Metals in Biology (eBook)

Prof. Graeme Hanson, located in the Centre for Magnetic Resonance at the University of Queensland, has applied a unique synergistic approach involving both theoretical and experimental aspects of multifrequency continuous wave and pulsed EPR spectroscopy to structurally (geometric and electronic) characterise the metal binding sites in metalloenzymes and transition metal ion complexes. The development and commercialisation of the XSophe-Sophe-XeprView (CW EPR) and Molecular Sophe(CW EPR, Pulsed EPR and ENDOR) computer simulation software suites has been crucial in the characterisation of these biological inorganic systems.   Dr. Lawrence J. Berliner is currently at the Department of Chemistry and Biochemistry, University of Denver, where he was Professor and Chair for the past 8 years. He retired from The Ohio State University, where he spent a 32-year career in the area of biological magnetic resonance (EPR and NMR). He has been recognized by the International EPR Society with the Silver Medal for Biology/Medicine in 2000. He also received the Lifetime Achievement Award in Biological EPR Spectroscopy at EPR-2005. He is the Series Editor for Biological Magnetic Resonance, which he launched in 1979.

CONTRIBUTORS 6
PREFACE 9
CONTENTS 11
LIST OF COLOR FIGURES AND WEBSITE MATERIALS 18
INTRODUCTION 19
1. IRON–SULFUR CLUSTER-CONTAINING PROTEINS 20
2. MOLYBDENUM ENZYMES 21
3. MANGANESE-CONTAINING ENZYMES 23
4. NOVEL METALLOENZYMES AND METALLOPROTEINS 23
5. CONCLUSIONS 24
IRON–SULFUR-CONTAINING MATERIALS 26
ELECTRON MAGNETIC RESONANCE OF IRON–SULFUR PROTEINS IN ELECTRON-TRANSFER CHAINS: RESOLVING COMPLEXITY 27
1. INTRODUCTION 28
1.1. Problems of Complex Electron-Transfer Systems 29
2. IRON–SULFUR PROTEINS 30
2.1. Types of Clusters 32
3. INFORMATION FROM ADVANCED EMR 33
3.1. Relaxation Rates 34
3.2. Identification of Cluster Ligands 34
3.3. Interactions with Protons and Paramagnets 34
3.4. Further Structural Information 35
3.5. Orientation-Selective ENDOR and ESEEM 35
3.6. Studies of Intact Membrane-Bound Complexes 36
3.7. Methods of Isolating Spectra of Individual Components 37
3.8. Results from 14N ESEEM 39
4. SELECTED EXAMPLES FROM ELECTRON-TRANSPORT CHAINS 43
4.1. Xanthine Dehydrogenase/Oxidase as a Model 43
4.2. Mitochondria and Aerobic Bacteria 45
4.3. Complex I (NADH:Ubiquinone Reductase) 45
4.4. Complex II (Succinate:Quinone Reductase) and Quinol:Fumarate Reductase 46
4.5. Complex III 48
4.6. Microbial Anaerobic Respiration 49
4.6.1. Nitrate Reductase 49
4.6.2. Methanogenesis: Heterodisulfide Reductase 50
4.6.3. Photosynthetic Electron-Transport Chains 51
5. CONCLUSIONS 51
ACKNOWLEDGMENTS 51
ABBREVIATIONS 52
NOTE 52
REFERENCES 52
CATALYSIS AND GENE REGULATION 61
ACKNOWLEDGMENTS 65
REFERENCES 65
IRON–SULFUR CLUSTERS IN “RADICAL SAM” ENZYMES: SPECTROSCOPY AND COORDINATION 68
1. INTRODUCTION 68
2. “RADICAL SAM” IRON-SULFUR ENZYMES: AN EXAMPLE OF A LOW-MOLECULAR-WEIGHT LIGAND TO A [4Fe–4S] CLUSTER 69
2.1. The Pyruvate Formate Lyase System 72
2.2. Lysine 2,3-Aminomutase 73
2.3. Anaerobic Ribonucleotide Reductase 73
3. DETECTION OF HYPERFINE COUPLING INTERACTIONS IN METALLOPROTEINS 75
3.1. ENDOR: Principles and General Considerations 77
3.2. ESEEM and HYSCORE 79
4. ANALYSIS OF LIGAND HYPERFINE COUPLING INTERACTIONS 81
5. APPLICATIONS TO METALLOPROTEINS 84
5.1. Pyruvate Formate Lyase-Activating Enzyme (PFL-AE) 84
5.2. Lysine 2,3-Aminomutase (LAM) 87
5.3. Anaerobic Ribonucleotide Reductase Activating Enzyme (aRNR-AE) 88
6. CONCLUSION 90
ACKNOWLEDGMENT 90
REFERENCES 90
MONONUCLEAR MOLYBDENUM ENZYMES 98
REFERENCES 101
EPR STUDIES OF XANTHINE OXIDOREDUCTASE AND OTHER MOLYBDENUM-CONTAINING HYDROXYLASES 105
1. INTRODUCTION 105
2. HISTORICAL CONTEXT 105
3. THE ACTIVE SITE STRUCTURE OF XANTHINEOXIDOREDUCTASE 107
4. ISOTOPIC SUBSTITUTION STUDIES 120
5. MAGNETIC INTERACTIONS BETWEEN CENTERS IN XANTHINE OXIDOREDUCTASE 125
6. CONCLUDING COMMENTS 128
REFERENCES 129
HIGH-RESOLUTION EPR SPECTROSCOPY OF MO ENZYMES. SULFITE OXIDASES:STRUCTURAL AND FUNCTIONAL IMPLICATIONS 135
1. INTRODUCTION AND STRUCTURES FROM X-RAY CRYSTALLOGRAPHY 136
2. EARLIER CW EPR INVESTIGATIONS 139
3. FREQUENCIES OBSERVED IN PULSED EPR FOR A SYSTEM OF ELECTRON SPIN S = 1/2 AND ARBITRARY NUCLEAR SPIN IN WEAK INTERACTION LIMIT 141
4. PULSED EPR TECHNIQUES USED IN THIS WORK 147
4.1. ENDOR 147
4.2. ESEEM Techniques 148
5. GENERAL PROBLEMS IN EXTRACTION OF STRUCTURAL PARAMETERS FROM MAGNETIC RESONANCE PARAMETERS 152
6. SAMPLE PREPARATION AND INSTRUMENTATION 153
7. HIGH-RESOLUTION PULSED EPR SPECTRA, MAGNETIC RESONANCE PARAMETERS, AND STRUCTURAL IMPLICATIONS FOR VARIOUS FORMS OF SO 154
7.1. Exchangeable Protons: Similarities and Differences in SOs from Different Organisms 154
7.1.1. High-pH Forms 154
7.1.2. The lpH forms of CSO, HSO, and Ti(III) Citrate-Reduced pl-SO 160
7.2. Groups Blocking Water Access to Mo(V) 162
7.2.1. Pi-Form of CSO [46] 162
7.2.2. pl-SO, Tentative Observation of –SO42– Ligation to Mo(V) [35] 164
7.3. Nonexchangeable Protons [50] 165
7.4. Exchangeable Oxygen Ligands 168
7.4.1. Equatorial Oxygen Ligand 168
7.4.2. Axial Oxygen Ligand (oxo group) 168
8. BIOLOGICAL IMPLICATIONS. 173
9. CONCLUSION 176
NOTE ADDED IN PROOF 176
ACKNOWLEDGMENTS 177
REFERENCES 177
DIMETHYLSULFOXIDE (DMSO) REDUCTASE, A MEMBER OF THE DMSO REDUCTASE FAMILY OF MOLYBDENUM ENZYMES 183
1. INTRODUCTION 183
2. EPR STUDIES OF MO(V) SPECIES 185
3. EPR STUDIES OF DMSO REDUCTASE 186
3.1. Respiratory DMSO Reductase 187
3.2. Periplasmic DMSO Reductase 187
3.2.1. Mo(V) EPR Signals from Periplasmic DMSO Reductase 189
3.2.1.1. Low-g Mo(V) EPR active species 189
3.2.1.2. Observation of a novel sulfur-centered radical signal 191
3.2.1.3. Mechanism of formation of the low-g type-1 species and the sulfur-centered radical 193
3.2.1.4. The borohydride signal 196
3.2.1.5. High-g unsplit type-1 and type-2 196
3.2.1.4. The high-g split signal 201
3.3. Catalytic Mechanism 202
4. CONCLUSIONS 206
NOTE 206
REFERENCES 206
MANGANESE-CONTAINING ENZYMES 214
THEMANGANESE-CALCIUM CLUSTER OF THE OXYGEN-EVOLVING SYSTEM: SYNTHETIC MODELS, EPR STUDIES, AND ELECTRONIC STRUCTURE CALCULATIONS 215
1. INTRODUCTION 215
2. THEORETICAL BACKGROUND FOR THE POLYNUCLEARMANGANESE CLUSTERS 217
2.1. Introduction to the Spin Physics of Exchange-Coupled Manganese Complexes 217
2.2. EPR Theory for Exchange Coupled Systems. 221
2.2.1. Dimeric Species 223
2.2.2. Clusters of Higher Nuclearity 227
2.3. Computational Methods for Magnetically Coupled Homonuclear Metal Clusters 230
2.3.1. Broken-Symmetry Approach 231
2.3.2. Calculations of EPR Parameters 233
3. SYNTHETIC MODELS FOR MANGANESE CLUSTER OF THE OEC 234
3.1. Current Structural Proposals for the Pentanuclear Mn4Ca Cluster of the OEC 234
3.2. EPR Characteristics of the Manganese Cluster of the OEC 237
3.3. Synthetic Models 240
3.3.1. Dimeric Species 240
3.3.2. Trimeric Species 251
3.3.3. Tetrameric Species 255
4. COMPUTATIONAL STUDIES OF THE OEC 260
4.1. Calculations on the Mechanistic Aspects of the Water Oxidation with DFT 260
4.2. Mixed Molecular Mechanics/Quantum Mechanics Studies of Water Oxidation 264
5. CONCLUSIONS AND PROSPECTIVES 265
ACKNOWLEDGMENTS 267
APPENDIX 267
NOTES 268
REFERENCES 270
MANGANESE METALLOPROTEINS 284
1. INTRODUCTION 284
2. MANGANESE CATALASES 287
2.1. Biochemical and Structural Characterization 287
2.2. Spectroscopic Characterization 289
2.2.1. Mn(II)Mn(II) 289
2.2.2. Mn(III)Mn(III) 290
2.2.3. Mn(II)Mn(III) 291
2.2.4. Mn(III)Mn(IV) 292
2.3. Mechanistic Implications 295
3. RIBONUCLEOTIDE REDUCTASE 296
3.1. Biochemical and Structural Characterization 296
3.2. Spectroscopic Characterization 298
3.2.1. Mn(III)–Fe(III) and Mn(IV)–Fe(III) 298
3.2.2. Mn(IV)–Fe(IV) 300
3.2.2. Interaction of H2O2 with Mn(II)–Fe(II), Mn(III)—Fe(III), and Mn(IV)–Fe(III) 303
3.3. Mechanistic Implications 305
4. CLASS IB RIBONUCLEOTIDE REDUCTASES 306
4.1. Biochemical and Structural Characterization 306
4.2. Spectroscopic Characterization 307
4.3. Mechanistic Implications 310
5. MANGANESE-IRON OXYGENASES 310
5.1. Biochemical and Structural Characterization 310
5.2. Spectroscopic Characterization 312
5.3. Mechanistic Implications 314
6. SOXB 315
6.1. Biochemical and Structural Characterization 315
6.2. Spectroscopic Characterization 316
6.3. Mechanistic Implications 317
7. BACTERIOPHAGE .. PROTEIN PHOSPHATASE 317
7.1. Biochemical and Structural Characterization 317
7.2. Spectroscopic Characterization 318
7.3. Mechanistic Implications 320
8. PURPLE ACID PHOSPHATASE 321
8.1. Biochemical and Structural Characterization 321
8.2. Spectroscopic Characterization 321
8.3. Mechanistic Implications 323
9. PHOSPHOTRIESTERASE 323
9.1. Biochemical and Structural Characterization 323
9.2. Spectroscopic Characterization 324
9.3. Mechanistic Implications 325
10. ARGINASE 328
10.1. Biochemical and Structural Characterization 328
10.2. Spectroscopic Characterization 328
10.3. Mechanistic Implications 333
11. METHIONYL AMINOPEPTIDASE 335
11.1. Biochemical and Structural Characterization 335
11.2. Spectroscopic Characterization 336
11.3. Mechanistic Implications 338
REFERENCES 339
NOVEL METALLOENZYMES AND METALLOPROTEINS 353
EPR OF COBALT-SUBSTITUTED ZINC ENZYMES 354
1. INTRODUCTION 354
2. REVIEW OF COBALT-SUBSTITUTED ENZYMES 355
3. METHODS OF Co(II) INSERTION 357
4. EPR EXPERIMENTAL TECHNIQUES AND CONSIDERATIONS 359
5. SPECTRAL INTERPRETATION 365
6. SPECTRAL INTERPRETATION: A CASE STUDY 373
7. COMPLEMENTARY TECHNIQUES 374
8. CONCLUSIONS 375
REFERENCES 375
HYPERFINE AND QUADRUPOLAR INTERACTIONS IN VANADYL PROTEINS AND MODEL COMPLEXES: THEORY AND EXPERIMENT 380
1. INTRODUCTION 381
1.1. Coordination Chemistry of VO2+ 381
1.2. EPR Properties 382
1.3. The Additivity Relationship for Predicting Ligand Environments 383
1.4. The Ground State and Ligand Hyperfine Couplings 383
2. ENDOR AND ESEEM OF VANADYL MODEL COMPLEXES 385
2.1. 14N Hyperfine and Quadrupole Coupling Constants 385
2.2. 1H and 17O Coupling Constants 388
2.3. 31P Hyperfine Coupling Constants 389
2.4. 51V Nuclear Quadrupole Coupling Constants 389
3. DENSITY FUNCTIONAL THEORY CALCULATIONS OF EPR PARAMETERS IN VANADYL MODEL COMPLEXES 390
3.1. Overview of DFT Methods for Calculations of EPR Parameters 390
3.2. DFT Calculations of Vanadium EPR Parameters 392
3.3. DFT Calculations of Ligand Hyperfine and Quadrupole Coupling Constants 396
3.4. Outlook 399
4. SELECT PROTEIN STUDIES 400
4.1. Pyruvate Kinase 400
4.2. S-Adenosylmethionine Synthetase 402
4.3. Imidazole Glycerol Phosphate Dehydratase 403
4.4. ATP Synthase 403
4.5. D-Xylose Isomerase 404
4.6. Transferrins 406
4.7. Ferritin 407
5. TISSUES 408
5.1. Kidney and Liver 408
5.2. Bone 410
6. CONCLUSIONS 411
ACKNOWLEDGMENTS 411
REFERENCES 411
INDEX 419