Biological Inorganic Chemistry

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  • Edition: 1st
  • Format: Hardcover
  • Copyright: 2006-10-01
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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 Contributorsp. xix
Prefacep. xxiii
Acknowledgmentsp. xxv
Introduction and Text Overviewp. 1
The Elements of Lifep. 1
Functional Roles of Biological Inorganic Elementsp. 1
A Guide to This Textp. 3
Overviews of Biological Inorganic Chemistryp. 5
Bioinorganic Chemistry and the Biogeochemical Cyclesp. 7
Introductionp. 7
The Origin and Abundance of the Chemical Elementsp. 8
The Carbon/Oxygen/Hydrogen Cyclesp. 12
The Nitrogen Cyclep. 16
The Sulfur Cyclep. 20
The Interaction and Integration of the Cyclesp. 24
Conclusionsp. 29
Metal Ions and Proteins: Binding, Stability, and Foldingp. 31
Introductionp. 31
The Metal Cofactorp. 31
Protein Residues as Ligands for Metal Ionsp. 33
Genome Browsingp. 37
Folding and Stability of Metalloproteinsp. 37
Kinetic Control of Metal Ion Deliveryp. 40
Special Cofactors and Metal Clustersp. 43
Why Special Metal Cofactors?p. 43
Types of Cofactors, Structural Features, and Occurrencep. 46
Cofactor Biosynthesisp. 54
Transport and Storage of Metal Ions in Biologyp. 57
Introductionp. 57
Metal Ion Bioavailabilityp. 59
General Properties of Transport Systemsp. 61
Iron Illustrates the Problems of Metal Ion Transportp. 66
Transport of Metal Ions Other Than Ironp. 70
Mechanisms of Metal Ion Storage and Resistancep. 71
Intracellular Metal Ion Transport and Traffickingp. 74
Summaryp. 76
Biominerals and Biomineralizationp. 79
Introductionp. 79
Biominerals: Types and Functionsp. 79
General Principles of Biomineralizationp. 83
Conclusionsp. 93
Metals in Medicinep. 95
Introductionp. 95
Metallotherapeuticsp. 96
Imaging and Diagnosisp. 114
Molecular Targetsp. 122
Metal Metabolism as a Therapeutic Targetp. 129
Conclusionsp. 132
Metal Ion Containing Biological Systemsp. 137
Metal Ion Transport and Storagep. 139
Transferrinp. 139
Introduction: Iron Metabolism and the Aqueous Chemistry of Ironp. 139
Transferrin: The Iron Transporting Protein of Complex Organismsp. 140
Iron-Donating Function of Transferrinp. 141
Interaction of Transferrin with HFEp. 143
Ferritinp. 144
Introduction: The Need for Ferritinsp. 144
Ferritin: Nature's Nanoreactor for Iron and Oxygenp. 145
Siderophoresp. 151
Introduction: The Need for Siderophoresp. 151
Siderophore Structuresp. 151
Thermodynamics of Ferric Ion Coordination by Siderophoresp. 152
Outer-Membrane Receptor Proteins for Ferric Siderophoresp. 153
Marine Siderophoresp. 154
Metallothioneinsp. 156
Introductionp. 157
Classes of Metallothioneinsp. 157
Induction and Isolationp. 157
Structural and Spectroscopic Propertiesp. 158
Reactivity and Functionp. 161
Copper-Transporting ATPasesp. 163
Introduction: Wilson and Menkes Diseasesp. 163
Structure and Functionp. 163
Metal Ion Binding and Conformational Changesp. 165
Metallochaperonesp. 166
Introductionp. 166
The Need for Metallochaperonesp. 167
COX17p. 169
ATX1p. 169
Copper Chaperone for SOD1p. 171
Metallochaperones for Other Metals?p. 172
Concluding Remarksp. 173
Hydrolytic Chemistryp. 175
Metal-Dependent Lyase and Hydrolase Enzymes. (I) General Metabolismp. 175
Introductionp. 175
Magnesiump. 176
Zincp. 179
Manganesep. 183
Metal-Dependent Lyase and Hydrolase Enzymes. (II) Nucleic Acid Biochemistryp. 185
Introductionp. 185
Magnesium-Dependent Enzymesp. 185
Calciump. 192
Zincp. 194
Ureasep. 198
Introductionp. 198
The Structure of Native Ureasep. 199
The Structure of Urease Complexed with Transition State and Substrate Analoguesp. 200
The Structure-Based Mechanismp. 202
The Structure of Urease Complexed with Competitive Inhibitorsp. 204
The Molecular Basis for in vivo Urease Activation and Nickel Traffickingp. 206
Aconitasep. 209
Introductionp. 209
Stereochemistry of the Citrate-Isocitrate Isomerase Reactionp. 210
Characterization and Function of the Fe-S Clusterp. 211
Active Site Amino Acid Residues and the Reaction Mechanismp. 212
Cluster Reactivity and Cellular Functionp. 214
Catalytic Nucleic Acidsp. 215
Introduction and Discovery of Catalytic Nucleic Acidsp. 215
Scope and Efficiency of Catalytic Nucleic Acidsp. 216
Classification of Catalytic Nucleic Acids with Hydrolytic Activityp. 217
Metal Ions as Important Cofactors in Catalytic Nucleic Acidsp. 219
Interactions between Metal Ions and Catalytic Nucleic Acidsp. 221
The Role of Metal Ions in Catalytic Nucleic Acidsp. 222
Expanding the Repertoire of Catalytic Nucleic Acids with Transition Metal Ionsp. 225
Application of Catalytic Nucleic Acidsp. 225
From Metalloproteins to Metallocatalytic Nucleic Acidsp. 226
Electron Transfer, Respiration, and Photosynthesisp. 229
Electron-Transfer Proteinsp. 229
Introductionp. 229
Determinants of Reduction Potentialsp. 230
Iron-Sulfur Proteinsp. 239
Cytochromesp. 245
Copper Proteinsp. 250
A Further Comment on the Size of the Cofactorp. 254
Donor-Acceptor Interactionsp. 255
Electron Transfer through Proteinsp. 261
Introductionp. 261
Basic Conceptsp. 261
Semiclassical Theory of Electron Transferp. 264
Photosynthesis and Respirationp. 278
Introductionp. 278
Qualitative Aspects of Mitchell's Chemiosmotic Hypothesis for Phosphorylationp. 279
An Interlude: Reduction Potentialsp. 279
Maximizing Free Energy and ATP Productionp. 281
Quantitative Aspects of Mitchell's Chemiosmotic Hypothesis for Phosphorylationp. 283
Cellular Structures Involved in the Energy Transduction Process: Similarities among Bacteria, Mitochondria, and Chloroplastsp. 284
The Respiratory Chainp. 285
The Photosynthetic Electron-Transfer Chainp. 291
A Common Underlying Theme in Biological O[subscript 2]/H[subscript 2]O Metabolism: Metalloradical Active Sitesp. 299
Dioxygen Production: Photosystem IIp. 302
Introductionp. 302
Photosystem II Activity: Light-Catalyzed Two- and Four-Electron Redox Chemistryp. 303
Photosystem II Protein Structure and Redox Cofactorsp. 305
Inorganic Ions of PSIIp. 308
Modeling the Structure of the PSII Mn Clusterp. 313
Proposals for the Mechanism of Photosynthetic Water Oxidationp. 314
Oxygen Metabolismp. 319
Dioxygen Reactivity and Toxicityp. 319
Introductionp. 319
Chemistry of Dioxygenp. 320
Dioxygen Toxicityp. 325
Superoxide Dismutases and Reductasesp. 331
Introductionp. 331
Superoxide Chemistryp. 332
Superoxide Dismutase and Superoxide Reductase Mechanistic Principlesp. 333
Superoxide Dismutase and Superoxide Reductase Enzymesp. 335
Peroxidase and Catalasesp. 343
Introductionp. 343
Overall Structurep. 344
Active-Site Structurep. 345
Mechanismp. 346
Reduction of Compounds I and IIp. 350
Dioxygen Carriersp. 354
Introduction: Biological Dioxygen Transport Systemsp. 354
Thermodynamic and Kinetic Aspects of Dioxygen Transportp. 357
Cooperativity and Dioxygen Transportp. 358
Biological Dioxygen Carriersp. 361
Protein Control of the Chemistry of Dioxygen, Iron, Copper, and Cobaltp. 370
Structural Basis of Ligand Affinities of Dioxygen Carriersp. 377
Final Remarksp. 385
Dioxygen Activating Enzymesp. 388
Introduction: Converting Carriers into Activatorsp. 388
Mononuclear Nonheme Metal Centers That Activate Dioxygenp. 400
Reducing Dioxygen to Water: Cytochrome c Oxidasep. 413
Introductionp. 414
Lessons from the X-Ray Structures of Bovine Heart Cytochrome c Oxidasep. 415
Reaction Mechanismp. 419
Reducing Dioxygen to Water: Multi-Copper Oxidasesp. 427
Introductionp. 427
Occurrence and General Propertiesp. 427
Functionsp. 428
X-Ray Structuresp. 429
Structure-Function Relationshipsp. 435
Perspectivesp. 437
Reducing Dioxygen to Water: Mechanistic Considerationsp. 440
Hydrogen, Carbon, and Sulfur Metabolismp. 443
Hydrogen Metabolism and Hydrogenasep. 443
Introduction: Microbiology and Biochemistry of Hydrogenp. 443
Hydrogenase Structuresp. 444
Biosynthesisp. 447
Hydrogenase Reaction Mechanismp. 447
Regulation by Hydrogenp. 450
Metalloenzymes in the Reduction of One-Carbon Compoundsp. 452
Introduction: Metalloenzymes in the Reduction of One-Carbon Compounds to Methane and Acetic Acidp. 452
Electron Donors and Acceptors for One-Carbon Redox Reactionsp. 455
Conversion to the "Formate" Oxidation Level by Two-Electron Reduction of Carbon Dioxidep. 455
Conversion from the "Formate" through the "Formaldehyde" to the "Methanol" Oxidation Levelp. 458
Interconversions at the Methyl Level: Methyltransferasesp. 459
Methyl Group Reduction or Carbonylationp. 461
Summaryp. 464
Biological Nitrogen Fixation and Nitrificationp. 468
Introductionp. 468
Biological Nitrogen Fixation: When and How Did Biological Nitrogen Fixation Evolve?p. 469
Nitrogen-Fixing Organisms and Crop Plantsp. 470
Relationships among Nitrogenasesp. 471
Structures of the Mo-Nitrogenase Component Proteins and Their Complexp. 474
Mechanism of Nitrogenase Actionp. 480
Future Perspectives for Nitrogen Fixationp. 485
Biological Nitrification: What Is Nitrification?p. 485
Enzymes Involved in Nitrification by Autotrophic Organismsp. 485
Nitrification by Heterotrophic Organismsp. 490
Anaerobic Ammonia Oxidation (Anammox)p. 491
Future Perspectives for Nitrificationp. 491
Nitrogen Metabolism: Denitrificationp. 494
Introductionp. 494
The Enzymes of Denitrificationp. 494
Summaryp. 505
Sulfur Metabolismp. 508
Introductionp. 508
Biological Role of Sulfur Compoundsp. 509
Biological Sulfur Cyclep. 510
Molybdenum Enzymesp. 518
Introductionp. 518
The Active Sites of the Molybdenum Enzymesp. 521
Molybdenum Enzymesp. 530
Conclusionsp. 542
Tungsten Enzymesp. 545
Introductionp. 545
Biochemical Properties of Tungstoenzymesp. 546
Structural Properties of Tungstoenzymesp. 550
Spectroscopic Properties of Tungstoenzymesp. 552
Mechanism of Action of Tungstoenzymesp. 553
Tungsten Model Complexesp. 554
Tungsten versus Molybdenump. 555
Metalloenzymes with Radical Intermediatesp. 557
Introduction to Free Radicalsp. 557
Introductionp. 557
Free Radical Stability and Reactivityp. 559
Electron Paramagnetic Resonance Spectroscopyp. 560
Biological Radical Complexesp. 560
Cobalaminsp. 562
Introductionp. 562
Nomenclature and Chemistryp. 562
Enzyme Systems Using AdoCblp. 565
Unresolved Issues in AdoCbl Requiring Enzymesp. 569
MeCbl Using Methionine Synthase as a Case Studyp. 570
Unresolved Issues in Methyl Transfer Reactions with MeCblp. 572
Ribonucleotide Reductasesp. 575
Introduction: Three Classes of Ribonucleotide Reductasesp. 575
Mechanisms of Radical Formationp. 577
Conclusionsp. 580
Fe-S Clusters in Radical Generationp. 582
Introductionp. 582
Glycyl Radical Generationp. 586
Isomerization Reactionsp. 589
Cofactor Biosynthesisp. 590
DNA Repairp. 592
Radical-SAM Enzymes: Unifying Themesp. 593
Galactose Oxidasep. 595
Introductionp. 595
Active Site Structurep. 596
Oxidation-Reduction Chemistryp. 597
Catalytic Turnover Mechanismp. 598
Mechanism of Cofactor Biogenesisp. 600
Amine Oxidasesp. 601
Introductionp. 601
Structural Characterizationp. 602
Structure-Function Relationshipp. 604
Mechanistic Considerationsp. 604
Biogenesis of Amine Oxidasesp. 606
Conclusionp. 606
Lipoxygenasep. 607
Introductionp. 607
Structurep. 608
Mechanismp. 608
Kineticsp. 611
Metal Ion Receptors and Signalingp. 613
Metalloregulatory Proteinsp. 613
Introduction: Structural Metal Sitesp. 613
Structural Zn Domainsp. 614
Metal Ion Signalingp. 618
Metalloregulatory Proteinsp. 620
Metalloregulation of Transcriptionp. 620
Metalloregulation of Post-Transcriptional Processesp. 625
Post-Translational Metalloregulationp. 626
Structural Zinc-Binding Domainsp. 628
Introductionp. 628
Molecular and Macromolecular Interactionsp. 628
Metal Coordination and Substitutionp. 630
Zinc Fingers and Protein Designp. 632
Calcium in Mammalian Cellsp. 635
Introductionp. 635
Concentration Levels of Ca[superscript 2+] in Higher Organismsp. 635
The Intracellular Ca[superscript 2+]-Signaling Systemp. 636
A Widespread Ca[superscript 2+]-Binding Motif: The EF-Handp. 639
Ca[superscript 2+] Induced Structural Changes in Modulator Proteins (Calmodulin, Troponin C)p. 641
Ca[superscript 2+] Binding in Buffer or Transporter Proteinsp. 645
Nitric Oxidep. 647
Introduction: Physiological Role and Chemistry of Nitric Oxidep. 647
Chemistry of Oxygen Activationp. 649
Overview of Nitric Oxide Synthase Architecturep. 650
Nitric Oxide Synthase Mechanismp. 651
Cell Biology, Biochemistry, and Evolution: Tutorial Ip. 657
Life's Diversityp. 657
Evolutionary Historyp. 666
Genomes and Proteomesp. 668
Cellular Componentsp. 670
Metabolismp. 685
Fundamentals of Coordination Chemistry: Tutorial IIp. 695
Introductionp. 695
Complexation Equilibria in Waterp. 695
The Effect of Metal Ions on the pK[subscript a] of Ligandsp. 698
Ligand Specificity: Hard versus Softp. 698
Coordination Chemistry and Ligand-Field Theoryp. 700
Consequences of Ligand-Field Theoryp. 703
Kinetic Aspects of Metal Ion Bindingp. 708
Redox Potentials and Electron-Transfer Reactionsp. 709
Abbreviationsp. 713
Glossaryp. 717
The Literature of Biological Inorganic Chemistryp. 727
Introduction to the Protein Data Bank (PDB)p. 729
Indexp. 731
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