Smallest Biomolecules: Diatomics and their Interactions with Heme Proteins (eBook)

Front Cover 1
The Smallest Biomolecules 4
Copyright Page 5
Table of Contents 6
Preface 10
PART I INTRODUCTORY OVERVIEWS 12
Chapter 1. Mammalian Myoglobin as a Model for Understanding Ligand Affinities and Discrimination in Heme Proteins 14
1. INTRODUCTION 14
2. LIGAND CONFORMATION AND DISCRIMINATION 15
3. WATER OR ENDOGENOUS LIGAND DISPLACEMENT 16
4. LIGAND ENTRY IN THE DISTAL PORTION OF THE HEME CAVITY 17
5. IRON-LIGAND BOND FORMATION 17
6. ELECTROSTATIC STABILIZATION OF BOUND LIGANDS 18
7. FeC–O STRETCHING FREQUENCY, ELECTROSTATIC FIELDS, AND O2 DISSOCIATION RATE CONSTANTS 19
8. FORMALISM FOR INTERPRETING LIGAND BINDING CONSTANTS 20
9. REGULATION OF O2 AFFINITY AND LIGAND DISCRIMINATION IN SOYBEAN Lba 23
10. COMPARISONS BETWEEN ASCARIS SUUM HEMOGLOBIN DOMAIN 1 (AscHb) AND CEREBRATULUS LACTEUS MINI-HEMOGLOBIN (CerHb), TWO GLOBINS CONTAINING TyrB10 23
11. NO BINDING TO FERRIC AND FERROUS HEME PROTEINS 25
12. SUMMARY 25
ACKNOWLEDGMENTS 26
REFERENCES 26
Chapter 2. A Surfeit of Biological Heme-based Sensors 29
1. INTRODUCTION 29
2. WHAT CONSTITUTES A BIOLOGICAL HEME-BASED SENSOR? 31
3. FAMILIES OF HEME-BASED SENSORS 35
4. FUTURE DIRECTIONS 70
ACKNOWLEDGMENTS 70
REFERENCES 71
Chapter 3. NO and NOx Interactions with Hemes 77
ABBREVIATIONS 77
1. INTRODUCTION: REACTIONS OF NO AND NOX IN SOLUTIONS 78
2. THE FORMATION AND DISSOCIATION OF FERRIC AND FERROUS PORPHYRIN NITROSYL COMPLEXES 81
3. TRANSFORMATIONS OF COORDINATED NOX 86
4. REACTIONS OF NO AND NOX WITH HEME MODELS AND PROTEINS IN AQUEOUS MEDIA 91
5. SUMMARY 98
ACKNOWLEDGMENTS 98
REFERENCES 99
PART II ELECTRONIC STRUCTURE AND SPECTROSCOPY 104
Chapter 4. CO, NO, and O2 as Vibrational Probes of Heme Protein Active Sites 106
ABBREVIATIONS 106
1. INTRODUCTION 107
2. FeCO VIBRATIONS 109
3. Fe(II)NO VIBRATIONS 120
4. Fe(III)NO VIBRATIONS 126
5. Fe(II)O2 VIBRATIONS 128
ACKNOWLEDGMENT 130
REFERENCES 130
Chapter 5. Nuclear Resonance Vibrational Spectroscopy — NRVS 135
ABBREVIATIONS 135
1. INTRODUCTION 135
2. EXPERIMENTAL METHODOLOGY 137
3. APPLICATIONS 144
SUMMARY 155
ACKNOWLEDGMENTS 155
REFERENCES 155
Chapter 6. EPR and Low-temperature MCD Spectroscopy of Ferrous Heme Nitrosyls 158
1. INTRODUCTION 158
2. GENERAL CONSIDERATIONS 160
3. EPR SPECTRA OF FIVE- AND SIX-COORDINATE Fe(II)–PORPHYRIN NO ADDUCTS 162
4. MCD SPECTROSCOPY ON FERROUS HEME NITROSYLS 172
5. CONCLUSIONS 179
ACKNOWLEDGMENT 179
REFERENCES 179
PART III ASPECTS OF HEMOGLOBINS (EXCEPT HEME—NOx INTERACTIONS) 184
Chapter 7. Protoglobin and Globin-coupled Sensors 186
1. BACKGROUND ON THE GLOBINS 186
2. HISTORY OF THE GLOBIN-COUPLED SENSORS AND THE PROTOGLOBIN 187
3. GCS FUNCTIONAL CLASSIFICATION 187
4. BIOPHYSICAL AND KINETIC CHARACTERISTICS 201
5. MECHANISM OF SIGNALING 203
6. GCS DIVERSITY AND EVOLUTION 205
7. PROTOGLOBINS IN THE ARCHAEA 207
8. ANCIENT OXYGEN SIGNALING AND THE FUTURE 210
ACKNOWLEDGMENTS 211
REFERENCES 211
Chapter 8. Neuroglobin and Cytoglobin 214
1. GLOBINS: THE ANCIENT PROTEIN SUPERFAMILY CONTAINS TWO NOVICES 214
2. NEUROGLOBIN: THE DISTANTLY RELATED COUSIN “ON OUR NERVES” 216
3. CYTOGLOBIN: MUSCLE MYOGLOBIN’S BROTHER IN FIBROBLASTS AND NEURONS 221
4. TWO GLOBINS IN SEARCH OF THEIR ROLES IN THE FAMILY (AND IN THE CELL) 223
ACKNOWLEDGMENTS 227
REFERENCES 227
Chapter 9. Extreme pH Sensitivity in the Binding of Oxygen to Some Fish Hemoglobins: The Root Effect 230
1. BACKGROUND 231
2. QUANTITATIVE ANALYSIS OF OXYGEN BINDING 231
3. THE ROOT EFFECT HEMOGLOBINS 237
4. EVOLUTION AND PHYSIOLOGICAL ROLE OF ROOT EFFECT HEMOGLOBINS 237
5. MECHANISTIC ORIGINS OF THE ROOT EFFECT 238
6. STRUCTURAL INTERPRETATIONS OF THE ORIGINS OF THE ROOT EFFECT 239
7. CONCLUSIONS 243
REFERENCES 243
Chapter 10. Microbial Hemoglobins: Structure, Function, and Folding 246
ABBREVIATIONS 246
1. HEMOGLOBIN SUPER FAMILY: AN OVERVIEW 246
2. MICROBIAL HEMOGLOBINS 248
3. STRUCTURES AND FUNCTIONS OF MICROBIAL HEMOGLOBINS 249
4. FOLDING STABILITIES OF MICROBIAL Hbs 268
5. CLOSING REMARKS 270
ACKNOWLEDGMENT 272
REFERENCES 272
PART IV HEME—NOx INTERACTIONS 278
Chapter 11. The Reaction between Nitrite and Hemoglobin: The Role of Nitrite in Hemoglobin-mediated Hypoxic Vasodilation 280
1. INTRODUCTION 280
2. THE CHEMISTRY OF THE NITRITE/HEMOGLOBIN REACTION 280
3. PHYSIOLOGICAL CONSEQUENCES OF THE NITRITE/HEMOGLOBIN REACTION 293
4. SUMMARY AND CONCLUSIONS 297
ACKNOWLEDGMENTS 298
REFERENCES 299
Chapter 12. Nitric Oxide Dioxygenase: An Ancient Enzymic Function of Hemoglobin 301
1. Hb FUNCTIONS 301
2. ROLE FOR Hbs AS NO-METABOLIZING ENZYMES 304
3. Hb STRUCTURE AND THE NOD MECHANISM 311
4. EVOLUTION OF Hb FUNCTION 324
5. INHIBITORS AND APPLICATIONS OF THE NOD REACTION 325
6. OTHER ENZYMIC FUNCTIONS FOR (FLAVO)Hbs AND Mbs? 328
7. CONCLUSIONS AND PROSPECTIVE 329
ACKNOWLEDGMENTS 330
REFERENCES 330
Chapter 13. Respiratory Nitric Oxide Reductases, NorB and NorZ, of the Heme–Copper Oxidase Type 338
1. INTRODUCTION 338
2. GENETIC ORGANIZATION AND FUNCTIONAL PROPERTIES OF nor GENE PRODUCTS 339
3. RESPIRATORY NITRIC OXIDE REDUCTASES ARE MEMBERS OF THE HEME–COPPER OXIDASE SUPERFAMILY 342
4. SHORT-CHAIN RESPIRATORY NITRIC OXIDE REDUCTASE, NorB, IS A COMPLEX WITH CYTOCHROME c 346
5. THE ACTIVE SITE 348
6. LONG-CHAIN RESPIRATORY NITRIC OXIDE REDUCTASE, NorZ, IS ALSO A QUINOL OXIDASE 354
7. STRUCTURAL AND FUNCTIONAL VARIATIONS AMONG RESPIRATORY NITRIC OXIDE REDUCTASES 355
8. NITRIC OXIDE SIGNALING AND nor GENE REGULATION 356
9. CONCLUSIONS 360
ACKNOWLEDGMENTS 360
REFERENCES 360
Chapter 14. Nitric Oxide Reductase (P450nor) from Fusarium oxysporum 365
1. INTRODUCTION 365
2. ISOLATION OF P450NOR AND MOLECULAR PROPERTIES 366
3. GENE STRUCTURE OF P450NOR 369
4. MECHANISTIC STUDIES 370
5. REACTIONS WITH PEROXYNITRITE 374
6. CRYSTALLOGRAPHY, X-RAY STRUCTURE, AND ENZYMOLOGY 377
7. IMPLICATIONS AND OUTLOOK 381
8. LATEST RESULTS ON THE MOLECULAR MECHANISM OF P450NOR BASED ON COMPUTATIONAL CALCULATIONS 383
ACKNOWLEDGMENTS 385
REFERENCES 385
Chapter 15. Nitric Oxide Interaction with Insect Nitrophorins and Possibilities for the Electron Configuration of the {FeNO}6 Complex 389
1. BACKGROUND 390
2. STRATEGIES USED BY BLOOD-SUCKING INSECTS TO INSURE THAT THEY OBTAIN A SUFFICIENT MEAL 391
3. PROTEIN SEQUENCES AND STRUCTURES OF THE NITROPHORINS FROM R. prolixus. 394
4. THE SPECIAL PROPERTIES OF NP7 398
5. NMR SPECTROSCOPIC STUDIES OF THE NITROPHORINS 400
6. SOURCE OF NO IN THE INSECT SALIVA: A SALIVARY GLAND NO SYNTHASE FROM R. prolixus 407
7. A NITROPHORIN FROM ANOTHER INSECT: STRUCTURE, SPECTROSCOPIC AND REDOX PROPERTIES OF cNP 408
8. NITRIC OXIDE REACTIVITY WITH HEME CENTERS 414
9. REDOX CHEMISTRY OF NO-HEME SYSTEMS INCLUDING THE NITROPHORINS OF R. prolixus 415
10. POSSIBLE ROLE OF HEME RUFFLING IN STABILIZING THE {FENO}6 CENTER OF THE NITROPHORIN–NO COMPLEXES 423
ACKNOWLEDGEMENTS 431
REFERENCES 431
Chapter 16. Bioinorganic Chemistry of the HNO Ligand 440
ABBREVIATIONS 440
1. NO AND HNO 441
2. PRODUCTION AND DETECTION OF HNO 442
3. NITROXYL REVISITED 442
4. PHYSIOLOGICAL EFFECTS OF FREE NITROXYL 444
5. THE ENEMAR/FELTHAM BONDING EXTREME 446
6. BIOLOGICAL ROLES OF NITROXYL INTERMEDIATES 447
7. NITRITE REDUCTASES 447
8. NITRIC OXIDE REDUCTASES 449
9. ELECTROCHEMICAL INVESTIGATIONS 451
10. NITROXYL ADDUCTS OF HEME PROTEINS 455
11. BONDING PARAMETERS IN Mb—HNO 459
12. NON-HEME NITROXYL COMPLEXES 462
13. SURVEY OF REACTIVITY 467
CONCLUSIONS 469
REFERENCES 469
PART V SELECTED ENZYMES AND SENSORS 474
Chapter 17. Ligand-Protein Interactions in Mammalian Nitric Oxide Synthase 476
ABBREVIATIONS 476
1. INTRODUCTION 477
2. SPECTROSCOPIC PROPERTIES OF NOS 480
3. CARBON MONOXIDE AS A PROBE OF THE CATALYTIC SITE 481
4. THE NITRIC OXIDE-BOUND COMPLEXES 486
5. THE EFFECT OF NO ON THE MONOMER/DIMER EQUILIBRIUM 492
6. OVERVIEW OF NO INTERACTIONS 504
7. CONCLUSIONS 505
ACKNOWLEDGMENTS 506
REFERENCES 506
Chapter 18. CooA: A Paradigm for Gas-sensing Regulatory Proteins 509
ABBREVIATIONS 509
1. INTRODUCTION 509
2. OVERVIEW OF THE SENSING MECHANISMS OF R. rubrum CooA 511
3. COMPARISON OF R. rubrum CooA STRUCTURE AND EFFECTOR RESPONSE TO THOSE OF CRP 514
4. HYPOTHESIS FOR ACTIVATION OF CooA BY CO 518
5. BASIS FOR THE SPECIFICITY FOR CO IN CooA ACTIVATION 528
6. COOPERATIVITY OF CO BINDING 530
7. SUMMARY AND FUTURE DIRECTIONS 531
ACKNOWLEDGMENTS 532
REFERENCES 532
Chapter 19. Soluble Guanylyl Cyclase and Its Evolutionary Relatives 535
1. INTRODUCTION 535
2. BIOINFORMATIC ANALYSIS OF sGC FAMILY AND GENEALOGY 536
3. MEASUREMENT OF sGC ACTIVITY AND REGULATION 540
4. STRUCTURAL HIGHLIGHTS 541
5. OXYGEN BINDING TO Tt-HNOX 544
6. REGULATION BY NO, CO, AND OTHER REGULATORY COMPOUNDS 545
7. OXYGEN-SENSING sGC PROTEINS? 546
8. FUTURE DIRECTIONS 548
ACKNOWLEDGMENTS 548
REFERENCES 548
Chapter 20. Resonance Raman Studies of the Activation Mechanism of Soluble Guanylate Cyclase 551
1. INTRODUCTION 551
2. STRUCTURAL CHARACTERISTICS OF sGC 553
3. ACTIVATORS OF sGC 555
4. SPECTROSCOPIC CHARACTERIZATION OF sGC 557
5. EFFECTS OF SUBSTRATE AND ANALOGUES 567
6. CHANGES IN HEME VIBRATIONS 568
7. MECHANISM OF ACTIVATION 568
8. PROSPECTS 571
REFERENCES 572
Chapter 21. Insights into Heme-based O2 Sensing from Structure–Function Relationships in the FixL Proteins 575
ABBREVIATIONS 576
1. INTRODUCTION 577
2. FixL PROTEINS 578
3. EARLY PHYSICAL CHARACTERIZATION OF FixLs AND THEIR HEME LIGAND COMPLEXES 580
4. STRUCTURAL STUDIES 585
5. NON-EQUILIBRIUM, LIGAND-COUPLED DYNAMICS AS A PROBE OF SIGNAL TRANSDUCTION 591
6. ROLE OF FixL ASSOCIATION 597
7. SITE-DIRECTED MUTAGENESIS STUDIES 598
8. PERSPECTIVES 604
REFERENCES 605
Index 608
Color Plates 616