Biological Inorganic Chemistry

by Bertini, Ivano

• ISBN13: 9781891389436
• ISBN10: 1891389432
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-10-01
• Publisher: UNIVERSITY SCIENCE BOOKS

Summary

Second author is Harry B. Gray, California Institute of Technology, Pasadena, CA. Text is divided into part A and part B. A discusses the unifying principles of the field, and B discusses specific systems in detail. Topics include metal ions and proteins, metals in medicine, hydrolytic chemistry, and more. For students and researchers. Expanded-outline format.

Table of Contents

List of Contributors	p. xix
Preface	p. xxiii
Acknowledgments	p. xxv
Introduction and Text Overview	p. 1
The Elements of Life	p. 1
Functional Roles of Biological Inorganic Elements	p. 1
A Guide to This Text	p. 3
Overviews of Biological Inorganic Chemistry	p. 5
Bioinorganic Chemistry and the Biogeochemical Cycles	p. 7
Introduction	p. 7
The Origin and Abundance of the Chemical Elements	p. 8
The Carbon/Oxygen/Hydrogen Cycles	p. 12
The Nitrogen Cycle	p. 16
The Sulfur Cycle	p. 20
The Interaction and Integration of the Cycles	p. 24
Conclusions	p. 29
Metal Ions and Proteins: Binding, Stability, and Folding	p. 31
Introduction	p. 31
The Metal Cofactor	p. 31
Protein Residues as Ligands for Metal Ions	p. 33
Genome Browsing	p. 37
Folding and Stability of Metalloproteins	p. 37
Kinetic Control of Metal Ion Delivery	p. 40
Special Cofactors and Metal Clusters	p. 43
Why Special Metal Cofactors?	p. 43
Types of Cofactors, Structural Features, and Occurrence	p. 46
Cofactor Biosynthesis	p. 54
Transport and Storage of Metal Ions in Biology	p. 57
Introduction	p. 57
Metal Ion Bioavailability	p. 59
General Properties of Transport Systems	p. 61
Iron Illustrates the Problems of Metal Ion Transport	p. 66
Transport of Metal Ions Other Than Iron	p. 70
Mechanisms of Metal Ion Storage and Resistance	p. 71
Intracellular Metal Ion Transport and Trafficking	p. 74
Summary	p. 76
Biominerals and Biomineralization	p. 79
Introduction	p. 79
Biominerals: Types and Functions	p. 79
General Principles of Biomineralization	p. 83
Conclusions	p. 93
Metals in Medicine	p. 95
Introduction	p. 95
Metallotherapeutics	p. 96
Imaging and Diagnosis	p. 114
Molecular Targets	p. 122
Metal Metabolism as a Therapeutic Target	p. 129
Conclusions	p. 132
Metal Ion Containing Biological Systems	p. 137
Metal Ion Transport and Storage	p. 139
Transferrin	p. 139
Introduction: Iron Metabolism and the Aqueous Chemistry of Iron	p. 139
Transferrin: The Iron Transporting Protein of Complex Organisms	p. 140
Iron-Donating Function of Transferrin	p. 141
Interaction of Transferrin with HFE	p. 143
Ferritin	p. 144
Introduction: The Need for Ferritins	p. 144
Ferritin: Nature's Nanoreactor for Iron and Oxygen	p. 145
Siderophores	p. 151
Introduction: The Need for Siderophores	p. 151
Siderophore Structures	p. 151
Thermodynamics of Ferric Ion Coordination by Siderophores	p. 152
Outer-Membrane Receptor Proteins for Ferric Siderophores	p. 153
Marine Siderophores	p. 154
Metallothioneins	p. 156
Introduction	p. 157
Classes of Metallothioneins	p. 157
Induction and Isolation	p. 157
Structural and Spectroscopic Properties	p. 158
Reactivity and Function	p. 161
Copper-Transporting ATPases	p. 163
Introduction: Wilson and Menkes Diseases	p. 163
Structure and Function	p. 163
Metal Ion Binding and Conformational Changes	p. 165
Metallochaperones	p. 166
Introduction	p. 166
The Need for Metallochaperones	p. 167
COX17	p. 169
ATX1	p. 169
Copper Chaperone for SOD1	p. 171
Metallochaperones for Other Metals?	p. 172
Concluding Remarks	p. 173
Hydrolytic Chemistry	p. 175
Metal-Dependent Lyase and Hydrolase Enzymes. (I) General Metabolism	p. 175
Introduction	p. 175
Magnesium	p. 176
Zinc	p. 179
Manganese	p. 183
Metal-Dependent Lyase and Hydrolase Enzymes. (II) Nucleic Acid Biochemistry	p. 185
Introduction	p. 185
Magnesium-Dependent Enzymes	p. 185
Calcium	p. 192
Zinc	p. 194
Urease	p. 198
Introduction	p. 198
The Structure of Native Urease	p. 199
The Structure of Urease Complexed with Transition State and Substrate Analogues	p. 200
The Structure-Based Mechanism	p. 202
The Structure of Urease Complexed with Competitive Inhibitors	p. 204
The Molecular Basis for in vivo Urease Activation and Nickel Trafficking	p. 206
Aconitase	p. 209
Introduction	p. 209
Stereochemistry of the Citrate-Isocitrate Isomerase Reaction	p. 210
Characterization and Function of the Fe-S Cluster	p. 211
Active Site Amino Acid Residues and the Reaction Mechanism	p. 212
Cluster Reactivity and Cellular Function	p. 214
Catalytic Nucleic Acids	p. 215
Introduction and Discovery of Catalytic Nucleic Acids	p. 215
Scope and Efficiency of Catalytic Nucleic Acids	p. 216
Classification of Catalytic Nucleic Acids with Hydrolytic Activity	p. 217
Metal Ions as Important Cofactors in Catalytic Nucleic Acids	p. 219
Interactions between Metal Ions and Catalytic Nucleic Acids	p. 221
The Role of Metal Ions in Catalytic Nucleic Acids	p. 222
Expanding the Repertoire of Catalytic Nucleic Acids with Transition Metal Ions	p. 225
Application of Catalytic Nucleic Acids	p. 225
From Metalloproteins to Metallocatalytic Nucleic Acids	p. 226
Electron Transfer, Respiration, and Photosynthesis	p. 229
Electron-Transfer Proteins	p. 229
Introduction	p. 229
Determinants of Reduction Potentials	p. 230
Iron-Sulfur Proteins	p. 239
Cytochromes	p. 245
Copper Proteins	p. 250
A Further Comment on the Size of the Cofactor	p. 254
Donor-Acceptor Interactions	p. 255
Electron Transfer through Proteins	p. 261
Introduction	p. 261
Basic Concepts	p. 261
Semiclassical Theory of Electron Transfer	p. 264
Photosynthesis and Respiration	p. 278
Introduction	p. 278
Qualitative Aspects of Mitchell's Chemiosmotic Hypothesis for Phosphorylation	p. 279
An Interlude: Reduction Potentials	p. 279
Maximizing Free Energy and ATP Production	p. 281
Quantitative Aspects of Mitchell's Chemiosmotic Hypothesis for Phosphorylation	p. 283
Cellular Structures Involved in the Energy Transduction Process: Similarities among Bacteria, Mitochondria, and Chloroplasts	p. 284
The Respiratory Chain	p. 285
The Photosynthetic Electron-Transfer Chain	p. 291
A Common Underlying Theme in Biological O[subscript 2]/H[subscript 2]O Metabolism: Metalloradical Active Sites	p. 299
Dioxygen Production: Photosystem II	p. 302
Introduction	p. 302
Photosystem II Activity: Light-Catalyzed Two- and Four-Electron Redox Chemistry	p. 303
Photosystem II Protein Structure and Redox Cofactors	p. 305
Inorganic Ions of PSII	p. 308
Modeling the Structure of the PSII Mn Cluster	p. 313
Proposals for the Mechanism of Photosynthetic Water Oxidation	p. 314
Oxygen Metabolism	p. 319
Dioxygen Reactivity and Toxicity	p. 319
Introduction	p. 319
Chemistry of Dioxygen	p. 320
Dioxygen Toxicity	p. 325
Superoxide Dismutases and Reductases	p. 331
Introduction	p. 331
Superoxide Chemistry	p. 332
Superoxide Dismutase and Superoxide Reductase Mechanistic Principles	p. 333
Superoxide Dismutase and Superoxide Reductase Enzymes	p. 335
Peroxidase and Catalases	p. 343
Introduction	p. 343
Overall Structure	p. 344
Active-Site Structure	p. 345
Mechanism	p. 346
Reduction of Compounds I and II	p. 350
Dioxygen Carriers	p. 354
Introduction: Biological Dioxygen Transport Systems	p. 354
Thermodynamic and Kinetic Aspects of Dioxygen Transport	p. 357
Cooperativity and Dioxygen Transport	p. 358
Biological Dioxygen Carriers	p. 361
Protein Control of the Chemistry of Dioxygen, Iron, Copper, and Cobalt	p. 370
Structural Basis of Ligand Affinities of Dioxygen Carriers	p. 377
Final Remarks	p. 385
Dioxygen Activating Enzymes	p. 388
Introduction: Converting Carriers into Activators	p. 388
Mononuclear Nonheme Metal Centers That Activate Dioxygen	p. 400
Reducing Dioxygen to Water: Cytochrome c Oxidase	p. 413
Introduction	p. 414
Lessons from the X-Ray Structures of Bovine Heart Cytochrome c Oxidase	p. 415
Reaction Mechanism	p. 419
Reducing Dioxygen to Water: Multi-Copper Oxidases	p. 427
Introduction	p. 427
Occurrence and General Properties	p. 427
Functions	p. 428
X-Ray Structures	p. 429
Structure-Function Relationships	p. 435
Perspectives	p. 437
Reducing Dioxygen to Water: Mechanistic Considerations	p. 440
Hydrogen, Carbon, and Sulfur Metabolism	p. 443
Hydrogen Metabolism and Hydrogenase	p. 443
Introduction: Microbiology and Biochemistry of Hydrogen	p. 443
Hydrogenase Structures	p. 444
Biosynthesis	p. 447
Hydrogenase Reaction Mechanism	p. 447
Regulation by Hydrogen	p. 450
Metalloenzymes in the Reduction of One-Carbon Compounds	p. 452
Introduction: Metalloenzymes in the Reduction of One-Carbon Compounds to Methane and Acetic Acid	p. 452
Electron Donors and Acceptors for One-Carbon Redox Reactions	p. 455
Conversion to the "Formate" Oxidation Level by Two-Electron Reduction of Carbon Dioxide	p. 455
Conversion from the "Formate" through the "Formaldehyde" to the "Methanol" Oxidation Level	p. 458
Interconversions at the Methyl Level: Methyltransferases	p. 459
Methyl Group Reduction or Carbonylation	p. 461
Summary	p. 464
Biological Nitrogen Fixation and Nitrification	p. 468
Introduction	p. 468
Biological Nitrogen Fixation: When and How Did Biological Nitrogen Fixation Evolve?	p. 469
Nitrogen-Fixing Organisms and Crop Plants	p. 470
Relationships among Nitrogenases	p. 471
Structures of the Mo-Nitrogenase Component Proteins and Their Complex	p. 474
Mechanism of Nitrogenase Action	p. 480
Future Perspectives for Nitrogen Fixation	p. 485
Biological Nitrification: What Is Nitrification?	p. 485
Enzymes Involved in Nitrification by Autotrophic Organisms	p. 485
Nitrification by Heterotrophic Organisms	p. 490
Anaerobic Ammonia Oxidation (Anammox)	p. 491
Future Perspectives for Nitrification	p. 491
Nitrogen Metabolism: Denitrification	p. 494
Introduction	p. 494
The Enzymes of Denitrification	p. 494
Summary	p. 505
Sulfur Metabolism	p. 508
Introduction	p. 508
Biological Role of Sulfur Compounds	p. 509
Biological Sulfur Cycle	p. 510
Molybdenum Enzymes	p. 518
Introduction	p. 518
The Active Sites of the Molybdenum Enzymes	p. 521
Molybdenum Enzymes	p. 530
Conclusions	p. 542
Tungsten Enzymes	p. 545
Introduction	p. 545
Biochemical Properties of Tungstoenzymes	p. 546
Structural Properties of Tungstoenzymes	p. 550
Spectroscopic Properties of Tungstoenzymes	p. 552
Mechanism of Action of Tungstoenzymes	p. 553
Tungsten Model Complexes	p. 554
Tungsten versus Molybdenum	p. 555
Metalloenzymes with Radical Intermediates	p. 557
Introduction to Free Radicals	p. 557
Introduction	p. 557
Free Radical Stability and Reactivity	p. 559
Electron Paramagnetic Resonance Spectroscopy	p. 560
Biological Radical Complexes	p. 560
Cobalamins	p. 562
Introduction	p. 562
Nomenclature and Chemistry	p. 562
Enzyme Systems Using AdoCbl	p. 565
Unresolved Issues in AdoCbl Requiring Enzymes	p. 569
MeCbl Using Methionine Synthase as a Case Study	p. 570
Unresolved Issues in Methyl Transfer Reactions with MeCbl	p. 572
Ribonucleotide Reductases	p. 575
Introduction: Three Classes of Ribonucleotide Reductases	p. 575
Mechanisms of Radical Formation	p. 577
Conclusions	p. 580
Fe-S Clusters in Radical Generation	p. 582
Introduction	p. 582
Glycyl Radical Generation	p. 586
Isomerization Reactions	p. 589
Cofactor Biosynthesis	p. 590
DNA Repair	p. 592
Radical-SAM Enzymes: Unifying Themes	p. 593
Galactose Oxidase	p. 595
Introduction	p. 595
Active Site Structure	p. 596
Oxidation-Reduction Chemistry	p. 597
Catalytic Turnover Mechanism	p. 598
Mechanism of Cofactor Biogenesis	p. 600
Amine Oxidases	p. 601
Introduction	p. 601
Structural Characterization	p. 602
Structure-Function Relationship	p. 604
Mechanistic Considerations	p. 604
Biogenesis of Amine Oxidases	p. 606
Conclusion	p. 606
Lipoxygenase	p. 607
Introduction	p. 607
Structure	p. 608
Mechanism	p. 608
Kinetics	p. 611
Metal Ion Receptors and Signaling	p. 613
Metalloregulatory Proteins	p. 613
Introduction: Structural Metal Sites	p. 613
Structural Zn Domains	p. 614
Metal Ion Signaling	p. 618
Metalloregulatory Proteins	p. 620
Metalloregulation of Transcription	p. 620
Metalloregulation of Post-Transcriptional Processes	p. 625
Post-Translational Metalloregulation	p. 626
Structural Zinc-Binding Domains	p. 628
Introduction	p. 628
Molecular and Macromolecular Interactions	p. 628
Metal Coordination and Substitution	p. 630
Zinc Fingers and Protein Design	p. 632
Calcium in Mammalian Cells	p. 635
Introduction	p. 635
Concentration Levels of Ca[superscript 2+] in Higher Organisms	p. 635
The Intracellular Ca[superscript 2+]-Signaling System	p. 636
A Widespread Ca[superscript 2+]-Binding Motif: The EF-Hand	p. 639
Ca[superscript 2+] Induced Structural Changes in Modulator Proteins (Calmodulin, Troponin C)	p. 641
Ca[superscript 2+] Binding in Buffer or Transporter Proteins	p. 645
Nitric Oxide	p. 647
Introduction: Physiological Role and Chemistry of Nitric Oxide	p. 647
Chemistry of Oxygen Activation	p. 649
Overview of Nitric Oxide Synthase Architecture	p. 650
Nitric Oxide Synthase Mechanism	p. 651
Cell Biology, Biochemistry, and Evolution: Tutorial I	p. 657
Life's Diversity	p. 657
Evolutionary History	p. 666
Genomes and Proteomes	p. 668
Cellular Components	p. 670
Metabolism	p. 685
Fundamentals of Coordination Chemistry: Tutorial II	p. 695
Introduction	p. 695
Complexation Equilibria in Water	p. 695
The Effect of Metal Ions on the pK[subscript a] of Ligands	p. 698
Ligand Specificity: Hard versus Soft	p. 698
Coordination Chemistry and Ligand-Field Theory	p. 700
Consequences of Ligand-Field Theory	p. 703
Kinetic Aspects of Metal Ion Binding	p. 708
Redox Potentials and Electron-Transfer Reactions	p. 709
Abbreviations	p. 713
Glossary	p. 717
The Literature of Biological Inorganic Chemistry	p. 727
Introduction to the Protein Data Bank (PDB)	p. 729
Index	p. 731
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