Nitric Oxide, Part F (eBook)

Cover 1
Contents 6
Contributors 16
Volumes in Series 22
Section 1: Molecular Methods 48
Chapter 1: Mass Spectrometric Characterization of Proteins Modified by Nitric Oxide-Derived Species 50
Abstract 50
1. Introduction 51
2. Reagents 53
3. Preparation of Nitrated BSA 53
4. In-Gel Protein Digestion and Mass Spectrometric Analysis 53
5. Data Analysis 54
6. MALDI-TOF Peptide Mass Fingerprinting 55
7. LC-ESI-IT Fragment Fingerprinting upon Collisional Fragmentation 56
8. Concluding Remarks 56
Acknowledgments 59
References 59
Chapter 2: Detecting Nitrated Proteins by Proteomic Technologies 64
Abstract 64
1. Introduction 65
2. Methods 67
3. Conclusions 77
Acknowledgments 77
References 77
Chapter 3: Using Tandem Mass Spectrometry to Quantify Site-Specific Chlorination and Nitration of Proteins: Model System Studies with High-Density Lipoprotein Oxidized by Myeloperoxidase 80
Abstract 81
1. Introduction 81
2. High-Density Lipoprotein Biology 83
3. Advantages of HDL as a Model System 83
4. Advantages of LC-ESI-MS/MS When Analyzing Posttranslational Modifications of Proteins 84
5. Isolating HDL, ApoA-I, and MPO 85
6. Oxidative Reactions 85
7. Proteolytic Digestion of Proteins 86
8. Liquid Chromatography-Electrospray Ionization Mass Spectrometry (LC-ESI-MS and MS/MS) 86
9. A Combination of Tryptic and Glu-C Digests Provides Complete Sequence Coverage of ApoA-I 87
10. HOCl or MPO Preferentially Chlorinates Tyrosine 192 in Lipid-Free ApoA-I 87
11. Reagent ONOO-and MPO Nitrate All the Tyrosine Residues in Lipid-Free ApoA-I, but Tyrosine 192 Is the Main Target 91
12. HOCl Quantitatively Converts All Three Methionine Residues in ApoA-I to Methionine Sulfoxide 95
13. HOCl Generates Hydroxytryptophan and Dihydroxytryptophan Residues in ApoA-I 100
14. Reactive Nitrogen Species Generates Nitrotryptophan Residues in Lipid-Free ApoA-I 104
15. The YXXK Motif Directs ApoA-I Chlorination 104
16. Quantitative Analysis of Posttranslational Modifications of Proteins 105
17. ApoA-I Oxidation Impairs Cholesterol Transport by the ABCA1 System 105
18. Conclusions 106
Acknowledgments 107
References 107
Chapter 4: Influence of Intramolecular Electron Transfer Mechanism in Biological Nitration, Nitrosation, and Oxidation of Redox-Sensitive Amino Acids 112
Abstract 113
1. Introduction 113
2. Methods 114
3. Results 117
Acknowledgments 137
References 137
Chapter 5: Protein Thiol Modification by Peroxynitrite Anion and Nitric Oxide Donors 142
Abstract 142
1. Introduction 143
2. Protein Cysteine Oxidation by ONOO- 144
3. Methodology to Detect Protein Thiol Modification 144
4. Iodoacetamide Labeling of Proteins after Oxidant Treatment 145
5. HPLC Separation of Fluorescein-Labeled Peptides 146
6. Detection of Interchain Disulfides by Western Blot 147
7. Repair of Protein Disulfides by Thioredoxin Reductase and Glutaredoxin Systems 148
8. Thioredoxin Reductase Repair of Protein Disulfides 149
9. Quantitation of Protein Disulfides by Measuring NADPH Oxidation 150
10. Quantitation of Total Cysteine Oxidation Using DTNB 150
11. Glutaredoxin/Glutathione (GSH) Reductase Repair of Protein Disulfides 151
12. Detection of Protein S-Glutathionylation 152
13. Thiol/disulfide Exchange with Oxidized Glutathione 152
14. Protein Thiol Modification by Nitric Oxide Donors 153
15. Conclusions 155
References 155
Chapter 6: Indirect Mechanisms of DNA Strand Scission by Peroxynitrite 158
Abstract 158
1. Introduction 159
2. Materials and Methods 159
3. Results and Discussion 163
Acknowledgments 166
References 166
Chapter 7: Nitric Oxide: Interaction with the Ammonia Monooxygenase and Regulation of Metabolic Activities in Ammonia Oxidizers 168
Abstract 168
1. Ammonia-Oxidizing Bacteria 169
2. Aerobic Ammonia Oxidation 169
3. Anaerobic Ammonia Oxidation with Nitrogen Dioxide as Oxidant Releases NO as Product 170
4. Aerobic Ammonia Oxidation with Nitrogen Dioxide as Oxidant 172
5. Regulation of Metabolic Activities in Ammonia Oxidizers 174
6. Nitric Oxide Induces Denitrification in N. europaea 175
7. Nitric Oxide Induces the Biofilm Formation of N. europaea 176
8. Nitric Oxide Is Required in N. europaea to Restore Ammonia Oxidation after Chemoorganotrophic Denitrification 179
References 180
Chapter 8: Chemiluminescent Detection of S-Nitrosated Proteins: Comparison of Tri-iodide, Copper/CO/Cysteine, and Modified Copper/Cysteine Methods 184
Abstract 184
1. Introduction 185
2. Methods for Detection of S-Nitrosothiols 186
3. Chemiluminescent-Based Detection of S-Nitrosothiols 187
4. Advantages and Disadvantages 193
5. Comparisons and Validations 194
6. Conclusions 198
References 200
Chapter 9: S-Nitrosothiol Assays That Avoid the Use of Iodine 204
Abstract 204
1. Introduction 205
2. S-Nitrosothiol Synthesis 205
3. S-Nitrosothiol Assays 207
4. S-Nitrosothiols in Health and Disease: The Importance of Getting the Assay Right 218
5. Summary 218
References 218
Chapter 10: Analysis of Citrulline, Arginine, and Methylarginines Using High-Performance Liquid Chromatography 224
Abstract 224
1. Introduction 225
2. The HPLC Apparatus 226
3. Chemicals and Materials 226
4. General Precautions in Sample Preparation and HPLC Analysis 227
5. Analysis of Citrulline and Arginine in Physiological Samples 228
6. Analysis of Methylarginines in Physiological Samples 232
7. Conclusion 235
Acknowledgments 235
References 235
Chapter 11: Quantitative Proteome Mapping of Nitrotyrosines 238
Abstract 238
1. Introduction 239
2. Multidimensional LC-MS/MS Provides Large Data Sets for Identification of Nitrotyrosine-Modified Proteins 240
3. Retention of Complexity in Samples Prepared from Global Proteomic Analysis 242
4. Confident Identification of Nitrotyrosine-Containing Peptides 244
5. Comparative Quantitation of Nitrotyrosine-Modified Peptide/Proteins 245
6. Summary 250
References 250
Section 2: Cellular Methods 254
Chapter 12: Protein S-Nitrosation in Signal Transduction: Assays for Specific Qualitative and Quantitative Analysis 256
Abstract 256
1. Introduction 257
2. Examples Demonstrating the Contribution of Protein S-Nitrosation to Intracellular Signal Transduction 257
3. Assays for Analysis of S-Nitrosation of Specific Cellular Proteins 261
4. Conclusions 264
Acknowledgments 265
References 265
Chapter 13: Determination of Mammalian Arginase Activity 268
Abstract 268
1. Introduction 269
2. Principle of Assay 269
3. Preparation of Cell and Tissue Extracts 270
4. Buffers, Reagents and Other Materials for Assay Protocol I 271
5. Assay Protocol I 272
6. Buffers, Reagents, and Other Materials for Assay Protocol II 273
7. Assay Protocol II 273
8. Limitations of Assay 274
9. Determination of Arginase Activity in Cultured Cells 275
Acknowledgments 276
References 276
Chapter 14: Measurement of Protein S-Nitrosylation during Cell Signaling 278
Abstract 278
1. Introduction 279
2. Biotin Switch Technique 280
3. Protocol for Analyzing Protein S-Nitrosylation in Tissue Samples Using the Biotin Switch Assay 282
4. Chemical Reduction/Chemiluminescence 283
5. Protocol for Chemical Reduction/Chemiluminescence Measurements of S-Nitrosylation of Immunoprecipitated Proteins 285
6. Conclusion 287
References 287
Chapter 15: Pivotal Role of Arachidonic Acid in the Regulation of Neuronal Nitric Oxide Synthase Activity and Inducible Nitric Oxide Synthase Expression in Activated Astrocytes 290
Abstract 290
1. Introduction 291
2. Materials and Methods 292
3. Results and Discussion 293
Acknowledgments 297
References 297
Chapter 16: Red Blood Cells as a Model to Differentiate between Direct and Indirect Oxidation Pathways of Peroxynitrite 300
Abstract 301
1. Introduction 301
2. Direct Reactions of Peroxynitrite with Biological Targets 302
3. Peroxynitrite Homolysis: Indirect Radical Chemistry 303
4. Red Blood Cells as an Experimental Model to Test the Fate of Peroxynitrite in a Biological Environment 304
5. Red Blood Cell Modifications Induced by Extracellular Peroxynitrite Decay 307
6. Red Blood Cell Modifications Induced by Intracellular Peroxynitrite Decay 307
7. Peroxynitrite-Dependent Phosphorylation Signaling of RBC 308
8. Peroxynitrite-Induced Biomarkers of RBC Senescence 309
9. Peroxynitrite-Induced Biomarkers of RBC Apoptosis 311
10. Methods 312
11. Data and Statistics 315
Acknowledgments 316
References 316
Chapter 17: Detection and Proteomic Identification of S-Nitrosated Proteins in Human Hepatocytes 320
Abstract 320
1. Introduction 321
2. Preparation of CSNO 323
3. Preparation of Primary Human Hepatocytes and Cell Culture 323
4. Treatment of Hepatocytes and Sample Preparation 324
5. Biotin Switch Assay 324
6. Detection and Purification of Biotinylated Proteins 325
7. Final Considerations 326
Acknowledgments 327
References 327
Chapter 18: Identification of S-Nitrosylated Proteins in Plants 330
Abstract 330
1. Introduction 330
2. Generation of Protein Nitrosothiols 332
3. Blocking Reaction of Free Thiols 334
4. Reduction of Nitrosothiols and S-Biotinylation 335
5. Affinity Purification of Biotinylated Proteins by NeutrAvidin 336
6. Modified Techniques Related to the Biotin Switch Assay 337
References 338
Chapter 19: Identification of 3-Nitrotyosine-Modified Brain Proteins by Redox Proteomics 342
Abstract 343
1. Introduction 343
2. Materials 344
3. Method 345
4. Comments 352
Acknowledgments 352
References 352
Chapter 20: Slot-Blot Analysis of 3-Nitrotyrosine-Modified Brain Proteins 356
Abstract 356
1. Introduction 356
2. Materials 358
3. Solutions 359
4. Sample Preparation for 3-NT Determination 359
5. Comments 360
Acknowledgments 361
References 361
Chapter 21: Detection Assays for Determination of Mitochondrial Nitric Oxide Synthase Activity Advantages and Limitations364
Abstract 364
1. Introduction 365
2. Colorimetric Nitric Oxide Synthase Assay 366
3. Determination of Mitochondrial Nitric Oxide Synthase Activity Using Radioassay 367
4. Spectrophotometric Determination of Mitochondrial Nitric Oxide Synthase Activity 369
5. Polarographic Nitric Oxide Synthase Assays 369
6. Chemiluminescence Assay 370
7. Fluorescent-Based Nitric Oxide Detection Assays 373
8. Conclusion 378
References 379
Section 3: Organism Methods 382
Chapter 22: Assay of 3-Nitrotyrosine in Tissues and Body Fluids by Liquid Chromatography with Tandem Mass Spectrometric Detection 384
Abstract 384
1. 3-Nitrotyrosine (3-NT) in Physiological Systems 385
2. Measurement of 3-NT 386
3. Liquid Chromatography with Tandem Mass Spectrometric Detection (LC-MS/MS) Assay of 3-NT Residues and 3-NT-Free Adducts: Thornalley Group Method 387
4. Estimates of 3-NT Residues and Free 3-NT in Plasma and Red Blood Cells under Basal Conditions and Effect of Disease 389
5. 3-Nitrotyrosine Residues in Lipoproteins 398
6. 3-Nitrotyrosine Residues and Free Adduct in Cerebrospinal Fluid 400
7. 3-Nitrotyrosine Residue Content of Tissues 400
8. Concluding Remarks 401
Acknowledgments 402
References 402
Chapter 23: Nitrite and Nitrate Measurement by Griess Reagent in Human Plasma: Evaluation of Interferences and Standardization 408
Abstract 408
1. Introduction 409
2. Experimental Procedures 411
3. Results 413
4. Discussion 420
Acknowledgments 425
References 425
Chapter 24: Detection of Nitric Oxide and Its Derivatives in Human Mixed Saliva and Acidified Saliva 428
Abstract 428
1. Introduction 429
2. Formation of Reactive Nitrogen Oxide Species (RNOS) in Mixed Whole Saliva and the Bacterial Fraction 429
3. Detection of RNOS in Mixed Whole Saliva and the Bacterial Fraction 431
4. Formation of RNOS in Acidified Saliva 437
5. Detection of RNOS in Acidified Saliva 439
6. Concluding Remarks 440
References 441
Chapter 25: Imaging of Reactive Oxygen Species and Nitric Oxide In Vivo in Plant Tissues 444
Abstract 444
1. Introduction 445
2. Imaging Reactive Oxygen Species and Nitric Oxide In Vivo by Confocal Laser Microscopy 446
3. Plant Tissue Preparation and Procedure 449
4. Conclusions 453
Acknowledgments 453
References 453
Chapter 26: Examining Nitroxyl in Biological Systems 458
Abstract 459
1. Introduction 459
2. Nitroxyl Donors 459
3. Biological HNO Chemistry 466
4. Use of HNO Donors in Biological Studies 470
5. Nitroxyl Pharmacological Effects: In Vivo and In Vitro Studies 471
6. Summary 473
References 474
Author Index 480
Subject Index 506