Hanson / Berliner Metals in Biology

Applications of High-Resolution EPR to Metalloenzymes
1. Auflage 2010
ISBN: 978-1-4419-1139-1
Verlag: Springer-Verlag
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 419 Seiten

Metal ions in biology is an ever expanding area in science and medicine involving metal ions in proteins and enzymes, their biosynthesis, catalysis, electron transfer, metal ion trafficking, gene regulation and disease. While X-ray crystallography has provided snapshots of the geometric structures of the active site redox cofactors in these proteins, the application of high resolution EPR spectroscopy in conjunction with quantum chemistry calculations has enabled, in many cases, a detailed understanding of a metalloenzymes mechanism through investigations of the geometric and electronic structure of the resting, enzyme-substrate intermediates and product complexes. This volume, Part II of a two-volume set demonstrates the application of high resolution EPR spectroscopy in determining the geometric and electronic structure of active site metal ion centers in iron sulfur cluster containing metalloproteins, mononuclear molybdenum metalloenzymes, manganese-containing enzymes and novel metalloproteins.

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.

Autoren/Hrsg.

Hanson, Graeme

Berliner, Lawrence

Inhaltsverzeichnis

1;CONTRIBUTORS;6
2;PREFACE;9
3;CONTENTS;11
4;LIST OF COLOR FIGURES AND WEBSITE MATERIALS;18
5;INTRODUCTION;19
5.1;1. IRON–SULFUR CLUSTER-CONTAINING PROTEINS;20
5.2;2. MOLYBDENUM ENZYMES;21
5.3;3. MANGANESE-CONTAINING ENZYMES;23
5.4;4. NOVEL METALLOENZYMES AND METALLOPROTEINS;23
5.5;5. CONCLUSIONS;24
6;IRON–SULFUR-CONTAINING MATERIALS;26
7;ELECTRON MAGNETIC RESONANCE OF IRON–SULFUR PROTEINS IN ELECTRON-TRANSFER CHAINS: RESOLVING COMPLEXITY;27
7.1;1. INTRODUCTION;28
7.1.1;1.1. Problems of Complex Electron-Transfer Systems;29
7.2;2. IRON–SULFUR PROTEINS;30
7.2.1;2.1. Types of Clusters;32
7.3;3. INFORMATION FROM ADVANCED EMR;33
7.3.1;3.1. Relaxation Rates;34
7.3.2;3.2. Identification of Cluster Ligands;34
7.3.3;3.3. Interactions with Protons and Paramagnets;34
7.3.4;3.4. Further Structural Information;35
7.3.5;3.5. Orientation-Selective ENDOR and ESEEM;35
7.3.6;3.6. Studies of Intact Membrane-Bound Complexes;36
7.3.7;3.7. Methods of Isolating Spectra of Individual Components;37
7.3.8;3.8. Results from 14N ESEEM;39
7.4;4. SELECTED EXAMPLES FROM ELECTRON-TRANSPORT CHAINS;43
7.4.1;4.1. Xanthine Dehydrogenase/Oxidase as a Model;43
7.4.2;4.2. Mitochondria and Aerobic Bacteria;45
7.4.3;4.3. Complex I (NADH:Ubiquinone Reductase);45
7.4.4;4.4. Complex II (Succinate:Quinone Reductase) and Quinol:Fumarate Reductase;46
7.4.5;4.5. Complex III;48
7.4.6;4.6. Microbial Anaerobic Respiration;49
7.4.6.1;4.6.1. Nitrate Reductase;49
7.4.6.2;4.6.2. Methanogenesis: Heterodisulfide Reductase;50
7.4.6.3;4.6.3. Photosynthetic Electron-Transport Chains;51
7.5;5. CONCLUSIONS;51
7.6;ACKNOWLEDGMENTS;51
7.7;ABBREVIATIONS;52
7.8;NOTE;52
7.9;REFERENCES;52
8;CATALYSIS AND GENE REGULATION;61
8.1;ACKNOWLEDGMENTS;65
8.2;REFERENCES;65
9;IRON–SULFUR CLUSTERS IN “RADICAL SAM” ENZYMES: SPECTROSCOPY AND COORDINATION;68
9.1;1. INTRODUCTION;68
9.2;2. “RADICAL SAM” IRON-SULFUR ENZYMES: AN EXAMPLE OF A LOW-MOLECULAR-WEIGHT LIGAND TO A [4Fe–4S] CLUSTER;69
9.2.1;2.1. The Pyruvate Formate Lyase System;72
9.2.2;2.2. Lysine 2,3-Aminomutase;73
9.3;2.3. Anaerobic Ribonucleotide Reductase;73
9.4;3. DETECTION OF HYPERFINE COUPLING INTERACTIONS IN METALLOPROTEINS;75
9.4.1;3.1. ENDOR: Principles and General Considerations;77
9.4.2;3.2. ESEEM and HYSCORE;79
9.5;4. ANALYSIS OF LIGAND HYPERFINE COUPLING INTERACTIONS;81
9.6;5. APPLICATIONS TO METALLOPROTEINS;84
9.6.1;5.1. Pyruvate Formate Lyase-Activating Enzyme (PFL-AE);84
9.6.2;5.2. Lysine 2,3-Aminomutase (LAM);87
9.6.3;5.3. Anaerobic Ribonucleotide Reductase Activating Enzyme (aRNR-AE);88
9.7;6. CONCLUSION;90
9.8;ACKNOWLEDGMENT;90
9.9;REFERENCES;90
10;MONONUCLEAR MOLYBDENUM ENZYMES;98
10.1;REFERENCES;101
11;EPR STUDIES OF XANTHINE OXIDOREDUCTASE AND OTHER MOLYBDENUM-CONTAINING HYDROXYLASES;105
11.1;1. INTRODUCTION;105
11.2;2. HISTORICAL CONTEXT;105
11.3;3. THE ACTIVE SITE STRUCTURE OF XANTHINEOXIDOREDUCTASE;107
11.4;4. ISOTOPIC SUBSTITUTION STUDIES;120
11.5;5. MAGNETIC INTERACTIONS BETWEEN CENTERS IN XANTHINE OXIDOREDUCTASE;125
11.6;6. CONCLUDING COMMENTS;128
11.7;REFERENCES;129
12;HIGH-RESOLUTION EPR SPECTROSCOPY OF MO ENZYMES. SULFITE OXIDASES:STRUCTURAL AND FUNCTIONAL IMPLICATIONS;135
12.1;1. INTRODUCTION AND STRUCTURES FROM X-RAY CRYSTALLOGRAPHY;136
12.2;2. EARLIER CW EPR INVESTIGATIONS;139
12.3;3. FREQUENCIES OBSERVED IN PULSED EPR FOR A SYSTEM OF ELECTRON SPIN S = 1/2 AND ARBITRARY NUCLEAR SPIN IN WEAK INTERACTION LIMIT;141
12.4;4. PULSED EPR TECHNIQUES USED IN THIS WORK;147
12.4.1;4.1. ENDOR;147
12.4.2;4.2. ESEEM Techniques;148
12.5;5. GENERAL PROBLEMS IN EXTRACTION OF STRUCTURAL PARAMETERS FROM MAGNETIC RESONANCE PARAMETERS;152
12.6;6. SAMPLE PREPARATION AND INSTRUMENTATION;153
12.7;7. HIGH-RESOLUTION PULSED EPR SPECTRA, MAGNETIC RESONANCE PARAMETERS, AND STRUCTURAL IMPLICATIONS FOR VARIOUS FORMS OF SO;154
12.7.1;7.1. Exchangeable Protons: Similarities and Differences in SOs from Different Organisms;154
12.7.1.1;7.1.1. High-pH Forms;154
12.7.1.2;7.1.2. The lpH forms of CSO, HSO, and Ti(III) Citrate-Reduced pl-SO;160
12.7.2;7.2. Groups Blocking Water Access to Mo(V);162
12.7.2.1;7.2.1. Pi-Form of CSO [46];162
12.7.2.2;7.2.2. pl-SO, Tentative Observation of –SO42– Ligation to Mo(V) [35];164
12.7.3;7.3. Nonexchangeable Protons [50];165
12.7.4;7.4. Exchangeable Oxygen Ligands;168
12.7.4.1;7.4.1. Equatorial Oxygen Ligand;168
12.7.4.2;7.4.2. Axial Oxygen Ligand (oxo group);168
12.8;8. BIOLOGICAL IMPLICATIONS.;173
12.9;9. CONCLUSION;176
12.10;NOTE ADDED IN PROOF;176
12.11;ACKNOWLEDGMENTS;177
12.12;REFERENCES;177
13;DIMETHYLSULFOXIDE (DMSO) REDUCTASE, A MEMBER OF THE DMSO REDUCTASE FAMILY OF MOLYBDENUM ENZYMES;183
13.1;1. INTRODUCTION;183
13.2;2. EPR STUDIES OF MO(V) SPECIES;185
13.3;3. EPR STUDIES OF DMSO REDUCTASE;186
13.3.1;3.1. Respiratory DMSO Reductase;187
13.3.2;3.2. Periplasmic DMSO Reductase;187
13.3.2.1;3.2.1. Mo(V) EPR Signals from Periplasmic DMSO Reductase;189
13.3.2.2;3.2.1.1. Low-g Mo(V) EPR active species;189
13.3.2.3;3.2.1.2. Observation of a novel sulfur-centered radical signal;191
13.3.2.4;3.2.1.3. Mechanism of formation of the low-g type-1 species and the sulfur-centered radical;193
13.3.2.5;3.2.1.4. The borohydride signal;196
13.3.2.6;3.2.1.5. High-g unsplit type-1 and type-2;196
13.3.2.7;3.2.1.4. The high-g split signal;201
13.3.3;3.3. Catalytic Mechanism;202
13.4;4. CONCLUSIONS;206
13.5;NOTE;206
13.6;REFERENCES;206
14;MANGANESE-CONTAINING ENZYMES;214
15;THEMANGANESE-CALCIUM CLUSTER OF THE OXYGEN-EVOLVING SYSTEM: SYNTHETIC MODELS, EPR STUDIES, AND ELECTRONIC STRUCTURE CALCULATIONS;215
15.1;1. INTRODUCTION;215
15.2;2. THEORETICAL BACKGROUND FOR THE POLYNUCLEARMANGANESE CLUSTERS;217
15.2.1;2.1. Introduction to the Spin Physics of Exchange-Coupled Manganese Complexes;217
15.2.2;2.2. EPR Theory for Exchange Coupled Systems.;221
15.2.2.1;2.2.1. Dimeric Species;223
15.2.2.2;2.2.2. Clusters of Higher Nuclearity;227
15.2.3;2.3. Computational Methods for Magnetically Coupled Homonuclear Metal Clusters;230
15.2.3.1;2.3.1. Broken-Symmetry Approach;231
15.2.3.2;2.3.2. Calculations of EPR Parameters;233
15.3;3. SYNTHETIC MODELS FOR MANGANESE CLUSTER OF THE OEC;234
15.3.1;3.1. Current Structural Proposals for the Pentanuclear Mn4Ca Cluster of the OEC;234
15.3.2;3.2. EPR Characteristics of the Manganese Cluster of the OEC;237
15.3.3;3.3. Synthetic Models;240
15.3.3.1;3.3.1. Dimeric Species;240
15.3.3.2;3.3.2. Trimeric Species;251
15.3.3.3;3.3.3. Tetrameric Species;255
15.4;4. COMPUTATIONAL STUDIES OF THE OEC;260
15.4.1;4.1. Calculations on the Mechanistic Aspects of the Water Oxidation with DFT;260
15.4.2;4.2. Mixed Molecular Mechanics/Quantum Mechanics Studies of Water Oxidation;264
15.5;5. CONCLUSIONS AND PROSPECTIVES;265
15.6;ACKNOWLEDGMENTS;267
15.7;APPENDIX;267
15.8;NOTES;268
15.9;REFERENCES;270
16;MANGANESE METALLOPROTEINS;284
16.1;1. INTRODUCTION;284
16.2;2. MANGANESE CATALASES;287
16.2.1;2.1. Biochemical and Structural Characterization;287
16.2.2;2.2. Spectroscopic Characterization;289
16.2.2.1;2.2.1. Mn(II)Mn(II);289
16.2.2.2;2.2.2. Mn(III)Mn(III);290
16.2.2.3;2.2.3. Mn(II)Mn(III);291
16.2.2.4;2.2.4. Mn(III)Mn(IV);292
16.2.3;2.3. Mechanistic Implications;295
16.3;3. RIBONUCLEOTIDE REDUCTASE;296
16.3.1;3.1. Biochemical and Structural Characterization;296
16.3.2;3.2. Spectroscopic Characterization;298
16.3.2.1;3.2.1. Mn(III)–Fe(III) and Mn(IV)–Fe(III);298
16.3.2.2;3.2.2. Mn(IV)–Fe(IV);300
16.3.2.3;3.2.2. Interaction of H2O2 with Mn(II)–Fe(II), Mn(III)—Fe(III), and Mn(IV)–Fe(III);303
16.3.3;3.3. Mechanistic Implications;305
16.4;4. CLASS IB RIBONUCLEOTIDE REDUCTASES;306
16.4.1;4.1. Biochemical and Structural Characterization;306
16.4.2;4.2. Spectroscopic Characterization;307
16.4.3;4.3. Mechanistic Implications;310
16.5;5. MANGANESE-IRON OXYGENASES;310
16.5.1;5.1. Biochemical and Structural Characterization;310
16.5.2;5.2. Spectroscopic Characterization;312
16.5.3;5.3. Mechanistic Implications;314
16.6;6. SOXB;315
16.6.1;6.1. Biochemical and Structural Characterization;315
16.6.2;6.2. Spectroscopic Characterization;316
16.6.3;6.3. Mechanistic Implications;317
16.7;7. BACTERIOPHAGE .. PROTEIN PHOSPHATASE;317
16.7.1;7.1. Biochemical and Structural Characterization;317
16.7.2;7.2. Spectroscopic Characterization;318
16.7.3;7.3. Mechanistic Implications;320
16.8;8. PURPLE ACID PHOSPHATASE;321
16.8.1;8.1. Biochemical and Structural Characterization;321
16.8.2;8.2. Spectroscopic Characterization;321
16.8.3;8.3. Mechanistic Implications;323
16.9;9. PHOSPHOTRIESTERASE;323
16.9.1;9.1. Biochemical and Structural Characterization;323
16.9.2;9.2. Spectroscopic Characterization;324
16.9.3;9.3. Mechanistic Implications;325
16.10;10. ARGINASE;328
16.10.1;10.1. Biochemical and Structural Characterization;328
16.10.2;10.2. Spectroscopic Characterization;328
16.10.3;10.3. Mechanistic Implications;333
16.11;11. METHIONYL AMINOPEPTIDASE;335
16.11.1;11.1. Biochemical and Structural Characterization;335
16.11.2;11.2. Spectroscopic Characterization;336
16.11.3;11.3. Mechanistic Implications;338
16.12;REFERENCES;339
17;NOVEL METALLOENZYMES AND METALLOPROTEINS;353
18;EPR OF COBALT-SUBSTITUTED ZINC ENZYMES;354
18.1;1. INTRODUCTION;354
18.2;2. REVIEW OF COBALT-SUBSTITUTED ENZYMES;355
18.3;3. METHODS OF Co(II) INSERTION;357
18.4;4. EPR EXPERIMENTAL TECHNIQUES AND CONSIDERATIONS;359
18.5;5. SPECTRAL INTERPRETATION;365
18.6;6. SPECTRAL INTERPRETATION: A CASE STUDY;373
18.7;7. COMPLEMENTARY TECHNIQUES;374
18.8;8. CONCLUSIONS;375
18.9;REFERENCES;375
19;HYPERFINE AND QUADRUPOLAR INTERACTIONS IN VANADYL PROTEINS AND MODEL COMPLEXES: THEORY AND EXPERIMENT;380
19.1;1. INTRODUCTION;381
19.1.1;1.1. Coordination Chemistry of VO2+;381
19.1.2;1.2. EPR Properties;382
19.1.3;1.3. The Additivity Relationship for Predicting Ligand Environments;383
19.1.4;1.4. The Ground State and Ligand Hyperfine Couplings;383
19.2;2. ENDOR AND ESEEM OF VANADYL MODEL COMPLEXES;385
19.2.1;2.1. 14N Hyperfine and Quadrupole Coupling Constants;385
19.2.2;2.2. 1H and 17O Coupling Constants;388
19.2.3;2.3. 31P Hyperfine Coupling Constants;389
19.2.4;2.4. 51V Nuclear Quadrupole Coupling Constants;389
19.3;3. DENSITY FUNCTIONAL THEORY CALCULATIONS OF EPR PARAMETERS IN VANADYL MODEL COMPLEXES;390
19.3.1;3.1. Overview of DFT Methods for Calculations of EPR Parameters;390
19.3.2;3.2. DFT Calculations of Vanadium EPR Parameters;392
19.3.3;3.3. DFT Calculations of Ligand Hyperfine and Quadrupole Coupling Constants;396
19.3.4;3.4. Outlook;399
19.4;4. SELECT PROTEIN STUDIES;400
19.4.1;4.1. Pyruvate Kinase;400
19.4.2;4.2. S-Adenosylmethionine Synthetase;402
19.4.3;4.3. Imidazole Glycerol Phosphate Dehydratase;403
19.4.4;4.4. ATP Synthase;403
19.4.5;4.5. D-Xylose Isomerase;404
19.4.6;4.6. Transferrins;406
19.4.7;4.7. Ferritin;407
19.5;5. TISSUES;408
19.5.1;5.1. Kidney and Liver;408
19.5.2;5.2. Bone;410
19.6;6. CONCLUSIONS;411
19.7;ACKNOWLEDGMENTS;411
19.8;REFERENCES;411
20;INDEX;419