Redox Proteomics: From Protein Modifications to Cellular Dysfunction and Diseases(Wiley Series on Mass Spectrometry)

Methodology and applications of redox proteomics The relatively new and rapidly changing field of redox proteomics has the potential to revolutionize how we diagnose disease, assess risks, determine prognoses, and target therapeutic strategies for people with inflammatory and aging-associated diseases. This collection brings together, in one comprehensive volume, a broad array of information and insights into normal and altered physiology, molecular mechanisms of disease states, and new applications of the rapidly evolving techniques of proteomics. Written by some of the finest investigators in this area, Redox Proteomics: From Protein Modifications to Cellular Dysfunction and Diseases examines the key topics of redox proteomics and redox control of cellular function, including: * The role of oxidized proteins in various disorders * Pioneering studies on the development of redox proteomics * Analytical methodologies for identification and structural characterization of proteins affected by oxidative/nitrosative modifications * The response and regulation of protein oxidation in different cell types * The pathological implications of protein oxidation for conditions, including asthma, cardiovascular disease, diabetes, preeclampsia, and Alzheimer's disease Distinguished by its in-depth discussions, balanced methodological approach, and emphasis on medical applications and diagnosis development, Redox Proteomics is a rich resource for all professionals with an interest in proteomics, cellular physiology and its alterations in disease states, and related fields.

Table of Contents:
Preface xxiii Contributors xxvii Part I Oxidatively Modified Proteins and Proteomic Technologies 1 1 Chemical Modification of Proteins by Reactive Oxygen Species 3 Earl R. Stadtman and Rodney L. Levine 1.1 Introduction 3 1.2 Peptide Bond Cleavage 5 1.3 β-Scission 6 1.4 Oxidation of Amino Acid Residue Side Chains 7 2 The Chemistry of Protein Modifications Elicited by Nitric Oxide and Related Nitrogen Oxides 25 Douglas D. Thomas, Lisa Ridnour, Sonia Donzelli, Michael Graham Espey, Daniele Mancardi, Jeffery S. Isenberg, Martin Feelisch, David D. Roberts, and David A. Wink 2.1 Introduction 25 2.2 Chemical Biology of NO 26 2.3 Chemistry of Metabolite Formation 40 3 Mass Spectrometry Approaches for the Molecular Characterization of Oxidatively/Nitrosatively Modified Proteins 59 Andrea Scaloni 3.1 Introduction 59 3.2 Mass Spectrometry Analysis of Oxidatively/Nitrosatively Modified Proteins 61 3.3 Proteomic Strategies for the Identification of ROS/RNS Protein Targets in Biological Matrices 76 3.4 Conclusions 84 4 Thiol-Disulfide Oxidoreduction of Protein Cysteines: Old Methods Revisited for Proteomics 101 Valentina Bonetto and Pietro Ghezzi 4.1 Introduction: Protein Thiols from Oxidative Stress to Redox Regulation 101 4.2 Different Redox States of Protein Cysteines 102 4.3 Methodologies to Identify and Quantify the Redox State of Protein Cysteines 104 4.4 Methods to Detect Specific Modifications 108 4.5 Methods for Enriching Redox-Regulated Proteins 111 4.6 Structural and Physicochemical Determinants for the Susceptibility of Cysteines toward Oxidation 112 4.7 Perspective 114 5 Carbonylated Proteins and Their Implication in Physiology and Pathology 123 Rodney L. Levine and Earl. R. Stadtman 5.1 Introduction 123 5.2 Types of Oxidative Modifications and Choice of Marker 133 5.3 Methodological Considerations 134 5.4 Selected Studies 136 5.5 Carbonylation during Aging 136 6 S-Nitrosation of Cysteine Thiols as a Redox Signal 169 Yanhong Zhang and Neil Hogg 6.1 Introduction 169 6.2 Mechanisms of Formation of S-Nitrosothiols 170 6.3 Cellular Transduction of the S-Nitroso Group 176 6.4 S-Nitrosothiols and Redox Proteomics 178 6.5 S-Nitrosothiols as an Intracellular Signal 179 6.6 Conclusions 182 7 Detection of Glycated and Glyco-Oxidated Proteins 189 Annunziata Lapolla, Elisa Basso, and Pietro Traldi 7.1 Introduction 189 7.2 MALDI-MS in the Study of In vitro Glycated Proteins 196 7.3 MALDI-MS in the Evaluation of Glycation Levels of HSA and IgG in Diabetic Patients 201 7.4 HbA1c and the Real Globin Glycation and Glyco-Oxidation 205 7.5 Determination of Dicarbonyl Compound Levels in Diabetic and Nephropathic Patients 209 7.6 AGE/Peptides: An In vitro Study and In vivo Preliminary Results 212 7.7 Expected Future Trends 226 8 MudPIT (Multidimensional Protein Identification Technology) for Identification of Post-translational Protein Modifications in Complex Biological Mixtures 233 Stefani N. Thomas, Bing-Wen Lu, Tatiana Nikolskaya, Yuri Nikolsky, and Austin J. Yang 8.1 Introduction 233 8.2 Proteomic Analysis of Oxidatively Modified Proteins 234 8.3 Statistical Validation and Interpretation of MudPIT Data 241 8.4 Concluding Remarks 249 9 Use of a Proteomic Technique to Identify Oxidant-Sensitive Thiol Proteins in Cultured Cells 253 Mark B. Hampton, James W. Baty, and Christine C. Winterbourn 9.1 Introduction 253 9.2 Fluorescence Labeling and Proteomic Analysis of Oxidized Thiol Proteins 254 9.3 Detection of Thiol Protein Oxidation in Jurkat Cells 256 9.4 Detection of Reversible and Irreversible Thiol Oxidation 258 9.5 Oxidized Thiol Compared with Reduced Thiol Measurements 259 9.6 More Selective Thiol Labeling Protocols 260 9.7 Identification of Oxidant-Sensitive Proteins 261 9.8 Conclusions and Future Directions 261 10 ICAT (Isotope-Coded Affinity Tag) Approach to Redox Proteomics: Identification and Quantification of Oxidant-Sensitive Protein Thiols 267 Mahadevan Sethuraman, Mark E. McComb, Hua Huang, Sequin Huang, Tyler Heibeck, Catherine E. Costello, and Richard A. Cohen 10.1 Introduction 267 10.2 Oxidant-Sensitive Cys 268 10.3 Challenges in Redox Proteomics 268 10.4 Iodoacetamide-Based Redox Proteomics 269 10.5 ICAT Approach to Redox Proteomics 271 10.6 Validation of the ICAT Approach Using the Recombinant Protein Creatine Kinase 271 10.7 ICAT Approach to the Complex Protein Mixtures 275 10.8 Perspectives 282 11 Quantitative Determination of Free and Protein-Associated 3-Nitrotyrosine and S-Nitrosothiols in the Circulation by Mass Spectrometry and Other Methodologies: A Critical Review and Discussion from the Analytical and Review Point of View 287 Dimitrios Tsikas 11.1 Introduction 287 11.2 Methods of Analysis 295   11.3 S-Nitrosothiols and 3-Nitrotyrosine in Health and Disease 314 11.4 Considerations from the Analytical and Review Points of View 326 11.5 Concluding Remarks and Future Prospects 329 Part II Cellular Aspects of Protein Oxidation 343 12 The Covalent Advantage: A New Paradigm for Cell Signaling Mediated by Thiol Reactive Lipid Oxidation Products 345 Dale A. Dickinson, Victor M. Darley-Usmar, and Aimee Landar 12.1 Introduction 345 12.2 Cyclooxygenase and the Conversion of Nonreactive Lipids to Thiol Switching Molecules 346 12.3 Lipid Peroxidation and the Nonenzymatic Formation of Lipid Adducts Capable of Modifying Proteins 349 12.4 The Thiol Switch and Redox Cell Signaling 351 12.5 Biological Responses to Endogenous Electrophilic Lipid Production 353 12.6 A New Paradigm of Oxidized Lipid Signaling—The Covalent Advantage 353 12.7 Implications for the Pathophysiology of Disease 356 12.8 Summary 358 13 Early Molecular Events during Response to Oxidative Stress in Human Cells by Differential Proteomics 369 Gianluca Tell 13.1 Introduction 369 13.2 Cellular Response to Oxidative Stress: From Membrane Receptors to Gene Expression Control 374 13.3 Gene Expression Control during Cell Response to Oxidative Stress: Redox-Regulated Transcription Factors 382 13.4 The Power of Differential Proteomics in Detecting Early Molecular Markers of Oxidative Stress: Examples from Human Cell Lines 383 13.5 Conclusions 388 14 Oxidative Damage to Proteins: Structural Modifications and Consequences in Cell Function 399 Elisa Cabiscol and Joaquim Ros 14.1 Introduction 399 14.2 Glycolysis 400 14.3 Pyruvate Metabolism 426 14.4 Tricarboxylic Acid Cycle 432 14.5 Electron Transport Chain and Oxidative Phosphorylation 437 14.6 Antioxidant Defenses 443 14.7 Molecular Chaperones 447 14.8 Cytoskeleton 451 14.9 Conclusions 454 15 Oxidative Damage and Cellular Senescence: Lessons from Bacteria and Yeast 473 Thomas Nyström 15.1 Microbial Senescence 473 15.2 Protein Carbonylation—An Irreversible Oxidative Damage to Proteins 474 15.3 Bacterial Senescence and Protein Carbonylation 476 15.4 Replicative Senescence and Segregation of Carbonylated Proteins 478 15.5 Yeast Senescence, Protein Oxidation, and Oncogenesis 479 15.6 Perspective 479 Part III Redox Proteomic Analysis in Human Diseases 485 16 Proteins as Sensitive Biomarkers of Human Conditions Associated with Oxidative Stress 487 Isabella Dalle-Donne, Ranieri Rossi, Fabrizio Ceciliani, Daniela Giustarini, Roberto Colombo, and Aldo Milzani 16.1 Introduction 487 16.2 Oxidative Stress in Human Diseases and Animal Models 489 16.3 Biomarkers of Oxidative Stress Status (BOSS) 493 16.4 Proteins as Biomarkers of Oxidative Stress Status 504 16.5 Conclusions 512 17 Degradation and Accumulation of Oxidized Proteins in Age-Related Diseases 527 Peter Voss and Tilman Grune 17.1 Oxidative Modifications of Amino Acids and Protein Damage 527 17.2 Degradation and Accumulation of Oxidatively Modified Proteins 532 17.3 Oxidized Proteins in Age-Related Diseases 543 17.4 Summary 547 18 Redox Proteomics: A New Approach to Investigate Oxidative Stress in Alzheimer’s Disease 563 D. Allan Butterfield, Rukhsana Sultana, and H. Fai Poon 18.1 Introduction 563 18.2 Brain Tissue and Models Used in Studying Aβ(1–42)-Induced Oxidative Stress and Neurotoxicity in AD 565 18.3 Redox Proteomics 567 18.4 Oxidatively Modified Proteins in AD and AD Models by Redox Proteomics 572 18.5 Conclusion 585 19 Oxidized Proteins in Cardiac Ischemia and Reperfusion 605 Jonathan P. Brennan and Philip Eaton 19.1 Introduction to Cardiac Ischemia and Reperfusion 605 19.2 Oxidatively Modified Proteins in the Heart 616 19.3 Established Targets of Post-translational Oxidation 624 19.4 Oxidative Stress in Myocardial Adaptation to Ischemia and Reperfusion 628 19.5 Conclusions, Therapeutic Implications, and Future Directions 631 20 Proteome Analysis of Oxidative Stress: Glutathionyl Hemoglobin in Diabetic and Uremic Patients 651 Toshimitsu Niwa 20.1 Introduction 651 20.2 Glutathionyl Hb as a Marker of Oxidative Stress 653 20.3 Conclusion 663 21 Glyco-oxidative Biochemistry in Diabetic Renal Injury 669 Toshio Miyata 21.1 Presence of Local, but not Generalized, Oxidative Stress in Diabetes 669 21.2 Oxidative Protein Damage In vivo 670 21.3 Antioxidative Properties of Medical Agents 671 21.4 Therapeutic Perspectives for AGE Inhibitors 672 21.5 AGE Inhibition and Renoprotection 673 21.6 Future Prospects 676 22 Quantitative Screening of Protein Glycation, Oxidation, and Nitration Adducts by LC-MS/MS: Protein Damage in Diabetes, Uremia, Cirrhosis, and Alzheimer’s Disease 681 Paul J. Thornalley 22.1 Introduction: Derivatization Free Detection with Application to Modified Proteins and Amino Acids 681 22.2 Physiological Sources of Glycated, Oxidized, and Nitrated Amino Acid Residues and Free Adducts 689 22.3 Protein Glycation and Oxidation in Diabetes: Damage to Cellular and Extracellular Proteins 694 22.4 Profound Mishandling of Glycated, Oxidized, and Nitrated Amino Acids in Uremia 702 22.5 Increased Glycated and Oxidized Amino Acids of Blood Plasma in Liver Cirrhosis—A Signature of Hepatic Oxidative Stress 704 22.6 Increased Methylglyoxal-Derived Hydroimidazolone and 3-Nitrotyrosine Free Adducts in Cerebrospinal Fluid of Subjects with Alzheimer’s Disease—A Signature of Neuronal Damage 707 22.7 Glycation Adducts in Food and Beverages 710 22.8 Concluding Remarks: Physiological Formation and Proteolytic Processing of Glycated, Oxidized, and Nitrated Proteins in Disease Processes—The Importance of Measuring “Damage and Debris” 714 23 Protein Targets and Functional Consequences of Tyrosine Nitration in Vascular Disease 729 Laura M. S. Baker, Bruce A. Freeman, and Mutay Aslan 23.1 Association of Vascular Disease with Increased Production of Reactive Oxygen/Nitrogen Species and Accumulation of Nitrated Proteins 729 23.2 Production of Reactive Oxygen and Nitrogen Species in the Vasculature 731 23.3 Tyrosine Nitration Mechanisms 734 23.4 Methods for Detecting Nitrotyrosine 742 23.5 Selectivity of Tyrosine Nitration 745 23.6 Mechanistic Consequences of Nitrotyrosine Formation: Protein Nitration In vivo and Vascular Disease 747 23.7 Metabolism, Reversibility, and Stability of the Nitrated Tyrosine 764 23.8 Tyrosine Nitration as a Cell Signaling Event 767 23.9 Summary 769 24 Oxidation of Artery Wall Proteins by Myeloperoxidase: A Proteomics Approach 787 Tomas Vaisar and Jay W. Heinecke 24.1 Oxidative Stress in Atherosclerosis 787 24.2 Potential Role of Redox-Active Metal Ions and Glucose in Oxidative Stress 789 24.3 Potential Role of Cellular Pathways in Oxidative Stress 790 24.4 Evidence for Oxidative Modification of LDL in the Human Artery Wall 793 24.5 Oxidative Modification of HDL 796 24.6 Oxidative Regulation of Matrix Metalloproteinases 798 24.7 Conclusions 804 25 Oxidative Stress and Protein Oxidation in Pre-Eclampsia 813 Maarten T. M. Raijmakers, Wilbert H. M. Peters, Christianne J. de Groot, and Eric A. P. Steegers 25.1 Introduction 813 25.2 Oxidative Stress and Pre-Eclampsia 814 25.3 Proteomics 820 26 Involvement of Oxidants in the Etiology of Chronic Airway Diseases: Proteomic Approaches to Identify Redox Processes in Epithelial Cell Signaling and Inflammation 831 Albert van der Vliet, Niki L. Reynaert, Peter F. Bove, Karina Ckless, Anne-Katrin Greul, Milena Hristova, and Yvonne M. Janssen-Heininger 26.1 Introduction 831 26.2 Chronic Airway Inflammation: Conditions Associated with Oxidative and Nitrosative Stress 832 26.3 Biological Significance of Protein Oxidation 836 26.4 Proteomic Approaches to Study Protein Oxidation in Airway Disease 847 26.5 Tissue Proteomics and Application to Study Protein Oxidation 857 26.6 Summary and Conclusions 861 27 Sequestering Agents of Intermediate Reactive Aldehydes as Inhibitors of Advanced Lipoxidation End-Products (ALEs) 877 Marina Carini, Giancarlo Aldini, and Roberto Maffei Facino 27.1 Introduction 877 27.2 Lipoxidation-Derived Reactive Aldehydes 880 27.3 Intervention against Lipoxidation-Derived Carbonyl Stress: ALE Inhibitors 893 27.4 Conclusions and Future Perspective 913 Index 931

About the Author :
ISABELLA DALLE-DONNE, PHD, is Assistant Professor in the Department of Biology at the University of Milan, Italy. She has a PhD in cellular and molecular biology from the University of Milan. ANDREA SCALONI, PHD, is First Investigator at the Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council in Naples, Italy. He received his PhD in chemical sciences from the University of Rome "La Sapienza" in Italy. D. ALLAN BUTTERFIELD, PHD, is Alumni Professor of Chemistry and Director of the University of Kentucky Center of Membrane Sciences in Lexington, Kentucky, USA. He received his PhD in physical chemistry from Duke University.

Review :
"...a major book...readers interested in mass spectrometry methods in proteomics will find much that is of interest here." (Journal of the American Society for Mass Spectrometry, March 2007) "Every laboratory that uses redox proteomics in both clinical and academic research should possess a copy of this excellent book." (Doody's Health Services) "…highly recommended as a reference text…Redox Proteomics is thought to be a milestone in this field…" (Biotechnology Journal, March 2007)