Chemistry of Metalloproteins Problems and Solutions in Bioinorganic Chemistry

by Stephanos, Joseph J.; Addison, Anthony W.

• ISBN13: 9781118470442
• ISBN10: 1118470443
• Edition: 1st
• Format: Paperback
• Copyright: 2014-08-04
• Publisher: Wiley

Summary

Addresses the full gamut of questions in metalloprotein science

Formatted as a question-and-answer guide, this book examines all major families of metal binding proteins, presenting our most current understanding of their structural, physicochemical, and functional properties. Moreover, it introduces new and emerging medical applications of metalloproteins. Readers will discover both the underlying chemistry and biology of this important area of research in bioinorganic chemistry.

Chemistry of Metalloproteins features a building block approach that enables readers to master the basics and then advance to more sophisticated topics. The book begins with a general introduction to bioinorganic chemistry and metalloproteins. Next, it covers:

• Alkali and alkaline earth cations
• Metalloenzymes
• Copper proteins
• Iron proteins
• Vitamin B₁₂
• Chlorophyll

Chapters are richly illustrated to help readers fully grasp all the chemical concepts that govern the biological action of metalloproteins. In addition, each chapter ends with a list of suggested original research articles and reviews for further investigation of individual topics.

Presenting our most current understanding of metalloproteins, Chemistry of Metalloproteins is recommended for students and researchers in coordination chemistry, biology, and medicine.

Each volume of the Wiley Series in Protein and Peptide Science addresses a specific facet of the field, reviewing the latest findings and presenting a broad range of perspectives. The volumes in this series constitute essential reading for biochemists, biophysicists, molecular biologists, geneticists, cell biologists, and physiologists as well as researchers in drug design and development, proteomics, and molecular medicine with an interest in proteins and peptides.

Author Biography

JOSEPH J. STEPHANOS, PHD, is Associate Professor of Bioinorganic, Biophysical, and Inorganic Chemistry at Menofia University. His research examines metalloprotein chemistry, ligand-binding, and coordination chemistry of biologically active compounds.

ANTHONY W. ADDISON, PHD, is Professor of Inorganic Chemistry at Drexel University. His research focuses on bioinorganic chemistry; chemistry of dioxygen- and NO-binding metalloproteins; and the design, synthesis, and properties of novel chelating agents and macrocyclic and oligonuclear metal complexes. His numerous research articles and conference presentations have earned over 8,000 citations and a Hirsch Index of 37.

Table of Contents

Chapter 1 1

Introduction

Bio-inorganic Chemistry 1

General roles of metal ions in biological system 3

Proteins: Formation, Structure, and Metalloprotins 5

The cell 5

DNA 7

RNA 7

DNA replication 10

mRNA 11

Protein synthesis 12

tRNA 13

Amino acids 14

Polypeptide chains 16

Physiological roles of proteins 16

Primary, secondary, tertiary, quaternary structures and the factors that control each 17

Metalloproteins 23

Enzymes, coenzymes, and cofactors 23

Nicotinamide adenine dinucleitide, NADH 24

Ubiquinone, Coenzyme-Q 24

Flavin mononucleotide, FMN 25

Tetrapyrrolic cofactors, porphyrin, and chlorine 25

Phosphate 26

Comparison between P and S 27

Bioenergetics molecules 28

Suggestions for Further Reading 29

Chapter 2 31

The Alkali and Alkaline Earth Cations

Introduction 31

The roles of Na⁺, and K⁺ in the biological systems 32

The mechanisms for solvent and solute movement through the membrane’s cell 33

Osmosis 34

Passive transport 34

Active transport 36

Na⁺/K⁺ATPas 36

Ionophores (antibiotics) and receptors 40

Synthetic ionophores 42

Crown ether 42

Octopus molecule 43

Lariat ether 43

Cryptand ligands 43

Natural ionophores 44

Macrocyclic Esters 44

Macrotetrolides or Actins 44

Depsipeptide macrocycle 44

Valinomycin 44

Carboxylate ionophores 45

Macrocycles 45

Alamethicin 45

Non-macrocycle 46

Nigericin 46

Monensin 46

Dianemycin 46

Antibiotic X-206 46

Antibiotic X-537A 46

Ionophores and metal selection 47

Stereochemistry of metal-ionophores 50

Nerve impulse 53

Magnesium Enzymes 55

DNA- and RNA- polymerase 55

Pyruvate kinase 57

Phosphoglucomutase 60

Creatine kinase 62

Calcium proteins 64

Calsequestrin 64

Parvalbumin 64

Troponin complex 64

Troponin–C 64

Staphylococcal nuclease 65

Thermolysin 65

Concanavalin A 65

Muscle contractions 66

Magnesium and calcium 66

Suggestion for Further Reading 67

Chapter 3 70

Metalloenzymes

Introduction 70

Metal-Ions acting as Lewis acids in organic reactions 70

Metal-Ions acting as Lewis acids in biological processes 71

Hydrolysis of ethyl glycinate 71

Decarboxylation of oxaloacetic acid 72

Roles of zinc ions in the biological processes 73

Carboxypeptidases 74

Types of carboxypeptidases 74

Requirements to stimulate carboxypeptidase–A, and carboxypeptidase–B 74

Structural features 75

Zinc ion and reactivity 76

Spectral studies 77

The role of Zn (II) in carboxypeptidase–A, and carboxypeptidase–B 78

Models to mimic the role of the metal ion in

carboxypeptidase–A, and carboxypeptidase–B 79

Carbonic Anhydrase 83

Structural and chemical features of carbonic anhydrase 83

The role of the metal ion in carbonic anhydrase 85

Mechanisms that describe the action of carbonic anhydrase 85

Models for the carbonic anhydrase 87

Alcohol Dehydrogenase 88

Role and the chemical structural features of the alcohol dehydrogenase 88

The reaction mechanism of the alcohol dehydrogenase 89

Models for alcohol dehydrogenase 90

Suggestions for further Reading 91

Chapter 4 94

Copper Proteins

Introduction 94

Electronic Spectra of Copper Ions 95

Ground state term 95

Electronic spectral selection rules 96

Spectrochemical Series 97

Jahn–Teller effect 98

Symmetry of Cu²⁺–complexes and the electronic spectra 99

Copper(II)–peptide complexes 102

ESR Spectra of Copper Ions 104

The anisotropic effect 106

Isotropic effect 108

The hyperfine and superhyperfine splitting 109

ESR selection rules 111

The g-values 113

A_ll–g_ll trend 116

Classification of Copper Proteins and significant roles 117

Type-I 120

Plastocyanin 120

Biological function of plastocyanin and the role of the cooper ion 120

The role the polypeptide chain in the biological function of plastocyanin 120

The upper and lower limits of redox potential of  the biological systems 121

Factors that may account for the unusual rapid electron transfer in plastocyanin 123

Azurin 127

Stellacyanin 130

Models for plastocyanin 131

Type-II 132

Superoxide Dismutase and the significant role of metal ion 133

Toxicity of superoxide “O₂” 134

Structural features of superoxide dismutase 136

Type-III 137

Hemocyanin 137

Structures of the active site 137

Biomimetic model for hemocyanin 130

Multiple–type 141

Ascorbic oxidase and the significant of copper ion 141

Model systems 143

Suggestions for further Reading 144

Chapter 5 148

Iron proteins

Introduction 148

Classification of iron proteins 149

Electronic Spectra of Iron Ions 150

Electronic ground states 150

The electronic spectra and the selection role 152

Mössbauer Spectroscopy of Iron Ions 158

Electronic and nuclear resonance absorbance 158

Bases of the Mössbauer spectroscopy 158

Quadrupole splitting 160

Isomer shift 163

ESR Spectra of Iron (III) 165

Advantages of using ESR technique 165

The factors that affect the g–values 166

Iron – Bioavailability 170

Siderophores 175

Role of siderophores 175

Main classes of siderophores 176

The hydroxamates class 176

Ferrichrome family 176

Fluopsin 178

Ferrioxamines family 179

Rhodotorulic acid family 179

Coprogen 180

Aerobactin family 181

Mycobactin family 182

Fusarinine family 182

Phenolate siderophores class 183

2,3–Dihydroxybenzoylglycine (itoic acid) 183

2,3–Dihydroxy–N– benzoyl–L–serine 183

2–N,6–N–Di(2,3–dihydroxybenzoyl)–L–lysine 183

Enterobactin 184

a-Hydroxycarboxylate class 186

Rhizoferrin 186

Mugineic acid 186

Pseudobactin 186

Synthetic siderophores 187

Iron-Storage and Transfer Proteins 188

Ferritin 188

Binding and the release of iron 190

Transferrin 191

Binding Synergism 192

Metal Binding Sites 193

Delivery of iron 193

Mode of ligation influence the Fe³⁺/Fe²⁺ redox–cycle 195

The implications of the mode of ligation on the ESR and the electronic spectra 196

Dioxygenase Iron–Proteins 200

Reactions of O₂-molecule that are catalyzed by metal ion in the biological systems 200

Reaction of organic compounds and oxygen molecules 201

Roles of dioxygenases in the biological systems 201

Intradiol O₂–ase 202

Extradiol O₂–ase 202

Catechol–1,2–dioxygenase 202

Protocatechuate–3, 4–dioxygenase (metapyrocatechase) 203

Protocatechuate–4, 5–dioxygenase 204

Protocatechuate–2, 3–dioxygenase 205

Spectroscopic properties of protocatechuate–3, 4–dioxygenase 205

The active site of protocatechuate–3, 4–dioxygenase 205

Mechanism explain the action of dioxygenase 206

Intradiol dioxygenase 208

Extradiol dioxygenase 210

Intradiol versus extradiol 211

Model system 211

Iron–Sulfur Proteins 212

Roles of iron–sulfur proteins 212

Examples of simple and complex iron sulfur proteins 212

Simple iron sulfur proteins

Rubredoxin 214

Biological roles, sources, and the main characters 214

Spectroscopic features 215

2Fe–2S Ferredoxins 218

Simplest form, sources, structural, and chemical characteristics 218

Iron atoms and the active–center 219

Sulfur of the active site 220

As valence-trapped dimmer 221

Exchang-coupling, J 222

4Fe–4S Ferredoxins and HiPIP 227

Active site and chemical features 227

“High potential iron sulfur protein”, HiPIP 227

Bacterial ferredoxins, Fd 228

Redox potential 228

Active site analogues 230

Aconitase 232

Biological role 232

Active and inactive forms 232

Reaction mechanism 234

Conjugated Fe-S proteins 235

Hydroxylases 236

Hydroxylases and metabolism 236

Chemical properties 236

Mechanism 238

Hydrogenases 239

Biological role 239

Reactions catalyzed by hydrogenase 240

Ni ion and hydrogenase 241

Structural features 242

Dihydrogen and dihydride complexes 244

Mechanism 245

Nitrogenases 247

Biological role 247

Reaction catalyzed by nitrogenase 247

Unfavorable N₂-reduction and the possible pathways 248

Structural and nitrogenase components 249

Role of each components 253

Dinitrogen complexes 255

Possible mechanisms for N₂ fixation 257

Binuclear-Fe-Proteins 261

Examples 261

Hemerythrin 261

Sources 261

Comparison among oxygen-carrier proteins 262

Biological characterizations and the chemical forms 262

Oxygen binding 262

Electronic spectra and magnetic studies 266

Mössbauer data of hemerythrin derivatives 267

Ribotide Reductase 269

Function and Requirements 269

Purple acid phosphate 270

Role and reaction mechanism 270

Methane mono-oxygenase 272

Source and role 272

Chemical properties of diiron enzymes 272

Active sites and model compounds 273

Heme proteins; classification and behavior of heme in absence of globins 276

Prosthetics group 276

Examples and biological role 278

General conformations 279

m-Oxo-diiron(III)heme difficulty 280

Myoglobin and hemoglobin 285

Necessity of oxygen carriers 285

Myoglobin 285

Role and main characters 285

Oxymyoglobin and the observed diamagnetism 286

Axial ligand binding and saturation curve 289

Hemoglobin 290

Properties and biological role 290

Oxygen binding 291

Difficulties in the statistical oxygen binding 298

Bohr effect 298

Quaternary structure and oxygen binding 299

Oxygen binding (Adair constants) in term of the allosteric parameters using Monod-Wyman-and Chaneux model 300

Oxygen binding and homotropic interaction 305

Cytochromes 309

Cytochrome–c 309

Biological function and structural features 309

Adduct formation 310

Electronic spectra 310

Redox reactions 312

Electron transfer mechanism 313

Axial electron transfer, requirements 313

Bond cleavage 313

Metal addition 315

Through ligand 316

Peripheral electron transfer, requirements 318

p–Bonding ligands 320

s–Meso addition 321

Catalases 323

Biological role 323

Mechanism 323

Site of oxidation and axial ligand 326

Models 327

Peroxidase 328

Biological role and examples 328

Biological properties of horseradish peroxidase, HRP 329

Route for HRP' action 330

Example of peroxidase reactions 332

Models 333

Cytochrome p–450 335

Role and properties 335

Electronic spectra 337

p-450 and p420 339

Catalytic cycles for p–450 339

 p-450 versus HRP and cyto. c peroxidase 340

Examples for the action of p-450 342

Electronic Spectra of Hemoproteins 344

Possible electronic transitions 344

Molecular orbital and the molecular energy wave functions of the porphyrin molecule 345

The p ? p optical transitions in the hemoproteins 348

Molecular symmetry orbitals for a simplified iron porphyrin complex without axial ligands 349

Characterization of expected electronic transitions 362

Vibronic excitation, b–band (Q_v), in electronic–spectra of hemoprotein's derivatives 365

Symmetry and 3d orbital of the iron-heme 368

Electronic spectrum of aquomethemoglobin 370

Electronic spectrum of Hb(III)CN 371

Electronic spectrum of Hb(II) 372

Electronic spectrum of Hb(II)CO 373

Electronic spectrum of Hb(II)O₂ 374

ESR Spectra of Hemoproteins 376

ESR and magnetic moment 376

Splitting pattern of d-orbital 376

Rhombicity, tetragonal-field and mode of ligation 378

Distortion, spin orbital interaction, applied magnetic field and g-value 381

Mixed-Spin in hemoproteins 385

Two components spin–systems 385

Quantum–mechanically mixed spin system 386

ESR and reduction of cyto.c in alkaline pH 388

ESR and structural description of cytochrome P-450 389

ESR and nitrosyl hemoproteins 390

Suggestions for further reading 393

Chapter 6 405

Vitamin B₁₂ 405

Structural differences among B₁₂, B_12r, B_12s, B_12a, and B₁₂ coenzyme 405

Enzymatic reactions 407

One carbon transfer 407

Formation of methyl mercury from methyl-B₁₂ 407

Formation of methionine from homocysteine 408

Formation of serine from glycine 409

Conversion of CO₂ to acetate 409

The isomerase reactions 409

1,2-shift reactions and examples 409

The reduction of the –CHOH– group of ribonucleotide 412

Possible mechanisms 412

Substrate dissociation and olefin complex formation 412

Substrate dissociation into radical or carbanion 413

Hydrogen cleavage as hydride, hydrogen atom or proton 414

Chemical properties of B₁₂ 416

Model compounds 417

Suggestions for further reading 418

Chapter 7 420

Chlorophyll 420

Chlorophyll and photosynthesis process 420

Molecular structure and role of chlorophyll 421

Light and dark reactions 424

Structure of the chlorophyll serves its function 428

Model for photosynthetic process and synthetic leaf 429

Environments and chlorophyll association 431

Photo–oxidation of chlorophyll 432

Suggestions for further reading 434