Globins and Other Nitric Oxide-Reactive Proteins

Contributors to Volume 436......Page 1
Preface......Page 9
Volume in Series......Page 11
Chemistry of Nitric Oxide and Related Species......Page 37
Introduction......Page 38
Properties of the NO molecule......Page 39
Reaction of NO with oxygen......Page 41
Nitroxyl HNO......Page 42
Nitrous Acid, Nitrosation, and S-Nitrosothiols......Page 45
Reactions of Peroxynitrite, ONOO-......Page 46
Nitrogen Dioxide......Page 47
NO Complexes with Metal Centers......Page 48
Mobilization of Metal Ions from Biological Sites by NO......Page 49
References......Page 50
Introduction......Page 54
The bullNO Dioxygenase Mechanism......Page 55
Stopped-Flow Analysis of NO Ferrous Cytochrome cprime Formation......Page 61
References......Page 65
The Preparation and Purification of NO Gas and the Use of NO Releasers: The Application of NO Donors and Other Agents of Nitrosative Stress in Biological Systems......Page 67
Introduction......Page 68
NO from cylinders and lecture bottles......Page 69
Generation of NO in the laboratory......Page 70
Determination of NO concentration......Page 71
S-nitrosothiols......Page 72
NOR, NOC, and NONOate compounds......Page 73
Cellular fate of NO2 and the level of nitrosative stress......Page 76
Microbes and nitrosative stress......Page 77
References......Page 578
The Chemistry of Peroxynitrite: Implications for Biological Activity......Page 81
Introduction......Page 82
Mechanism of Peroxynitrite Decomposition in Aqueous Solutions......Page 83
Susceptibility of the bullNO Dioxygenase to bullNO Inhibition......Page 246
The Radical Model In Vivo......Page 86
Nitration of Tyrosine......Page 87
Structural Background......Page 89
References......Page 308
Nitric Oxide Selective Electrodes......Page 94
Methods of NO Measurement in Physiology......Page 95
Principles of Determination of NO by Electrochemical Sensors......Page 96
Fabrication of Electrodes for NO Determination......Page 97
Calibration of NO Electrodes......Page 102
Characterization of NO Electrodes......Page 105
Selected Applications of NO Electrodes......Page 109
References......Page 119
NO, N2O, and O2 Reaction Kinetics: Scope and Limitations of the Clark Electrode......Page 127
Introduction......Page 128
Materials......Page 129
Measurement of NO Scavenging Activity......Page 403
Discussion......Page 239
AHb: Structural and biochemical properties......Page 173
Determination of NO reduction activity of Nor......Page 133
Determination of N2O reduction activity of N2OR......Page 136
O2 measurements......Page 137
Scope and Limitations of the Clark Electrode......Page 139
Acknowledgments......Page 140
Chemiluminescence Quantification of NO and Its Derivatives in Liquid Samples......Page 143
The myriad roles of NO......Page 144
The NO-ozone reaction and the chemiluminescence analyzer......Page 145
Procedures......Page 147
Reagents preparation......Page 149
Procedure......Page 150
Procedure......Page 151
Procedure......Page 152
Procedure......Page 153
Measurement of nitrate/nitrite in cell supernatants......Page 154
Final Remarks......Page 155
References......Page 156
Interactions of NO with Hemoglobin: From Microbes to Man......Page 158
Introduction......Page 159
Microbes, Plants, and Invertebrates......Page 160
FHbs......Page 161
NO reductase mechanism (denitrosylase)......Page 162
Monomeric Hbs......Page 163
Truncated Hbs......Page 165
FHbs......Page 166
Lbs......Page 167
nsHbs......Page 169
Cysteine-mediated dioxygenase mechanism (NO-dependent deoxygenase)......Page 174
Tetrameric hemoglobins......Page 176
Tetrameric Hb: Structural and biochemical properties......Page 177
Tetrameric Hb: Physiological role and biochemical mechanisms......Page 180
Tetrameric Hb micropopulations......Page 181
Tetrameric Hb oxidation and Hb-SNO formation......Page 183
Conclusions......Page 184
References......Page 186
A Survey of Methods for the Purification of Microbial Flavohemoglobins......Page 196
Introduction......Page 197
An overview of recent methods for flavohemoglobin expression and purification......Page 205
Expression and purification of E. coli Hmp in pBR322, a multicopy vector......Page 206
Expression and purification of E. coli Hmp from the vector pPL452 and thermal induction......Page 207
Expression of E. coli hmp in pBAD......Page 208
Acknowledgments......Page 209
Structural Studies on Flavohemoglobins......Page 214
Introduction......Page 215
Data collection, data analysis, and structure solution......Page 216
Lipid analysis......Page 218
Data collection, analysis, and structure solution......Page 219
Overall fold......Page 220
FAD-binding domain......Page 221
NAD-binding domain......Page 223
Heme-binding domain......Page 224
References......Page 228
Flavohemoglobin of Staphylococcus aureus......Page 230
Preparation of Recombinant S. aureus Hmp......Page 231
Protein purification......Page 232
Redox titration and analysis......Page 233
Catalytic properties of S. aureus Hmp......Page 235
Construction of S. aureus hmp deletion strain......Page 236
Complementation analysis......Page 238
Acknowledments......Page 241
References......Page 242
Assay and Characterization of the NO Dioxygenase Activity of Flavohemoglobins......Page 244
Introduction......Page 245
Autooxidation of Hemoglobins and bullNO Decomposition......Page 249
Methemoglobin Reduction......Page 250
Heme and Flavin Cofactors......Page 251
Reagents......Page 252
Reagents and materials......Page 256
Reagents......Page 259
Reagents......Page 260
Reagents......Page 261
References......Page 262
Globin Interactions with Lipids and Membranes......Page 265
Introduction......Page 266
Extraction method......Page 267
Hemichrome Formation and Detection......Page 268
Gel-filtration experiments......Page 269
Overview......Page 271
Interaction of VHb with E. coli lipid monolayer......Page 272
Lipid binding to VHb and HMP......Page 274
References......Page 376
References......Page 278
Assessment of Biotechnologically Relevant Characteristics of Heterologous Hemoglobins in E. coli......Page 280
Introduction......Page 281
Gene placement and plasmid copy number......Page 285
Transcriptional regulation......Page 286
Overview......Page 287
Cofactor Imitation......Page 288
Conclusions......Page 289
Small-scale bioreactor cultivations (300 ml)......Page 290
Laboratory-scale bioreactor cultivations (1.3 l)......Page 291
DO, growth, carbon dioxide production, and oxygen uptake......Page 292
By-product formation......Page 293
Western blotting......Page 294
References......Page 295
Applications of the VHb Gene VGB for Improved Microbial Fermentation Processes......Page 298
Introduction......Page 299
VHb Application in Microbial Metabolic Engineering......Page 300
Effect of VHB on Protein Production......Page 301
Effect of VHB on Polyhydroxyalkanoate Production......Page 304
Application of VHB in Bioremediation......Page 306
Application of VGB Promoter......Page 307
Expression and Purification of CGB and CTB, the NO-Inducible Globins of the Foodborne Bacterial Pathogen C. Jejuni......Page 313
Introduction......Page 314
Materials......Page 317
Purification of Cgb......Page 318
Histidine-tagged Cgb: A cautionary note......Page 319
Cloning and expression of C. jejuni trHb in E. coli......Page 320
Visible absorbance spectroscopy......Page 322
References......Page 324
Mapping Heme-Ligand Tunnels in Group I Truncated(2/2) Hemoglobins......Page 327
Introduction......Page 328
An In Silico Method for Predicting the Tertiary Structure of Rice HB2......Page 329
Protein Cavities/Tunnel and Ligand Entry......Page 330
The use of Xe atoms to map cavities in 2/2HbN......Page 332
Mapping of protein matrix tunnels in 2/2HbN......Page 334
2/2HbN-Xe derivatives......Page 335
Conclusions......Page 336
Acknowledgments......Page 337
Scavenging of Reactive Nitrogen Species by Mycobacterial Truncated Hemoglobins......Page 340
Introduction......Page 341
Mycobacterial trHbs......Page 342
Chemicals......Page 343
Overview of the Combined Spectroscopic/Crystallographic Approach to the Characterization of Hemichrome in Tetrameric HBS......Page 344
Assay protocol......Page 347
Overview......Page 349
Assay protocol......Page 351
Overview......Page 352
Assay protocol......Page 354
Acknowledgments......Page 355
References......Page 356
Expression, Purification, and Crystallization of Neuro-and Cytoglobin......Page 361
Introduction......Page 362
Expression of NGB......Page 363
DEAE Sepharose Fast Flow chromatography......Page 364
Sephacryl S-200 high-resolution chromatography......Page 365
Preparation of a crude Cygb extract......Page 367
Sephacryl S-200 high-resolution chromatography......Page 368
Alternative Methods for the Preparative Purification of Recombinant Ngb and Cygb and their Mutants......Page 369
Analytical Purification of Recombinant Ngb and Cygb......Page 370
Gel filtration on Superose 12 column: Separation of aggregates......Page 371
Anion-exchange chromatography on a HiTrap DEAE fast-flow column......Page 373
Crystal form II......Page 375
Measurement of Distal Histidine Coordination Equilibrium and Kinetics in Hexacoordinate Hemoglobins......Page 378
Introduction......Page 379
Ligand Binding to HX......Page 380
Methods......Page 382
Scenario 1: Fp is appreciable (KH < 10) and k'L[L] >> K-H and KH......Page 383
Scenario 2: Fp is not appreciable (KH > 10) and K' L[L] >> K-H and KH......Page 385
Methods......Page 386
Scenario 4: Fp is not appreciable (KH > 10) and K'L[L] << K-H and KH......Page 388
Measurement of KH in the Ferrous Oxidation State Using Absorbance Spectroscopy......Page 389
Measurement of KH by Electrochemistry......Page 390
Methods......Page 392
Analysis......Page 394
Conclusions......Page 395
Purification of Class 1 Plant Hemoglobins and Examination of Their Functional Properties......Page 398
Introduction......Page 399
Available data sets......Page 526
Extraction and purification of recombinant barley Hb......Page 400
Purification protocol......Page 401
Characterization of barley Hb......Page 402
Identification of a Methemoglobin Reductase......Page 405
Purification protocol for MDHA reductase......Page 406
Conclusion......Page 408
References......Page 427
Use of In Silico (Computer) Methods to Predict and Anazlyze the Tertiary Structure of Plant Hemoglobins......Page 411
Overview......Page 412
Reported amino acid sequences and tertiary structures for plant hemoglobins......Page 419
Image Editing to Generate High-Quality Figures......Page 424
Editing of the amino acid residues at the heme pocket......Page 426
A Self-Induction Method to Produce High Quantities of Recombinant Functional Flavo-Leghemoglobin Reductase......Page 429
Introduction......Page 430
Medium growth and incubating conditions of the recombinant cells......Page 432
Purification of recombinant FLbR2......Page 433
Assays for the catalysis of Lb3+reduction......Page 434
Representative purification and protein production yield......Page 435
UV-Vis spectra of the flavoenzyme......Page 436
Functionality of the recombinant rFLbR-2......Page 438
References......Page 440
Spectroscopic and Crystallographic Characterization of bis-Histidyl Adducts in Tetrameric Hemoglobins......Page 442
Introduction......Page 443
Antarctic Fish Hemoglobins......Page 444
Hemichrome occurrence in Hbs......Page 446
The exceptional behavior of Antarctic fish Hbs......Page 447
Spectroscopic markers......Page 448
Crystallization......Page 451
The available three-dimensional structural models......Page 452
Atomic resolution structure of HbTb in partial hemichrome state......Page 455
References......Page 457
Dinitrosyl Iron Complexes Bind with Hemoglobin as Markers of Oxidative Stress......Page 462
Introduction......Page 463
Synthesis of DNIC......Page 464
Experiments on animals......Page 465
Spin adducts of DEPMPO with free radicals......Page 466
Study of Oxidative HB Modification by SDS Electrophoresis......Page 468
Influence of Hb-DNIC on Oxidative Modification of HB Under the Action of Hydrogen Peroxide......Page 469
Study of HB-DNIC destruction by hydroperoxides......Page 470
Influence of tert-Butyl Hydroperoxide and Hydrogen Peroxide on Hb-DNIC......Page 471
Superoxide-Dependent Destruction of HB-DNIC......Page 473
Acknowledgments......Page 476
Linked Analysis of Large Cooperative Allosteric Systems: The Case of the Giant HBL Hemoglobins......Page 479
Introduction......Page 480
Models......Page 482
Nested MWC model......Page 483
Influence of allosteric effectors......Page 485
Constraints on the allosteric equilibrium constants......Page 487
Statistics......Page 488
HBL HB from L. terrestris......Page 489
HBL HB from M. decora......Page 492
What Is the Advantage of Hierarchical Function?......Page 494
Concluding Remarks......Page 496
Appendix A......Page 497
References......Page 499
Mass Mapping of Large Globin Complexes by Scanning Transmission Electron Microscopy......Page 502
Description of STEM Mass Mapping......Page 503
Advantages of STEM......Page 505
STEM Specimen Preparation......Page 507
Sequence search in the databases......Page 559
Molecular mass......Page 508
Buffers and salts......Page 509
Substrate......Page 510
Interactive Mass Mapping with PCMass......Page 511
Performance Checks......Page 513
Applications......Page 514
References......Page 516
Introduction......Page 517
Anesthesia......Page 518
Tissue Hb isolation......Page 519
Tissue Hb purification......Page 520
Red Blood Cells......Page 521
Collecting Nemerteans......Page 522
Comparative and Evolutionary Genomics of Globin Genes in Fish......Page 524
Introduction......Page 525
Identifying or thologous and paralogous genes......Page 529
Data set production......Page 530
Phylogenetic analysis......Page 531
Type of selection acting on codons/amino acid residues......Page 533
Detecting functionally diverging amino acid residues......Page 534
Inferring ancestral globin sequences......Page 535
An Example of Comparative Genomics in Fish Globins......Page 536
Cytogenetic Methods for Comparative Genomics: Fluorescence In Situ Hybridization......Page 539
Mapping of globin genes by FISH on fish......Page 540
The FISH procedure......Page 541
Preparation of high-quality metaphase chromosomes......Page 542
Hybridization......Page 543
General remarks......Page 544
References......Page 545
Inferring Evolution of Fish Proteins: The Globin Case Study......Page 552
Globin separation......Page 555
Protein cleavage......Page 556
Deacylation of alpha-chain N terminus......Page 557
Cloning and sequencing of globin cDNAs......Page 558
Sequence alignment......Page 560
Overview of tree-building methods and topology interpretation......Page 561
Multiple markers......Page 564
Some refer ence species trees for Actinopterygians......Page 565
Reconstruction of the history of a gene family......Page 566
Reciprocal illumination......Page 568
Alternative reconstructions and interpretations......Page 570
Adaptations and disadaptations......Page 571
Identification of structural motifs......Page 572
Molecular modeling......Page 573
Functional divergence......Page 574
General Remarks......Page 577
Tracing Globin Phylogeny Using PSIBLAST Searches Based on Groups of Sequences......Page 584
Introduction......Page 585
Statistical Evaluation of Sequence Similarity......Page 586
Verification of Globin Sequence Alignments......Page 587
A New Paradigm in Globin Classification......Page 588
Tracing Phylogenetic Relationships via PSIBLAST Searches......Page 589
Author Index......Page 597
Subject Index......Page 626