(according to Clare et al., Biochim. Biophys. Acta 1504: 196–219, 2001).

Peroxyl radicals undergo a number of reactions that result in the formation of carbonyl groups (aldehydes or ketones), alcohols, and hydroperoxides. Peroxyl radicals undergo ready dimerization reactions with other peroxyl radicals or related species such as O2−/HOO; reactions with the latter species are more likely with proteins for steric reasons (46).

α-Carbon peroxyl radicals undergo a complex series of reactions which result in backbone cleavage (63). These species have been assumed to rapidly eliminate HOO to give acyl imines that subsequently react with water to form the corresponding amides and carbonyl compounds. However, studies on cyclo(Gly2) and cyclo(Ala2) have shown that these peroxyl radicals undergo only a slow loss of HOO. At high pH, ionization of the -NH- group (pKa 10.8 and 11.2 for cyclo(Gly2) and cyclo(Ala2), respectively) results in the rapid (base-catalyzed) elimination of O2−. This process gives a single product (Fig. 1.2, reaction 4), whereas at lower pH values, where slow loss of HOO is observed, bimolecular decay predominates and multiple species are formed (Fig. 1.2, reaction 5). Hydrogen atom abstraction by backbone α-carbon peroxyl radicals yields to α-carbon hydroperoxides, whereas cross-termination reactions with O2− and HOO yields alkoxyl radicals (73).

FIG. 1.2 Reaction 4 shows the reaction of cyclo(Gly2, R=H) or cyclo(Ala2, R=CH3): after abstraction of an H-atom by an OH radical followed by reaction with O2, the resulting peroxyl radical releases O2− very quickly at high pH. At lower pH, release of hydroperoxyl (OOH) happens at a much slower rate and different products are formed (reaction 5)

(according to Clare et al., Biochim. Biophys. Acta 1504: 196–219, 2001).

Side-chain aminyl radicals (e.g., those formed from the ε-amino group of Lys side chains) undergo intramolecular abstraction, and this generates carbon-centered radicals at either C3 or the α-carbon (69).

Hydrogen abstraction from the α-carbon position accounts for more than 90% of the radicals formed with a series of alanine-derived peptides on reaction with HO. This is due to the greater stability of the α-carbon radical over the primary alkyl radical formed on hydrogen atom abstraction from the methyl side chain (74). However, the yield of such backbone-derived radicals decreases markedly when there are side chains present, which can form stabilized radicals, or when steric factors play a role. α-Carbon radicals decay mainly by dimerization in the absence of O2 (75). In the former case, significant yields of cross-links involving side chain-derived radicals have been identified; in the presence of O2, peroxyl and alkoxyl species are also generated (76).

α-Carbon-centered radicals are also generated on addition of the solvated electron to backbone carbonyl groups (Fig. 1.3, reaction 6). The resulting midchain α-hydroxy α-amido radicals, formed on protonation of the initial adduct, decay primarily via reaction with other radicals in the absence of O2. Thus, the reaction with an α-carbon radical results in the repair of both species (Fig. 1.3, reaction 7). The initial adduct species also undergo electron transfer reactions with acceptors such as disulfide (Fig. 1.3, reaction 8) or His residues. The main chain cleavage via reaction 9 (Fig. 1.3) is believed to be a minor process.

FIG. 1.3 After addition of a solvated electron, an α-carbon-centered radical is generated at the backbone carbon (reaction 6). The formed midchain α-hydroxy α-amido radical decays in the absence of O2 via the reaction with other radicals (reaction 7), in this case resulting in the repair of both species. Electron transfer reactions are possible between disulfides or histidine residues (reaction 8). A cleavage of the main chain is a minor process in this scenario (reaction 9)

(according to Clare et al., Biochim. Biophys. Acta 1504: 196–219, 2001).

1.1.1.2 Thiyl Radicals 

Thiyl radicals (RS) are generated by either hydrogen abstraction from a free thiol group or by cleavage of disulfide linkages. The latter reaction can occur photolytically (Fig. 1.4, reaction 10) and by addition of an electron (reduction), followed by rapid fragmentation of the radical anion (Fig. 1.4, reaction 11) (77). Thiyl radicals react rapidly, but reversibly, with O2 to form peroxyl radicals RSOO (Fig. 1.5, reaction 12); these can isomerize to sulfonyl radicals RS(= O)O and give rise to oxyacids and sulfinyl (RSO) radicals (78). At physiological pH values, reaction with excess thiol anion (RS−) to give a disulfide radical anion (Fig. 1.5, reaction 13) competes with reaction with O2. The disulfide radical anion also reacts readily with O2 via electron transfer to give the disulfide and O2− (Fig. 1.5, reaction 14). Thiyl radicals readily dimerize, and thereby give rise to (inter- or intramolecular) protein cross-links, though the occurrence of such reactions may be limited by steric and electronic factors (52).

FIG. 1.4 Radical formation by photooxidation (reaction 10) or reduction (i.e., electron absorption) (reaction 11) of a disulfide bond

(according to Clare et al., Biochim. Biophys. Acta 1504: 196–219, 2001).

FIG. 1.5 Formation of a peroxyl radical by O2 absorption of a thiyl radical (reaction 12), reaction of a thiol anion with a thiyl radical producing a disulfide radical anion (reaction 13), and further electron transfer from that radical anion to O2, forming a disulfide (RSSR) and a superoxide radical anion (O2−) (reaction 14)

(according to Clare et al., Biochim. Biophys. Acta 1504: 196–219, 2001).

1.1.1.3 Aromatic Ring-Derived Radicals 

Reactions with aromatic side chains generally start by addition to the aromatic ring, and the initial adducts may undergo rapid further reactions. In addition, hydrogen abstraction from the aromatic ring and side chain methylene (-CH2-) groups can be seen. 3,4-DOPA (Fig. 1.6, reactions 15 and 16) is formed following the disproportionation of two initial ring-derived radicals in the absence of O2. In this reaction, HO reacts with Tyr residues and the formed adduct radicals react further, resulting in DOPA, or rapidly eliminate water, in both acid- and base-catalyzed reactions, to give phenoxyl radicals (Fig. 1.6, reaction 16). In the presence of O2 peroxyl radical formation is followed by rapid elimination of HOO (Fig. 1.6, reaction 17) and higher yields of DOPA are generated compared with the situation in the absence of O2. This DOPA formation has been used as a tyrosine and protein oxidation marker (79), however this species can also give rise to cellular damage, including DNA damage (80).

FIG. 1.6 In reactions with aromatic amino residues, generally additions to the ring occur (first step of reaction 15) and the formed products rapidly undergo further reactions. Oxidation of a tyrosine residue by a hydroxyl radical (OH) forms adduct radicals that can undergo further reactions to form DOPA (3,4-dihydroxyphenylalanine, end products of the reactions 15 and 17) of form phenoxyl radicals (reaction16). “R” indicates the rest of the protein containing the shown modified side chain

(according to Clare et al., Biochim. Biophys. Acta 1504: 196–219, 2001).

Additionally, phenoxyl species are generated by selective oxidants, such as N3, via one-electron oxidation of the phenolic ring to form a radical cation and subsequent rapid loss of the phenolic proton. They are also generated on a large number of heme, and other proteins, via enzymatic reactions (81, 82). Phenoxyl radicals can dimerize to yield hydroxylated biphenyls (di- or bi-tyrosine; Fig. 1.7, reaction 18), resulting in protein cross-linking. Cross-links between the ortho site and the oxygen atom have also been characterized (Fig. 1.7, reaction 18). Phenoxyl radicals have been implicated in the oxidation of a number of biological targets, including other amino acids, peptides, proteins, lipoproteins, and antioxidants (83, 84).

FIG. 1.7 This figure shows the dimerization of phenoxyl radicals to hydroxylated biphenyls, causing cross-linking of proteins. Both cross-links have been detected

(according to Clare et al., Biochim. Biophys. Acta 1504: 196–219, 2001).

Similar reactions are observed with Trp, with initial addition occurring to either the benzene ring (Fig. 1.8, reaction 19) or the pyrrole moiety (Fig. 1.8, reaction 20) (85). In the absence of O2, the benzene ring-derived radicals give either low yields of 4-, 5-, 6-, and 7-hydroxytryptophans or lose water to give the neutral indolyl radical (Fig. 1.8, reaction 21) (86). Indolyl radicals react slowly with O2 (87), but react rapidly with O2− to give a hydroperoxide (Fig. 1.8, reaction 22) (88). The remaining benzene ring-derived radicals react with O2 to form peroxyl radicals, some 30% of which eliminate HOO/O2− to give hydroxylated products. The peroxyl radicals formed on reaction of the initial C3 pyrrole ring-derived radical with O2 undergo a ring-opening reaction to give N-formylkynurenine (Fig. 1.8, reaction 23). The formation of hydroxylated products and N-formylkynurenine, and the loss of fluorescence from the parent amino acid, have been employed as markers of Trp oxidation (79).

FIG. 1.8 Reactions of tryptophan with hydroxyl radicals result in an initial addition to the benzene ring (reaction 19) or to the pyrole moiety (reaction 20). In the absence of O2, the radicals derived from the benzene ring form low amounts of 4-, 5-, 6-, and 7-hydroxytryptophans (reaction 20) or the neutral indolyl radical (reaction 21). With a slow rate, indolyl radicals react with O2, and with a very fast rate with superoxide (O2−), forming a hydroperoxide (reaction 23). The peroxyl radicals from the reaction with the initial C3 pyrrole ring (from reaction 20) can react with O2, resulting in N-formylkynurenine after a ring opening (reaction 22)

(according to Clare et al., Biochim. Biophys. Acta 1504: 196–219, 2001).

Electron transfer reactions resulting in the formation of radical anions and radical cations are also common with aromatic side chains. Thus, the reaction of the solvated electron with Phe generates a transient radical anion which rapidly protonates to give a cyclohexadienyl radical (Fig. 1.9, reaction 24). Ring radical cations are generated with all the aromatic amino acids on reaction with powerful oxidants, such as SO4− (Fig. 1.9, reaction 25), and on direct photoionization (89). The charge of these species is rapidly lost by a number of processes, including hydration (thereby yielding hydroxylated products) and loss of a proton from an adjacent C-H (Phe), N-H (with His or Trp), or O-H bond (with Tyr) (90).

FIG. 1.9 Reaction of a solvated electron with phenylalanine followed by protonation forms a cyclohexadienyl radical (reaction 24). Strong oxidants like SO4− or direct photoionization are able to induce ring radical cations at all aromatic amino acids (reaction 25)

(according to Clare et al., Biochim. Biophys. Acta 1504: 196–219, 2001).

1.1.1.4 Transfer between Sites 

Transfer reactions between side chains and from side chain to backbone and vice versa may occur. Several transfer reactions between aromatic side chain-derived radicals have been defined. The reduction potentials of peptide radicals suggest that the ultimate source for oxidizing equivalents is likely to be Tyr residues (or Trp in the absence of these side chains). Thus, peptide radicals are able to oxidize Tyr residues via the formation of the ring radical cation, and subsequent deprotonation to give the phenoxyl radical. These reactions are in equilibrium, so Tyr phenoxyl radicals can be repaired by high concentrations of thiols such as Cys, yielding thiyl radicals. This process is enhanced by excess of thiol anions, as the thiyl radicals generated are removed via the formation of the disulfide radical anion.

Reaction of Trp with N3 results in the generation of the neutral indolyl radical. If such species are generated on peptides or proteins that also contain Tyr residues, rapid oxidation of the latter residues to give phenoxyl radicals is observed via electron transfer (91). This type of transfer process has been investigated in a 62-amino-acid peptide (erabutoxin B) that contains single Trp (Trp-25) and Tyr (Tyr-29) residues. Slow transfer is observed in this case; this is attributed to the rigid nature of this peptide that contains four disulfide bonds (92). This study suggests that rapid electron transfer requires either direct contact of the reactive residues or contact via suitable intermediate species, and that the peptide backbone does not provide a transfer pathway.

Disulfide bonds (cystine residues) can act as a major source for electrons arising from electron transfer by reducing species. Thus, initial addition of solvated electrons to both the backbone carbonyl groups of peptide bonds and at some side chain sites (e.g., aromatic residues) can result in the ultimate reduction of cystine groups. The yield of initial electrons that end up at disulfide sites depends on the protein; with lysozyme, it is nearly 65%, whereas with RNase A, it is nearly 20%. The latter observation is of particular interest as the disulfide groups in this protein are internalized and inaccessible to species in bulk solution. Transfer occurs via hydrogen bonding networks, with the backbone acting as an efficient conduit, unlike the oxidative pathway (93). Information on the rates and pathways of transfer cannot be readily obtained in many of these systems due to the random nature of the initial electron addition. Studies with modified metalloproteins have, however, provided information about the mechanisms and control of electron transfer within proteins (94, 95).

Only the transfer to the most readily oxidized side chains (aromatic, Cys, and cystine) is observed in the transfer between side chain and backbone. Reaction of α-carbon radicals with cystine occurs by homolytic substitution to give cross-linked thioethers (96).

Backbone to side chain transfers can occur readily when the radical is centered on other sites apart from the α-carbon. Thus (nitrogen-centered) amidyl radicals generated by photolysis of N-haloamino acid derivatives (e.g., those formed on reaction of HOCl with backbone amide groups) readily abstract hydrogen atoms from side chain sites, with intramolecular 1,5-hydrogen abstraction being particularly rapid. Abstraction of side-chain hydrogen atoms has also been shown to occur with excited-state carbonyl functions on the backbone, particularly when geometrical restraints prevent intramolecular reactions to give α-carbon-centered radicals; these reactions can also occur with excited carbonyl functions on side chains (97). While 1,5- and 1,6-hydrogen atom transfer reactions are not unusual, the efficiency of intramolecular hydrogen abstraction decreases as the transition state ring size increases. Larger transition states have been invoked to explain some long-range photochemically induced transfer reactions of oligopeptide-linked anthraquinones. These reactions involve 1,19- and 1,21-hydrogen atom transfer, and are highly regioselective for coupling of the α-carbon of a Gly residue to a specific carbonyl group on the anthraquinone (98).

Hydrogen abstraction at the γ-carbon position on side chains can yield dehydropeptides via peroxyl radical formation (63). The dehydropeptides undergo base hydrolysis to give a new amide function and a keto acid. Thus, initial side-chain damage can result in backbone cleavage via the intermediacy of a peroxyl species. The three-dimensional structure of a peptide can also affect the chemistry of side chain-derived peroxyl radicals (46).

Alkoxyl radicals formed at C3 on peptides and proteins undergo L-scission reactions to give α-carbon species (99). Alkoxyl radicals formed on Ala side chains readily lose formaldehyde to generate the corresponding Gly α-carbon species (Fig. 1.10, reaction 26). This process predominates over other reactions of such alkoxyl radicals (e.g., 1,2-hydrogen shifts) due to the stability of the α-carbon radical, and appears to occur with a range of C3 side-chain alkoxyl radicals.

FIG. 1.10 An alkoxyl radical formed on alanine side chains releases formaldehyde while generating the corresponding glycine α-carbon species (reaction 26)

(according to Clare et al., Biochim. Biophys. Acta 1504: 196–219, 2001).

1.1.2 Reactive Compounds Mediating in Protein Oxidation

Metabolically, oxygen can be incorporated into amino acids by many reactions using a large variety of organic molecules and such abundant molecules as water. Indeed, amino acid biosynthesis rarely uses O2 directly, an exception being the synthesis of tyrosine from phenylalanine (1).

Free radicals are chemicals with unpaired electrons in their outer orbitals. Free radicals have different reactivities, ranging from the high reactivity of the hydroxyl radical to the low reactivity of melanins. Superoxide anion and nitric oxide are believed to be produced continuously in aerobic cells, the superoxide preferentially in the mitochondria. Superoxide anion is dismutated to hydrogen peroxide by the Mn-SOD located in the matrix of mitochondria. Superoxide and H2O2 are able to initiate Fenton or Haber–Weiss chemical reaction and OH formation (Fig. 1.11). This reaction is catalyzed by the Fe2+ ion (100).

FIG. 1.11 In this figure, Fenton chemistry is shown as the linked reduction of Fe3+ to Fe2+ in the reducing environment of a cell catalyzing the continuous formation of hydroxyl radicals (OH) from H2O2 (reactions 27 and 28). The Haber–Weiss reaction (reaction 29) describes the formation of hydroxyl radicals from H2O2 in the presence of an adequate electron donator (in this case, the superoxide radical anion, O2−).

Radical-mediated damage to proteins may be initiated by electron leakage, metal ion-dependent reactions, and autoxidation of lipids and sugars. The consequent protein oxidation is O2− dependent and involves several propagating radicals, notably alkoxyl radicals. Its products include several categories of reactive species and a range of stable products whose chemistry is currently being elucidated (44).

Two categories of reactive, but nonradical, intermediates in protein oxidation have been identified. Reductive moieties, notably DOPA formed from tyrosine, can reduce transition metal ions, thus enhancing reactions with hydroperoxides, and are also able to induce radical formation in reactions with O2 (101–102). The other category are the hydroperoxides formed particularly on aliphatic side chains, but probably also on main-chain α-carbons (72). These can be decomposed by transition metal ions to give further radicals, which may propagate reaction chains. The hydroperoxides may also be reductively detoxified to hydroxides, probably without radical formation (103).

3-NY formation involves reactive nitrogen intermediates. Nitric oxide, peroxynitrite, nitrite, and reactions between hypochlorite and nitrogen-containing compounds are the sources of many more intermediates. Several of these species can also give rise to both hydroxylated aromatic residues and tyrosyl (phenoxyl) radicals, and hence dityrosine. Dityrosine can also be formed by the myeloperoxidase (MPO)/chloride/H2O2 system, with either protein-bound or free tyrosine, as judged by model experiments. Whether this also plays a major role in vivo is not clear, since the dityrosine formation might be paralleled by 3-chlorotyrosine formation. This is complicated by the possible further oxidation of dityrosine (104).

1.1.2.1 Hydroxyl Radical 

During the oxidation of aliphatic amino acids by HO, hydroxylated derivatives, notably of the side chains, are formed. These were partially characterized by Kopoldova and coworkers (105), and have been fully designed for valine and leucine (103). During the oxidation of aromatic residues, the formation of phenoxyl radicals from tyrosine and their conversion into dityrosine and further products can occur, especially if there are no reductants to repair the tyrosyl radicals (e.g., thiols, vitamin E) and if there are vicinal tyrosyl radicals (106). Hydroxylation of phenylalanine, tyrosine, and tryptophan is also one of the characteristic reactions of hydroxyl radicals, and similar reactions of histidine (giving 2-oxohistidine) are important (58). In vitro studies demonstrate that the hydroxyl radical converts L-phenylalanine into M-tyrosine, an unnatural isomer of L-tyrosine (107).

The highly reactive OH radicals are also able to form protein radicals of various life spans. The involvement of such radicals in biological catalysis was suggested earlier (108). The electron desaturation of proteins can be produced by OH radicals so that the practically continuous depletion of electrons by OH radicals may represent the mechanisms involved in the overcome of the energetic barrier between the valency and the conductive bands of the proteins (109). OH radicals formed by the Fenton reaction are able to attack practically all amino acids and proteins even under mild chemical conditions (110). Therefore, it was shown that the reaction of OH with free Gly can give rise to nitrogen-centered radicals as a result of one-electron oxidation of the free amine group to give an aminium radical cation (RNH2+) or the neutral aminyl radical (RNH) (111).

Reactions of radicals such as OH with His are complex, with initial addition occurring at C2, C4, and C5 of the imidazole ring (Fig. 1.12). These radicals can react with O2 to give peroxyl radicals or undergo base-catalyzed loss of water to give a stabilized diazacyclopentadienyl radical. The final products of these reactions have not been completely characterized, but include 2-oxo-histidine, asparagine, aspartic acid, hydroxylated derivatives, and hydroperoxides (58).

FIG. 1.12 Different aducts from the reaction of a histidine residue with the hydroxyl radical at different C-atoms from the imidazole ring (reactions 30–32). After several intermediate steps, 2-oxihistidine can be one of the final products occurring (reaction 33)

(according to Clare et al., Biochim. Biophys. Acta 1504: 196–219, 2001).

1.1.2.2 Superoxide Radicals 

The superoxide anion is formed by the univalent reduction of triplet-state molecular oxygen (3O2). This process is mediated by enzymes such as NAD(P)H oxidases and xanthine oxidase or nonenzymatically by redox-reactive compounds such as the semiubiquinone compound of the mitochondrial electron transport chain. SODs convert superoxide enzymatically into hydrogen peroxide. In biological tissues, superoxide can also be converted nonenzymatically into the nonradical species hydrogen peroxide and singlet oxygen (1O2) (112).

The primary free radical in most oxygenated biological systems is the superoxide radical (O2−), which is in equilibrium with its protonated form, the hydroperoxyl radical (HO2) (113). The major sources of these radicals are modest leakages from the electron transport chains of mitochondria, chloroplasts, and endoplasmic reticulum (ER). Although O2− is relatively unreactive in comparison with many other radicals, biological systems can convert it into other more reactive species, such as peroxyl (ROO), alkoxyl (RO), and hydroxyl (OH) radicals. The last of these can originate from the Fenton reaction, in which the metal ion redox cycles, with reduction effected by O2− and oxidation effected by its dismutation product, hydrogen peroxide (H2O2). Iron and copper are biologically important transition metal ions, with their reduced forms capable of rapidly cleaving organic (including lipid) hydroperoxides, forming radicals that can initiate chain reactions, ultimately giving stable products such as lipid hydroxides (44).

The two-electron (nonradical) oxidant hypochlorite is a major product of stimulated neutrophils, which produce superoxide radicals which dismute to H2O2 and then convert it into hypohalous acids by the action of MPO in the presence of halides. Although the nonradical nature of this oxidant makes it chemically distinctive, its occurrence in biological systems is an important process for the organism and was reviewed in Reference 44.

Of the radicals formed in biological systems, the greatest attention has been focused on superoxide, the species formed when oxygen is reduced by a single electron (Fig. 1.13, reaction 34) (114). Superoxide undergoes a dismutation to form hydrogen peroxide (Fig. 1.13, reaction 35), therefore H2O2 is also generally present in superoxide-generating systems. In addition, superoxide can be protonated to form the hydroperoxyl radical (Fig. 1.13, reaction 36) (114).

FIG. 1.13 Superoxide (O2−) is the main primary radical formed in cellular systems by oxygen reduction by a single electron (reaction 34). Enzymes like SOD can form hydroperoxide (H2O2) by addition of two protons. In an acidic/neutral environment, superoxide can be protonated and forms the electroneutral hydroperoxyl radical (HOO) (reaction 36)

(according to Pryor, Annu. Rev. Physiol. 48: 657–667, 1986).

As mentioned, superoxide is found to be formed in all aerobically metabolizing cells. For example, electrons that appear to “leak” out of the mitochondrial respiratory chain are transferred to oxygen and generate superoxide; these radicals may cause cooxidation of xenobiotics and/or initiate pathological changes. In addition, macrophages and certain other phagocytic cells produce superoxide during the oxidative burst that follows their activation. Superoxide is formed when electronegative compounds intercept electrons from normal cellular electron transport and then reduce oxygen, a process called redox cycling.

It has become clear that superoxide is produced during the reperfusion of oxygenated blood into tissue that has briefly been anoxic (115–116). It was observed that organs can be maintained in an anoxic state for some time with little or no damage; however, when arteries are unclamped/reopened and aerated blood is allowed to reperfuse the organ, tissue damage can be induced suddenly and severely by oxidative damage. A number of investigators have discovered that this damage can be mitigated or prevented if SOD or other protective species (antioxidants) are added to the blood during reperfusion.

By comparing the superoxide anion-generating capacity of subcellular fractions from the lungs of neonatal and adult rats, the microsomal fractions from adult rats produced approximately three times more superoxide. This was explained on the basis that microsomes from adult rats was shown to contain almost a threefold greater content of CYP450 and a twofold greater concentration of NADPH cytochrome c reductase (117).

Boveris et al. (118) and Boveris and Chance (119) demonstrated that large amounts of superoxide anion were generated by mitochondria during the process of complex I and II reduction of coenzyme Q10 and its oxidation by complex III. Chance et al. in 1979 (120) estimated that 1–3% of inspired oxygen was converted to superoxide anions; such large amounts of product would indeed be potentially highly toxic to cells. Coenzyme Q10 is known to occur in all subcellular membranes and has a functional role in many known membrane oxidoreductase systems localized therein, notably in the mitochondria, plasmalemma, the Golgi apparatus (121), and lysosomes (122). Coenzyme Q10 oxidoreductase systems play a major role in the regulation of subcellular metabolism through the agency of superoxide anion formation and metabolome modulation. The global functions of coenzyme Q10 in relation to subcellular bioenergy systems, redox equilibrium, metabolic flux modulation, gene regulation, and oxygen radical formation are referred to in studies (123).

The activity of the important nuclear transcription factor nuclear factor κB (NFκB) is regulated by superoxide anion formation. NFκB is maintained in the cytosol in an inactive form bound to the inhibitor IκBα. Following plasma membrane superoxide and H2O2