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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