Coordination Chemistry in Protein Cages

TAKAFUMI UENO is Professor in the School and Graduate School of Bioscience and Biotechnology at Tokyo Institute of Technology. His current research interests involve the molecular design of artificial metalloproteins and exploitation of meso-scale materials with the coordination chemistry of protein assemblies. He was awarded the Young Investigator Award of the Japan Society of Coordination Chemistry in 2007 and the Young Scientists' Prize of the Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology, Japan, in 2008. YOSHIHITO WATANABE is Professor in the Department of Chemistry at Nagoya University. Since 2009, he has been appointed a Vice President of Research and International Affairs. His current research interests include the design of hydrogen peroxide-dependent monooxygenase and construction of metalloenzymes with synthetic complexes at their catalytic centers. He is a recipient of the Chemical Society of Japan Award for Creative Work in 1999, and the Japan Society of Coordination Chemistry in 2011. He sits on two editorial boards and an international advisory board.

Foreword xiii

Preface xv

Contributors xvii

PART I COORDINATION CHEMISTRY IN NATIVE PROTEIN CAGES

1 The Chemistry of Nature’s Iron Biominerals in Ferritin Protein Nanocages 3
Elizabeth C. Theil and Rabindra K. Behera

1.1 Introduction 3

1.2 Ferritin Ion Channels and Ion Entry 6

1.2.1 Maxi- and Mini-Ferritin 6

1.2.2 Iron Entry 7

1.3 Ferritin Catalysis 8

1.3.1 Spectroscopic Characterization of -1,2 Peroxodiferric Intermediate (DFP) 8

1.3.2 Kinetics of DFP Formation and Decay 12

1.4 Protein-Based Ferritin Mineral Nucleation and Mineral Growth 13

1.5 Iron Exit 16

1.6 Synthetic Uses of Ferritin Protein Nanocages 17

1.6.1 Nanomaterials Synthesized in Ferritins 18

1.6.2 Ferritin Protein Cages in Metalloorganic Catalysis and Nanoelectronics 19

1.6.3 Imaging and Drug Delivery Agents Produced in Ferritins 19

1.7 Summary and Perspectives 20

Acknowledgments 20

References 21

2 Molecular Metal Oxides in Protein Cages/Cavities 25
Achim M¨uller and Dieter Rehder

2.1 Introduction 25

2.2 Vanadium: Functional Oligovanadates and Storage of VO2+ in Vanabins 26

2.3 Molybdenum and Tungsten: Nucleation Process in a Protein Cavity 28

2.4 Manganese in Photosystem II 33

2.5 Iron: Ferritins, DPS Proteins, Frataxins, and Magnetite 35

2.6 Some General Remarks: Oxides and Sulfides 38

References 38

PART II DESIGN OF METALLOPROTEIN CAGES

3 De Novo Design of Protein Cages to Accommodate Metal Cofactors 45
Flavia Nastri, Rosa Bruni, Ornella Maglio, and Angela Lombardi

3.1 Introduction 45

3.2 De Novo-Designed Protein Cages Housing Mononuclear Metal Cofactors 47

3.3 De Novo-Designed Protein Cages Housing Dinuclear Metal Cofactors 59

3.4 De Novo-Designed Protein Cages Housing Heme Cofactor 66

3.5 Summary and Perspectives 79

Acknowledgments 79

References 80

4 Generation of Functionalized Biomolecules Using Hemoprotein Matrices with Small Protein Cavities for Incorporation of Cofactors 87
Takashi Hayashi

4.1 Introduction 87

4.2 Hemoprotein Reconstitution with an Artificial Metal Complex 89

4.3 Modulation of the O2 Affinity of Myoglobin 90

4.4 Conversion of Myoglobin into Peroxidase 95

4.4.1 Construction of a Substrate-Binding Site Near the Heme Pocket 95

4.4.2 Replacement of Native Heme with Iron Porphyrinoid in Myoglobin 99

4.4.3 Other Systems Used in Enhancement of Peroxidase Activity of Myoglobin 100

4.5 Modulation of Peroxidase Activity of HRP 102

4.6 Myoglobin Reconstituted with a Schiff Base Metal Complex 103

4.7 A Reductase Model Using Reconstituted Myoglobin 106

4.7.1 Hydrogenation Catalyzed by Cobalt Myoglobin 106

4.7.2 A Model of Hydrogenase Using the Heme Pocket of Cytochrome c 107

4.8 Summary and Perspectives 108

Acknowledgments 108

References 108

5 Rational Design of Protein Cages for Alternative Enzymatic Functions 111
Nicholas M. Marshall, Kyle D. Miner, Tiffany D. Wilson, and Yi Lu

5.1 Introduction 111

5.2 Mononuclear Electron Transfer Cupredoxin Proteins 112

5.3 CuA Proteins 116

5.4 Catalytic Copper Proteins 118

5.4.1 Type 2 Red Copper Sites 118

5.4.2 Other T2 Copper Sites 120

5.4.3 Cu, Zn Superoxide Dismutase 121

5.4.4 Multicopper Oxygenases and Oxidases 122

5.5 Heme-Based Enzymes 124

5.5.1 Mb-Based Peroxidase and P450 Mimics 124

5.5.2 Mimicking Oxidases in Mb 125

5.5.3 Mimicking NOR Enzymes in Mb 127

5.5.4 Engineering Peroxidase Proteins 128

5.5.5 Engineering Cytochrome P450s 129

5.6 Non-Heme ET Proteins 131

5.7 Fe and Mn Superoxide Dismutase 132

5.8 Non-Heme Fe Catalysts 133

5.9 Zinc Proteins 134

5.10 Other Metalloproteins 135

5.10.1 Cobalt Proteins 135

5.10.2 Manganese Proteins 136

5.10.3 Molybdenum Proteins 137

5.10.4 Nickel Proteins 137

5.10.5 Uranyl Proteins 138

5.10.6 Vanadium Proteins 138

5.11 Summary and Perspectives 139

References 142

PART III COORDINATION CHEMISTRY OF PROTEIN ASSEMBLY CAGES

6 Metal-Directed and Templated Assembly of Protein Superstructures and Cages 151
F. Akif Tezcan

6.1 Introduction 151

6.2 Metal-Directed Protein Self-Assembly 152

6.2.1 Background 152

6.2.2 Design Considerations for Metal-Directed Protein Self-Assembly 153

6.2.3 Interfacing Non-Natural Chelates with MDPSA 155

6.2.4 Crystallographic Applications of Metal-Directed Protein Self-Assembly 159

6.3 Metal-Templated Interface Redesign 162

6.3.1 Background 162

6.3.2 Construction of a Zn-Selective Tetrameric Protein Complex Through MeTIR 163

6.3.3 Construction of a Zn-Selective Protein Dimerization Motif Through MeTIR 166

6.4 Summary and Perspectives 170

Acknowledgments 171

References 171

7 Catalytic Reactions Promoted in Protein Assembly Cages 175
Takafumi Ueno and Satoshi Abe

7.1 Introduction 175

7.1.1 Incorporation of Metal Compounds 176

7.1.2 Insight into Accumulation Process ofMetal Compounds 177

7.2 Ferritin as a Platform for Coordination Chemistry 177

7.3 Catalytic Reactions in Ferritin 179

7.3.1 Olefin Hydrogenation 179

7.3.2 Suzuki–Miyaura Coupling Reaction in Protein Cages 182

7.3.3 Polymer Synthesis in Protein Cages 185

7.4 Coordination Processes in Ferritin 188

7.4.1 Accumulation of Metal Ions 188

7.4.2 Accumulation of Metal Complexes 192

7.5 Coordination Arrangements in Designed Ferritin Cages 194

7.6 Summary and Perspectives 197

Acknowledgments 198

References 198

8 Metal-Catalyzed Organic Transformations Inside a Protein Scaffold Using Artificial Metalloenzymes 203
V. K. K. Praneeth and Thomas R. Ward

8.1 Introduction 203

8.2 Enantioselective Reduction Reactions Catalyzed by Artificial Metalloenzymes 204

8.2.1 Asymmetric Hydrogenation 204

8.2.2 Asymmetric Transfer Hydrogenation of Ketones 206

8.2.3 Artificial Transfer Hydrogenation of Cyclic Imines 208

8.3 Palladium-Catalyzed Allylic Alkylation 211

8.4 Oxidation Reaction Catalyzed by Artificial Metalloenzymes 212

8.4.1 Artificial Sulfoxidase 212

8.4.2 Asymmetric cis-Dihydroxylation 215

8.5 Summary and Perspectives 216

References 218

PART IV APPLICATIONS IN BIOLOGY

9 Selective Labeling and Imaging of Protein Using Metal Complex 223
Yasutaka Kurishita and Itaru Hamachi

9.1 Introduction 223

9.2 Tag–Probe Pair Method Using Metal-Chelation System 225

9.2.1 Tetracysteine Motif/Arsenical Compounds Pair 225

9.2.2 Oligo-Histidine Tag/Ni(ii)-NTA Pair 227

9.2.3 Oligo-Aspartate Tag/Zn(ii)-DpaTyr Pair 230

9.2.4 Lanthanide-binding Tag 235

9.3 Summary and Perspectives 237

References 237

10 Molecular Bioengineering of Magnetosomes for Biotechnological Applications 241
Atsushi Arakaki, Michiko Nemoto, and Tadashi Matsunaga

10.1 Introduction 241

10.2 Magnetite Biomineralization Mechanism in Magnetosome 242

10.2.1 Diversity of Magnetotactic Bacteria 242

10.2.2 Genome and Proteome Analyses of Magnetotactic Bacteria 244

10.2.3 Magnetosome Formation Mechanism 246

10.2.4 Morphological Control of Magnetite Crystal in Magnetosomes 250

10.3 Functional Design of Magnetosomes 251

10.3.1 Protein Display on Magnetosome by Gene Fusion Technique 252

10.3.2 Magnetosome Surface Modification by In Vitro System 255

10.3.3 Protein-mediated Morphological Control of Magnetite Particles 257

10.4 Application 258

10.4.1 Enzymatic Bioassays 259

10.4.2 Cell Separation 260

10.4.3 DNA Extraction 262

10.4.4 Bioremediation 264

10.5 Summary and Perspectives 266

Acknowledgments 266

References 266

PART V APPLICATIONS IN NANOTECHNOLOGY

11 Protein Cage Nanoparticles for Hybrid Inorganic–Organic Materials 275
Shefah Qazi, Janice Lucon, Masaki Uchida, and Trevor Douglas

11.1 Introduction 275

11.2 Biomineral Formation in Protein Cage Architectures 277

11.2.1 Introduction 277

11.2.2 Mineralization 278

11.2.3 Model for Synthetic Nucleation-Driven Mineralization 279

11.2.4 Mineralization in Dps: A 12-Subunit Protein Cage 279

11.2.5 Icosahedral Protein Cages: Viruses 282

11.2.6 Nucleation of Inorganic Nanoparticles Within Icosahedral Viruses 282

11.3 Polymer Formation Inside Protein Cage Nanoparticles 283

11.3.1 Introduction 283

11.3.2 Azide–Alkyne Click Chemistry in sHsp and P22 285

11.3.3 Atom Transfer Radical Polymerization in P22 287

11.3.4 Application as Magnetic Resonance Imaging Contrast Agents 290

11.4 Coordination Polymers in Protein Cages 292

11.4.1 Introduction 292

11.4.2 Metal–Organic Branched Polymer Synthesis by Preforming Complexes 292

11.4.3 Coordination Polymer Formation from Ditopic Ligands and Metal Ions 295

11.4.4 Altering Protein Dynamics by Coordination: Hsp-Phen-Fe 296

11.5 Summary and Perspectives 298

Acknowledgments 298

References 298

12 Nanoparticles Synthesized and Delivered by Protein in the Field of Nanotechnology Applications 305
Ichiro Yamashita, Kenji Iwahori, Bin Zheng, and Shinya Kumagai

12.1 Nanoparticle Synthesis in a Bio-Template 305

12.1.1 NP Synthesis by Cage-Shaped Proteins for Nanoelectronic Devices and Other Applications 305

12.1.2 Metal Oxide or Hydro-Oxide NP Synthesis in the Apoferritin Cavity 307

12.1.3 Compound Semiconductor NP Synthesis in the Apoferritin Cavity 308

12.1.4 NP Synthesis in the Apoferritin with the Metal-Binding Peptides 311

12.2 Site-Directed Placement of NPs 312

12.2.1 Nanopositioning of Cage-Shaped Proteins 312

12.2.2 Nanopositioning of Au NPs by Porter Proteins 313

12.3 Fabrication of Nanodevices by the NP and Protein Conjugates 317

12.3.1 Fabrication of Floating Nanodot Gate Memory 318

12.3.2 Fabrication of Single-Electron Transistor Using Ferritin 321

References 326

13 Engineered “Cages” for Design of Nanostructured Inorganic Materials 329
Patrick B. Dennis, Joseph M. Slocik, and Rajesh R. Naik

13.1 Introduction 329

13.2 Metal-Binding Peptides 331

13.3 Discrete Protein Cages 332

13.4 Heat-Shock Proteins 334

13.5 Polymeric Protein and Carbohydrate Quasi-Cages 340

13.6 Summary and Perspectives 346

References 347

PART VI COORDINATION CHEMISTRY INSPIRED BY PROTEIN CAGES

14 Metal–Organic Caged Assemblies 353
Sota Sato and Makoto Fujita

14.1 Introduction 353

14.2 Construction of Polyhedral Skeletons by Coordination Bonds 355

14.2.1 Geometrical Effect on Products 356

14.2.2 Structural Extension Based on Rigid, Designable Framework 358

14.2.3 Mechanistic Insight into Self-Assembly 366

14.3 Development of Functions via Chemical Modification 366

14.3.1 Chemistry in the Hollow of Cages 367

14.3.2 Chemistry on the Periphery of Cages 368

14.4 Metal–Organic Cages for Protein Encapsulation 370

14.5 Summary and Perspectives 370

References 371

Index 375