PRINCIPLES OF Bioinorganic Chemistry

Stephen J. Lippard MASSACHUSETTS INSTITUTE OF TECHNOLOGY

Jeremy M. Berg JOHNS HOPKINS SCHOOL OF MEDICINE

f University Science Books V Mill Valley, California

Contents

Preface xv

CHAPTER 1 Overview of Bioinorganic Chemistry 1

1.1. What is Bioinorganic Chemistry? 1 1.2. Metal Functions in Metalloproteins 3

1.2.a. Dioxygen Transport 3 1.2.b. Electron Transfer 6 1.2.c. Structural Roles for Metal Ions 6

1.3. Metalloenzyme Functions 8 1.3.a. Hydrolytic Enzymes 8 1.3.b. Two-Electron Redox Enzymes 10 1.3.C Multielectron Pair Redox Enzymes 11 1.3.d. Rearrangements 12

1.4. Communication Roles for Metals in Biology 14 1.5. Interactions of Metal Ions and Nucleic Acids 14 1.6. Metal-Ion Transport and Storage 16 1.7. Metals in Mediane 16 1.8. Organization of This Book 18

Study Problems 19 Bibliography 19

CHAPTER 2 Principles of Coordination Chemistry Related to Bioinorganic Research 21

2.1. Thermodynamic Aspects 21 2.1.a. The Hard-Soft Acid-Base Concept 21 2.1.b. The Chelate Effect and the Irving-Williams Series 24 2.1.c. pKa Values of Coordinated Ligands 24 2.1.d. Tuning of Redox Potentials 26 2.1.e. Biopolymer Effects 28

2.2. Kinetic Aspects 28 2.2.a. Ligand Exchange Rates 28 2.2.b. Substitution Reactions 30 2.2.c. Electron Transfer Reactions 30 vii

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2.3. Electronic and Geometrie Structures of Metal Ions in Biology 31

2.4. Reactions of Coordinated Ligands 35 2.5. Model Complexes and the Concept of Spontaneous Self-

Assembly -37

Study Problems 40 Bibliography 41

CHAPTER 3 Properties of Biological Molecules 43

3.1. Proteins and Their Constituents 43 3.1.a. The Naturally Occurring Amino Acids 43 3.1.b. Proteins as Ligands 45 3.I.e. Protein Structure 47 3.1.d. Higher-Order Structures 50 3.1.e. The Manipulation of Proteins by Gene Cloning and

Expression 50 3.1.f. The Kinetic Analysis of Enzyme Reactions 55

3.2. Nucleic Acids and their Constituents 57 3.2.a. RNA, DNA, and Their Building Blocks 57 3.2.b. RNA Structure 60 3.2.c. DNA Structure 61 3.2.d. Metal Binding and Nucleic Acid Structure 64 3.2.e. Chromosome Structures 66 3.2.f. Nucleic-Acid Synthesis in Vitro 66 3.2.g. Sulfur Atoms in Nucleic Acids 69

3.3. Other Metal-Binding Biomolecules 69 3.3.a. Prosthetic Groups 69 3.3.b. CoenzymeB-12 70 3.3.C. Bleomycin and Siderophores 70 3.3.d. Complex Assemblies 72

Study Problems 73 Bibliography 73

CHAPTER 4 Physical Methods in Bioinorganic Chemistry 75

4.1. Purpose of this Chapter 75 4.2. A Comment on Time Scales 75 4.3. X-ray Methods 77

4.3.a. X-ray Diffraction 77 4.3.b. X-ray Absorption Spectroscopy (XAS) 82

4.4. Magnetic Resonance Methods 83 4.4.a. Electron Paramagnetic Resonance (EPR)

Spectroscopy 84 4.4.b. Nuclear Magnetic Resonance (NMR) Spectroscopy 88

4.5. Mössbauer Spectroscopy 91

Contents

4.6. Electronic and Vibrational Spectroscopy 92 4.6.a. Electronic Spectra 92 4.6.b. Vibrational Spectroscopy 94 4.6.C. Circular Dichroism and Magnetic Circular Dichroism

Spectroscopy 95 4.7. Magnetic Measurements 96 4.8. Reduction Potential Measurements 97 4.9. Electron Microprobe Analysis 98

Study Problems 99 Bibliography 100

CHAPTER 5 Choice, Uptake, and Assembly of Metal Containing Units in Biology 103

5.1. Bioavailability of Metal Ions 105 5.2. Enrichment Strategies and Intracellular Chemistry of Low-

Abundance Metals 111 5.3. Spontaneous Self-Assembly of Metal Clusters 115

5.3.a. Iron-Sulfur Clusters 115 5.3.b. Polyiron Oxo Clusters and Biomineralization 125

5.4. Specialized Units 131 5.4.a. Porphyrins 131 5.4.b. Corrins and Hydroporphyrins 131 5.4.c. Metal-Nucleotide Complexes 132 5.4.d. Molybdenum-Binding Cofactors 132

Study Problems 136 Bibliography 136

CHAPTER 6 Control and Utilization of Metal-Ion Concentration in Cells 139

6.1. Beneficial and Toxic Effects of Metal Ions 139 6.2. A Beneficial Metal Under Tight Regulation: Iron 141

6.2.a. Solubilization, Uptake and Transport 142 6.2.b. Metalloregulation of Uptake and Storage 145

6.3. An Example of a Toxic Metal: Mercury 148 6.3.a. The Enzymes Involved in Mercury Detoxification 149 6.3.b. Metalloregulation of the Mercury Detoxification Genes 151

6.4. The Generation and Uses of Metal-Ion-Concentration Gradients 152 6.4.a. Generation of Ionic Gradients 154 6.4.b. Ion Transport by Ion Channels 156 6.4.c. The Acetylcholine Receptor 156 6.4.d. The Voltage-Gated Sodium Channel 162 6.4.e. Synthetic Models for Ion Channels 167

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6.5. Tissue Selectivity in Metal Drug Distribution 168

Study Problems 170 Bibliography 171

CHAPTER 7 Metal Ion Folding and Cross-Linking of Biomolecules 175

7.1. Metal-Ion Stabilization of Protein Structure 175 7.1.a. Aspartate Transcarbamoylase 175 7.1.b. Zinc-Binding Domains in Nucleic-Acid-Binding

Proteins 178 7.I.C. Calcium-Binding Proteins: Transient Structural

Stabilization 184 7.2. Metal-Ion Stabilization of Nucleic-Acid Structure 192

7.2.a. Transfer RNA 193 7.2.b. Catalytic RNA Molecules 194 7.2.c. Telomeres 196

7.3 Protein Binding to Metallated DNA 198 7.3.a. Unwinding and Bending of DNA Modified by Platinum

Anticancer Drugs 198 7.3.b. Recognition and Binding of High-Mobility-Group (Box)

Proteins to DNA Containing Cisplatin IntraStrand d(GpG) or d(ApG) Cross-Links 200

7.4. Metal-Organized Structures as Probes for Conformation 206 7.4.a. Metallointercalators 206 7.4.b. Conformational Recognition 206

Study Problems 210 Bibliography 210

CHAPTER 8 Binding of Metal Ions and Complexes to Biomolecule-Active Centers 213

8.1. Selection and Insertion of Metal Ions for Protein Sites 213 8.1.a. Thermodynamic Control 214 8.1.b. Kinetic Control 217 8.1.C Bioavailability 218

8.2. Preservation of Electroneutrality 218 8.2.a. Mononuclear Sites 219 8.2.b. Polynuclear Sites 220

8.3. Metal-Ion and Metal-Complex Binding to Nucleic Acids 221 8.4. Biopolymer-Promoted Metal-Ligand Interactions 223

8.4.a. Ferrochelatase 223 8.4.b. DNA-Promoted Reaction Chemistry 227

Study Problems 229 Bibliography 229

Contents

CHAPTER 9 Electron-Transf er Proteins 231

9.1. Electron Carriers 231 9.1.a. Iron-Sulfur Proteins 232 9.1.b. Blue Copper Proteins 237 9.I.e. Cytochromes 243

9.2. Long-Distance Electron Transfer 244 9.3. Distance and Driving-Force Dependence of Electron

Transfer 247

Study Problems 253 Bibliography 254

CHAPTER 1 0 Substrate Binding and Activation by Nonredox Mechanisms 257

10.1. Hydrolytic Enzymes 258 lO.l.a. Carboxypeptidase A and Thermolysin: Structural

Studies 259 lO.l.b. Carboxypeptidase A: Metal Substitution and

Spectroscopy 262 10.I.e. Kinetic Studies and the Postulated Enzyme

Mechanism 263 lO.l.d. Alkaline Phosphatase 267

10.2. A Lyase, Carbonic Anhydrase 267 10.3. An Oxidoreductase, Alcohol Dehydrogenase 271 10.4. Nucleotide Activation 274

Study Problems 279 Bibliography 279

CHAPTER 11 Atom- and Group-Transfer Chemistry 283

11.1. Dioxygen Transport 284 ll.l.a. Hemoglobin and Myoglobin 285 ll.l.b. Hemerythrin 291 11.I.e. Hemocyanin 297

11.2. Oxygen-Atom-Transfer Reactions: Fe 302 11.2.a. Cytochrome P-450 303 11.2.b. Methane Monooxygenase 311 11.2.C. Catechol and Other Dioxygenases 315

11.3. Oxygen-Atom-Transfer Reactions: Mo 318 11.3.a. Molybdenum Oxotransferase Enzymes 318 11.3.b. Models for Molybdenum Oxotransferases 322

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11.4. Other Reactions of Dioxygen and Its Byproducts 325 11.4.a. Protective Metalloenzymes: The Cu-Zn Superoxide

Dismutase 325 11.4.b". A Protective Metalloenzyme, Catalase, and

Peroxidases 329 11.4.C. Dioxygen Radical-Generating Systems 333

11.5. Coenzyme B-12 Dependent Reactions 336 11.5.a. Historical Perspective 336 11.5.b. Enzymatic Reactions and the Catalytic Mechanism 337 11.5.C. Thermodynamic Considerations and the Role of the

Enzyme 340

Study Problems 344 Bibliography 344

CHAPTER 12 Protein Tuning of Metal Properties to Achieve Specific Functions 349

12.1. The Basic Concept 349 12.2. Control of Function by Protein Side Chains: Opening

Coordination Sites 351 12.2.a. Herne Proteins 351 12.2.b. Iron-Sulfur Proteins: Aconitase 352 12.2.C. Zinc Proteins 354

12.3. Control of Function by Ligand Type 355 12.3.a. Herne Proteins 356 12.3.b. Iron-Sulfur Proteins: Rieske Centers 358

12.4. Control of Function by Coordination Geometry: Blue Copper Proteins 359

12.5. Control of Function by Indirect Effects 360 12.5.a. [Fe4S4(Cys)4] Centers: Hydrophobicity and Hydrogen-

Bonding Effects 360 12.5.b. Cytochromes: Electrostatic Potential 362

12.6. Substrate Specificity 364 12.6.a. Proteases 365 12.6.b. Cytochromes P-450 366

12.7. Coupled Processes 369 12.7.BL. Electron Transfer Coupling—Sulfite Oxidase 369 12.7.b. Chemical and Electron-Transfer Coupling:

Nitrogenase 370 12.7.C. Substrate Binding: Cytochrome P-450 370 12.7.d. Membrane Transport: Photosynthetic Reaction

Center 372

Study Problems 376 Bibliography 377

Contents

CHAPTER 13 The Frontiers of Bioinorganic Chemistry 379

13.1 Choice and Uptake of Metal Ions 380 13.2. Control and Utilization of Metal-Ion Concentrations 381 13.3. Metal Folding and Cross-Linking 383 13.4. Binding of Metal Ions to Biomolecules 384 13.5. Electron-Transfer Proteins 385 13.6. Substrate Binding and Activation 385 13.7. Atom- and Group-Transfer Chemistry 386 13.8. Protein Tuning of the Active Sites 388

Study Problems 390 Bibliography 390

I n d e x 393