Elsevier S & T

Globins and Other Nitric Oxide-Reactive Proteins, Part B

Poole, Robert K.

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Table of contents
  • Contentsv
  • Contributorsxvii
  • Prefacexxvii
  • Volume in Seriesxxix
  • Section I. Nitric Oxide-Metabolising andDetoxifying Enzymes1
  • Chapter 1: Structural Studies on Flavodiiron Proteins3
  • 1. Introduction4
  • 2. Crystallization of Flavodiiron Proteins4
  • 3. Diffraction Data Collection, Structure Determination, and Refinement7
  • 4. Overall Description of Structures8
  • 5. Conclusion16
  • References17
  • Chapter 2: Biochemical, Spectroscopic, and Thermodynamic Properties of Flavodiiron Proteins21
  • 1. Introduction22
  • 2. Cloning of Genes Encoding Flavodiiron Proteins and Their Truncated Domains24
  • 3. Production and Purification of Recombinant Flavodiiron Proteins25
  • 4. Biochemical Characterization of Flavodiiron Proteins26
  • 5. Spectroscopic Properties29
  • 6. Redox Properties32
  • 7. Conclusions37
  • Acknowledments42
  • References42
  • Chapter 3: Kinetic Characterization of the Escherichia coli Nitric Oxide Reductase Flavorubredoxin47
  • 1. Introduction48
  • 2. Amperometric Measurements49
  • 3. Spectroscopic Measurements51
  • 4. Conclusions61
  • Acknowledments61
  • References61
  • Chapter 4: Escherichia coli Cytochrome c Nitrite Reductase NrfA63
  • 1. Introduction64
  • 2. Measurement of Cytochrome c Nitrite Reductase-Dependent Consumption of Nitric Oxide in Whole Cell66
  • 3. Growth of E. coli Optimized for Cytochrome c Nitrite Reductase Production for Use in Enzyme Purif66
  • 4. Purification of Cytochrome c Nitrite Reductase68
  • 5. Assaying the Cytochrome c Nitrite Reductase69
  • 6. Crystallization of E. coli Cytochrome c Nitrite Reductase73
  • 7. Concluding Remarks74
  • Acknowledments76
  • References76
  • Chapter 5: The Respiratory Nitric Oxide Reductase (NorBC) from Paracoccus denitrificans79
  • 1. Introduction80
  • 2. Purification of Native NorBC from Paracoccus denitrificans82
  • 3. Purification of Recombinant NorBC85
  • 4. Amperometric Assays of NO Consumption86
  • 5. Pseudoazurin as an Electron Donor in Assays of NorBC88
  • 6. Preparation of NOR for Spectroscopic Investigation91
  • 7. Electron Paramagnetic Resonance Spectroscopy96
  • 8. Concluding Remarks98
  • Acknowledments99
  • References99
  • Chapter 6: Redox-Controlled Dinitrosyl Formation at the Diiron-Oxo Center of NorA103
  • 1. Introduction104
  • 2. Genetic Context and Expression of the NorA Gene in R. eutropha105
  • 3. Purification of NorA106
  • 4. Disulfide Bridges in NorA107
  • 5. Iron Analysis and Preparation of Apo-NorA108
  • 6. Interconversion of Redox Forms of NorA109
  • 7. Generation of NorA-DNIC In Vitro111
  • 8. Preparation of NorA-DNIC Formed In Vivo113
  • 9. Quantification of NO from NorA-DNIC113
  • 10. Outlook114
  • References114
  • Chapter 7: Purification and Functional Analysis of Fungal Nitric Oxide Reductase Cytochrome P450nor117
  • 1. Introduction118
  • 2. Screening of P450nor Activity119
  • 3. Gas Analysis119
  • 4. Purification of P450nor120
  • 5. Nitric Oxide Reductase Activity Assay121
  • 6. Protein Sequencing122
  • 7. Isolation of cDNA123
  • 8. Subcellular Fractionation of T. cutaneum124
  • 9. Site-Directed Mutagenesis125
  • 10. Expression of Recombinant Proteins126
  • 11. Purification of Recombinant Proteins127
  • 12. Titration of NAD Analogs128
  • 13. Stopped-Flow Rapid Scan Analysis130
  • 14. Other Analysis131
  • 15. Conclusion131
  • Acknowledments131
  • References131
  • Chapter 8: A Quantitative Approach to Nitric Oxide Inhibition of Terminal Oxidases of the Respirator135
  • 1. Introduction136
  • 2. Evaluation of Current Techniques for Measuring pNO, pO2, and KM(O2)137
  • 3. Nitric Oxide Donor Compounds138
  • 4. Nitric Oxide Kinetics139
  • 5. Oxygen Kinetics149
  • 6. Optical Detection of Enzyme Intermediates in the Presence of Oxygen and NO151
  • Appendices153
  • Acknowledments156
  • References156
  • Section II. Sensor Proteins161
  • Chapter 9: Cloning, Expression, and Purification of the N-terminal Heme-Binding Domain of Globin-Cou163
  • 1. Introduction164
  • 2. Bioinformatic Search of Globin-Coupled Sensors164
  • 3. Functional Analysis of Globin-Coupled Sensors166
  • Acknowledments171
  • References171
  • Chapter 10: Oxygen-Sensing Histidine-Protein Kinases: Assays of Ligand Binding and Turnover of Respo173
  • 1. Introduction174
  • 2. Assays175
  • Acknowledments187
  • References187
  • Chapter 11: Reactions of Nitric Oxide and Oxygen with the Regulator of Fumarate and Nitrate Reductio191
  • 1. Introduction192
  • 2. Production of 4Fe-FNR Protein194
  • 3. Determination of Iron and Acid-Labile Sulfide Content of FNR197
  • 4. UV-Visible Absorbance Spectra of FNR198
  • 5. Cluster Reaction with Nitric Oxide and Oxygen198
  • 6. Purification of 2Fe-FNR204
  • 7. Detection of Other Reaction Products204
  • 8. Conclusions206
  • References207
  • Chapter 12: Genome-Wide Identification of Binding Sites for the Nitric Oxide-Sensitive Transcription211
  • 1. Introduction212
  • 2. Strain Construction214
  • 3. Reference and Control Samples216
  • 4. Culture Conditions217
  • 5. Immunoprecipitation of DNA Targets Associated with NsrR218
  • 6. DNA Labeling, Microarray Hybridization, and’Processing219
  • 7. Visualization and Analysis of DNA Microarray Data220
  • 8. A New Statistical Methodology for Treatment of ChIP-on-Chip Data222
  • 9. Conclusions231
  • Acknowledments231
  • References231
  • Chapter 13: Characterization of the Nitric Oxide-Reactive Transcriptional Activator NorR235
  • 1. Introduction236
  • 2. Measurement of NorR Activity In Vivo237
  • 3. Measurement of Transcriptional Activation by NorR In Vitro238
  • 4. Detection of the Ferrous-Nitrosyl Form of NorR by In Vivo Electron Paramagnetic Resonance (EPR)240
  • 5. In Vitro Reconstitution of the Iron Center in NorR242
  • 6. Measurement of NO Affinity243
  • 7. Standardization of the NO Electrode246
  • 8. Determination of NorRFe(NO) Kd247
  • 9. Conclusions248
  • Acknowledments248
  • References249
  • Section III. Advanced Spectroscopic Methods253
  • Chapter 14: Hemoglobins from Mycobacterium tuberculosis and Campylobacter jejuni: A Comparative Stud255
  • 1. Hemoglobin Superfamily: An Overview256
  • 2. Microbial Hemoglobins257
  • 3. Resonance Raman Spectroscopy: Applications in Hemeproteins258
  • 4. Structures and Functions of Microbial Hemoglobins266
  • 5. Closing Remarks281
  • Acknowledments282
  • References282
  • Chapter 15: The Power of Using Continuous-Wave and Pulsed Electron Paramagnetic Resonance Methods fo287
  • 1. Introduction288
  • 2. Electron Paramagnetic Resonance in a Nutshell289
  • 3. EPR Studies of NO-Ligated Globins295
  • 4. EPR Studies of Ferric Globins301
  • 5. Spin-Labeling Heme Proteins304
  • 6. Future Challenges and Possibilities305
  • Acknowledments305
  • References306
  • Chapter 16: Oxygen Binding to Heme Proteins in Solution, Encapsulated in Silica Gels, and in the Cry311
  • 1. Oxygen-Binding Curves to Heme Proteins313
  • 2. Determination of OBCs for Hemoglobin in Solution316
  • 3. Determination of K1 for Hemoglobin in Solution in the Absence of Allosteric Effectors318
  • 4. Determination of OBCs for T State Hemoglobin Gels in the Absence and Presence of Allosteric Effec318
  • 5. Determination of OBCs for T State Hemoglobin Crystals320
  • 6. Determination of OBCs for Hemocyanin in Solution and in Silica Gels323
  • Acknowledments325
  • References325
  • Chapter 17: Characterization of Ligand Migration Mechanisms inside Hemoglobins from the Analysis of329
  • 1. Introduction330
  • 2. Principles of Nanosecond Laser Flash Photolysis330
  • 3. Basic Experimental Layouts331
  • 4. Encapsulation of Hbs in Silica Gels335
  • 5. Enhancement of Geminate Rebinding and Advantages of Gel Encapsulation336
  • 6. Extraction of Kinetic Information337
  • Acknowledments342
  • References342
  • Chapter 18: Ligand Dynamics in Heme Proteins Observed by Fourier Transform Infrared Spectroscopy at347
  • 1. Introduction348
  • 2. Materials349
  • 3. Fourier Transform Infrared Cryospectroscopy353
  • 4. Low-Temperature FTIR Spectroscopy on NO-Ligated Heme Proteins365
  • 5. Concluding Remarks373
  • Acknowledments374
  • References374
  • Chapter 19: Time-Resolved X-Ray Crystallography of Heme Proteins379
  • 1. Introduction379
  • 2. Experiment381
  • 3. Data Processing and Analysis385
  • 4. A Case Study: Scapharca Dimeric Hemoglobin388
  • 5. Conclusions391
  • Acknowledments393
  • References393
  • Chapter 20: Structural Dynamics of Myoglobin397
  • 1. Background398
  • 2. Crystallographic Studies of Myoglobin States399
  • 3. Experimental Approaches400
  • Acknowledments413
  • References413
  • Chapter 21: Use of the Conjugate Peak Refinement Algorithm for Identification of Ligand-Binding Path417
  • 1. Introduction418
  • 2. Exploration of Oxygen-Binding Pathways in Myoglobin418
  • 3. Theoretical Models419
  • 4. Potential Energy Function420
  • 5. Transition Pathways421
  • 6. Methods425
  • 7. Results429
  • 8. Conclusions432
  • References433
  • Chapter 22: Finding Gas Migration Pathways in Proteins Using Implicit Ligand Sampling439
  • 1. Introduction440
  • 2. Methods442
  • 3. Example Calculation: Truncated Hemoglobin (trHb) from Paramecium caudatum446
  • 4. Discussion449
  • Acknowledments455
  • References456
  • Chapter 23: Identification of Ligand-Binding Pathways in Truncated Hemoglobins Using Locally Enhance459
  • 1. Introduction460
  • 2. Molecular Dynamics462
  • 3. Locally Enhanced Sampling Molecular Dynamics465
  • 4. Methods466
  • 5. Results468
  • 6. Conclusions471
  • References472
  • Chapter 24: Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation477
  • 1. Introduction478
  • 2. Molecular Dynamics (MD) Methods479
  • 3. Quantum Mechanical-Molecular Mechanical Methods485
  • 4. Illustrative Examples488
  • 5. Ligand Migration Profiles from MSMD and PELE Simulations: Exploring Ligand Entry Pathways in M. t490
  • 6. Conclusions494
  • Acknowledments495
  • References495
  • Chapter 25: Microbial Responses to Nitric Oxide and Nitrosative Stress: Growth, "Omic," and Physiolo499
  • 1. Introduction500
  • 2. Methods504
  • 3. Nitric Oxide, NO-R eleasing Agents, and Nitrosating Agents512
  • 4. Illustrative Results from Applications of These Methods514
  • References516
  • Chapter 26: Analysis of Nitric Oxide-Dependent Antimicrobial Actions in Macrophages and Mice521
  • 1. NO.-Dependent Antimicrobial Actions of Murine Macrophages522
  • 2. NO.-Dependent Antimicrobial Actions of Human Macrophages528
  • 3. NO.-Dependent Antimicrobial Actions in Laboratory Mice532
  • References536
  • Chapter 27: Measuring Nitric Oxide Metabolism in the Pathogen Neisseria meningitidis539
  • 1. Introduction540
  • 2. Safety Aspects of Handling N. meningitidis in the Laboratory541
  • 3. Metabolism of Neisseria sp.541
  • 4. Experimental Approaches to Analyzing Nitrogen Metabolism Relevant to NO544
  • 5. Simultaneous Measurement of Oxygen and NO during Pure Culture of N meningitidis547
  • 6. Measurement of NO Production/Disappearance in Tissue Culture Using Human Monocyte-Derived Macroph555
  • References558
  • Chapter 28: Localization of S-Nitrosothiols and Assay of Nitric Oxide Synthase and S-Nitrosoglutathi561
  • 1. Introduction562
  • 2. Determination of l-Arginine-Dependent NOS Activity by Ozone Chemiluminescence in Plant Tissues563
  • 3. Assay of GSNOR Activity566
  • 4. Localization of S-Nitrosothiols and S-Nitrosoglutathione in Plant Tissues by Confocal Laser-Scann567
  • 5. Conclusion571
  • Acknowledments572
  • References572
  • Chapter 29: Methods for Nitric Oxide Detection during Plant-Pathogen Interactions575
  • 1. Introduction576
  • 2. Nitric Oxide Detection by Mass Spectrometry577
  • 3. Nitric Oxide Detection by Laser Photoacoustic Spectroscopy579
  • 4. Nitric Oxide Detection by Chemiluminescence582
  • 5. Nitric Oxide Detection by Hemoglobin Conversion583
  • 6. Nitric Oxide Detection by Electron Paramagnetic Resonance (EPR) Spin Trap585
  • 7. Nitric Oxide Detection Using Diaminofluoresceins587
  • 8. Conclusion590
  • References591
  • Chapter 30: Bioimaging Techniques for Subcellular Localization of Plant Hemoglobins and Measurement595
  • 1. Introduction596
  • 2. Measuring Hemoglobin-Dependent NO Scavenging596
  • 3. Techniques for Determination of Subcellular Localization of Plant Hemoglobins597
  • 4. Imaging of Hemoglobin-Dependent NO Scavenging in Arabidopsis Plants598
  • 5. Engineering of GLB1-GFP/GLB2-GFP Constructs and Microscopic Analysis of A. thaliana Plants Expres600
  • References603
  • Chapter 31: Use of Recombinant Iron-Superoxide Dismutase as A Marker of Nitrative Stress605
  • 1. Introduction606
  • 2. Immunodetection of Nitrated Proteins: Metal-Mediated Tyrosine Nitration of BSA608
  • 3. Tyrosine Nitration of Purified Recombinant Vu_FeSOD Affects its Enzymatic Activity610
  • 4. Tyrosine Nitration in Vu_FeSOD can be Estimated Using Antibodies Against 3-Nitrotyrosine612
  • 5. SIN-1-Dependent Vu_FeSOD Nitration can be Detected by the Loss of Enzymatic Activity612
  • Acknowledments616
  • References616
  • Author Index619
  • Subject Index647
Book details
  • Vendor Elsevier S & T
  • SKU 9780123742780
  • ISBN-13 9780080877921
  • Author Poole, Robert K.
  • Category Science
  • Subject Biochemistry

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The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 400 volumes (all of them still in print), the series contains much material still relevant today—truly an essential publication for researchers in all fields of life sciences.


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This volume is the second of two planned volumes on the topic of globin and other nitric oxide-reactive proteins.