Redox Proteomics

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.

"...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)

• Preface xxiiiContributors xxviiPart I Oxidatively Modified Proteins and Proteomic Technologies 11 Chemical Modification of Proteins by Reactive Oxygen Species 3Earl R. Stadtman and Rodney L. Levine1.1 Introduction 31.2 Peptide Bond Cleavage 51.3 β-Scission 61.4 Oxidation of Amino Acid Residue Side Chains 72 The Chemistry of Protein Modifications Elicited by Nitric Oxide and Related Nitrogen Oxides 25Douglas D. Thomas, Lisa Ridnour, Sonia Donzelli, Michael Graham Espey, Daniele Mancardi, Jeffery S. Isenberg, Martin Feelisch, David D. Roberts, and David A. Wink2.1 Introduction 252.2 Chemical Biology of NO 262.3 Chemistry of Metabolite Formation 403 Mass Spectrometry Approaches for the Molecular Characterization of Oxidatively/Nitrosatively Modified Proteins 59Andrea Scaloni3.1 Introduction 593.2 Mass Spectrometry Analysis of Oxidatively/Nitrosatively Modified Proteins 613.3 Proteomic Strategies for the Identification of ROS/RNS Protein Targets in Biological Matrices 763.4 Conclusions 844 Thiol-Disulfide Oxidoreduction of Protein Cysteines: Old Methods Revisited for Proteomics 101Valentina Bonetto and Pietro Ghezzi4.1 Introduction: Protein Thiols from Oxidative Stress to Redox Regulation 1014.2 Different Redox States of Protein Cysteines 1024.3 Methodologies to Identify and Quantify the Redox State of Protein Cysteines 1044.4 Methods to Detect Specific Modifications 1084.5 Methods for Enriching Redox-Regulated Proteins 1114.6 Structural and Physicochemical Determinants for the Susceptibility of Cysteines toward Oxidation 1124.7 Perspective 1145 Carbonylated Proteins and Their Implication in Physiology and Pathology 123Rodney L. Levine and Earl. R. Stadtman5.1 Introduction 1235.2 Types of Oxidative Modifications and Choice of Marker 1335.3 Methodological Considerations 1345.4 Selected Studies 1365.5 Carbonylation during Aging 1366 S-Nitrosation of Cysteine Thiols as a Redox Signal 169Yanhong Zhang and Neil Hogg6.1 Introduction 1696.2 Mechanisms of Formation of S-Nitrosothiols 1706.3 Cellular Transduction of the S-Nitroso Group 1766.4 S-Nitrosothiols and Redox Proteomics 1786.5 S-Nitrosothiols as an Intracellular Signal 1796.6 Conclusions 1827 Detection of Glycated and Glyco-Oxidated Proteins 189Annunziata Lapolla, Elisa Basso, and Pietro Traldi7.1 Introduction 1897.2 MALDI-MS in the Study of In vitro Glycated Proteins 1967.3 MALDI-MS in the Evaluation of Glycation Levels of HSA and IgG in Diabetic Patients 2017.4 HbA1c and the Real Globin Glycation and Glyco-Oxidation 2057.5 Determination of Dicarbonyl Compound Levels in Diabetic and Nephropathic Patients 2097.6 AGE/Peptides: An In vitro Study and In vivo Preliminary Results 2127.7 Expected Future Trends 2268 MudPIT (Multidimensional Protein Identification Technology) for Identification of Post-translational Protein Modifications in Complex Biological Mixtures 233Stefani N. Thomas, Bing-Wen Lu, Tatiana Nikolskaya, Yuri Nikolsky, and Austin J. Yang8.1 Introduction 2338.2 Proteomic Analysis of Oxidatively Modified Proteins 2348.3 Statistical Validation and Interpretation of MudPIT Data 2418.4 Concluding Remarks 2499 Use of a Proteomic Technique to Identify Oxidant-Sensitive Thiol Proteins in Cultured Cells 253Mark B. Hampton, James W. Baty, and Christine C. Winterbourn9.1 Introduction 2539.2 Fluorescence Labeling and Proteomic Analysis of Oxidized Thiol Proteins 2549.3 Detection of Thiol Protein Oxidation in Jurkat Cells 2569.4 Detection of Reversible and Irreversible Thiol Oxidation 2589.5 Oxidized Thiol Compared with Reduced Thiol Measurements 2599.6 More Selective Thiol Labeling Protocols 2609.7 Identification of Oxidant-Sensitive Proteins 2619.8 Conclusions and Future Directions 26110 ICAT (Isotope-Coded Affinity Tag) Approach to Redox Proteomics: Identification and Quantification of Oxidant-Sensitive Protein Thiols 267Mahadevan Sethuraman, Mark E. McComb, Hua Huang, Sequin Huang, Tyler Heibeck, Catherine E. Costello, and Richard A. Cohen10.1 Introduction 26710.2 Oxidant-Sensitive Cys 26810.3 Challenges in Redox Proteomics 26810.4 Iodoacetamide-Based Redox Proteomics 26910.5 ICAT Approach to Redox Proteomics 27110.6 Validation of the ICAT Approach Using the Recombinant Protein Creatine Kinase 27110.7 ICAT Approach to the Complex Protein Mixtures 27510.8 Perspectives 28211 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 287Dimitrios Tsikas11.1 Introduction 28711.2 Methods of Analysis 295  11.3 S-Nitrosothiols and 3-Nitrotyrosine in Health and Disease 31411.4 Considerations from the Analytical and Review Points of View 32611.5 Concluding Remarks and Future Prospects 329Part II Cellular Aspects of Protein Oxidation 34312 The Covalent Advantage: A New Paradigm for Cell Signaling Mediated by Thiol Reactive Lipid Oxidation Products 345Dale A. Dickinson, Victor M. Darley-Usmar, and Aimee Landar12.1 Introduction 34512.2 Cyclooxygenase and the Conversion of Nonreactive Lipids to Thiol Switching Molecules 34612.3 Lipid Peroxidation and the Nonenzymatic Formation of Lipid Adducts Capable of Modifying Proteins 34912.4 The Thiol Switch and Redox Cell Signaling 35112.5 Biological Responses to Endogenous Electrophilic Lipid Production 35312.6 A New Paradigm of Oxidized Lipid Signaling—The Covalent Advantage 35312.7 Implications for the Pathophysiology of Disease 35612.8 Summary 35813 Early Molecular Events during Response to Oxidative Stress in Human Cells by Differential Proteomics 369Gianluca Tell13.1 Introduction 36913.2 Cellular Response to Oxidative Stress: From Membrane Receptors to Gene Expression Control 37413.3 Gene Expression Control during Cell Response to Oxidative Stress: Redox-Regulated Transcription Factors 38213.4 The Power of Differential Proteomics in Detecting Early Molecular Markers of Oxidative Stress: Examples from Human Cell Lines 38313.5 Conclusions 38814 Oxidative Damage to Proteins: Structural Modifications and Consequences in Cell Function 399Elisa Cabiscol and Joaquim Ros14.1 Introduction 39914.2 Glycolysis 40014.3 Pyruvate Metabolism 42614.4 Tricarboxylic Acid Cycle 43214.5 Electron Transport Chain and Oxidative Phosphorylation 43714.6 Antioxidant Defenses 44314.7 Molecular Chaperones 44714.8 Cytoskeleton 45114.9 Conclusions 45415 Oxidative Damage and Cellular Senescence: Lessons from Bacteria and Yeast 473Thomas Nyström15.1 Microbial Senescence 47315.2 Protein Carbonylation—An Irreversible Oxidative Damage to Proteins 47415.3 Bacterial Senescence and Protein Carbonylation 47615.4 Replicative Senescence and Segregation of Carbonylated Proteins 47815.5 Yeast Senescence, Protein Oxidation, and Oncogenesis 47915.6 Perspective 479Part III Redox Proteomic Analysis in Human Diseases 48516 Proteins as Sensitive Biomarkers of Human Conditions Associated with Oxidative Stress 487Isabella Dalle-Donne, Ranieri Rossi, Fabrizio Ceciliani, Daniela Giustarini, Roberto Colombo, and Aldo Milzani16.1 Introduction 48716.2 Oxidative Stress in Human Diseases and Animal Models 48916.3 Biomarkers of Oxidative Stress Status (BOSS) 49316.4 Proteins as Biomarkers of Oxidative Stress Status 50416.5 Conclusions 51217 Degradation and Accumulation of Oxidized Proteins in Age-Related Diseases 527Peter Voss and Tilman Grune17.1 Oxidative Modifications of Amino Acids and Protein Damage 52717.2 Degradation and Accumulation of Oxidatively Modified Proteins 53217.3 Oxidized Proteins in Age-Related Diseases 54317.4 Summary 54718 Redox Proteomics: A New Approach to Investigate Oxidative Stress in Alzheimer’s Disease 563D. Allan Butterfield, Rukhsana Sultana, and H. Fai Poon18.1 Introduction 56318.2 Brain Tissue and Models Used in Studying Aβ(1–42)-Induced Oxidative Stress and Neurotoxicity in AD 56518.3 Redox Proteomics 56718.4 Oxidatively Modified Proteins in AD and AD Models by Redox Proteomics 57218.5 Conclusion 58519 Oxidized Proteins in Cardiac Ischemia and Reperfusion 605Jonathan P. Brennan and Philip Eaton19.1 Introduction to Cardiac Ischemia and Reperfusion 60519.2 Oxidatively Modified Proteins in the Heart 61619.3 Established Targets of Post-translational Oxidation 62419.4 Oxidative Stress in Myocardial Adaptation to Ischemia and Reperfusion 62819.5 Conclusions, Therapeutic Implications, and Future Directions 63120 Proteome Analysis of Oxidative Stress: Glutathionyl Hemoglobin in Diabetic and Uremic Patients 651Toshimitsu Niwa20.1 Introduction 65120.2 Glutathionyl Hb as a Marker of Oxidative Stress 65320.3 Conclusion 66321 Glyco-oxidative Biochemistry in Diabetic Renal Injury 669Toshio Miyata21.1 Presence of Local, but not Generalized, Oxidative Stress in Diabetes 66921.2 Oxidative Protein Damage In vivo 67021.3 Antioxidative Properties of Medical Agents 67121.4 Therapeutic Perspectives for AGE Inhibitors 67221.5 AGE Inhibition and Renoprotection 67321.6 Future Prospects 67622 Quantitative Screening of Protein Glycation, Oxidation, and Nitration Adducts by LC-MS/MS: Protein Damage in Diabetes, Uremia, Cirrhosis, and Alzheimer’s Disease 681Paul J. Thornalley22.1 Introduction: Derivatization Free Detection with Application to Modified Proteins and Amino Acids 68122.2 Physiological Sources of Glycated, Oxidized, and Nitrated Amino Acid Residues and Free Adducts 68922.3 Protein Glycation and Oxidation in Diabetes: Damage to Cellular and Extracellular Proteins 69422.4 Profound Mishandling of Glycated, Oxidized, and Nitrated Amino Acids in Uremia 70222.5 Increased Glycated and Oxidized Amino Acids of Blood Plasma in Liver Cirrhosis—A Signature of Hepatic Oxidative Stress 70422.6 Increased Methylglyoxal-Derived Hydroimidazolone and 3-Nitrotyrosine Free Adducts in Cerebrospinal Fluid of Subjects with Alzheimer’s Disease—A Signature of Neuronal Damage 70722.7 Glycation Adducts in Food and Beverages 71022.8 Concluding Remarks: Physiological Formation and Proteolytic Processing of Glycated, Oxidized, and Nitrated Proteins in Disease Processes—The Importance of Measuring “Damage and Debris” 71423 Protein Targets and Functional Consequences of Tyrosine Nitration in Vascular Disease 729Laura M. S. Baker, Bruce A. Freeman, and Mutay Aslan23.1 Association of Vascular Disease with Increased Production of Reactive Oxygen/Nitrogen Species and Accumulation of Nitrated Proteins 72923.2 Production of Reactive Oxygen and Nitrogen Species in the Vasculature 73123.3 Tyrosine Nitration Mechanisms 73423.4 Methods for Detecting Nitrotyrosine 74223.5 Selectivity of Tyrosine Nitration 74523.6 Mechanistic Consequences of Nitrotyrosine Formation: Protein Nitration In vivo and Vascular Disease 74723.7 Metabolism, Reversibility, and Stability of the Nitrated Tyrosine 76423.8 Tyrosine Nitration as a Cell Signaling Event 76723.9 Summary 76924 Oxidation of Artery Wall Proteins by Myeloperoxidase: A Proteomics Approach 787Tomas Vaisar and Jay W. Heinecke24.1 Oxidative Stress in Atherosclerosis 78724.2 Potential Role of Redox-Active Metal Ions and Glucose in Oxidative Stress 78924.3 Potential Role of Cellular Pathways in Oxidative Stress 79024.4 Evidence for Oxidative Modification of LDL in the Human Artery Wall 79324.5 Oxidative Modification of HDL 79624.6 Oxidative Regulation of Matrix Metalloproteinases 79824.7 Conclusions 80425 Oxidative Stress and Protein Oxidation in Pre-Eclampsia 813Maarten T. M. Raijmakers, Wilbert H. M. Peters, Christianne J. de Groot, and Eric A. P. Steegers25.1 Introduction 81325.2 Oxidative Stress and Pre-Eclampsia 81425.3 Proteomics 82026 Involvement of Oxidants in the Etiology of Chronic Airway Diseases: Proteomic Approaches to Identify Redox Processes in Epithelial Cell Signaling and Inflammation 831Albert van der Vliet, Niki L. Reynaert, Peter F. Bove, Karina Ckless, Anne-Katrin Greul, Milena Hristova, and Yvonne M. Janssen-Heininger26.1 Introduction 83126.2 Chronic Airway Inflammation: Conditions Associated with Oxidative and Nitrosative Stress 83226.3 Biological Significance of Protein Oxidation 83626.4 Proteomic Approaches to Study Protein Oxidation in Airway Disease 84726.5 Tissue Proteomics and Application to Study Protein Oxidation 85726.6 Summary and Conclusions 86127 Sequestering Agents of Intermediate Reactive Aldehydes as Inhibitors of Advanced Lipoxidation End-Products (ALEs) 877Marina Carini, Giancarlo Aldini, and Roberto Maffei Facino27.1 Introduction 87727.2 Lipoxidation-Derived Reactive Aldehydes 88027.3 Intervention against Lipoxidation-Derived Carbonyl Stress: ALE Inhibitors 89327.4 Conclusions and Future Perspective 913Index 931