Coordination chemistry in protein cages: principles, design, and applications (Hoboken, 2013). - ОГЛАВЛЕНИЕ / CONTENTS

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ОбложкаCoordination chemistry in protein cages: principles, design, and applications / ed. by T.Ueno, Y.Watanabe. - Hoboken: Wiley, 2013. - xix, 387 p., [6] l. ill.: ill. - Bibliogr. at the end of the chapters. - Ind.: p.375-387. - ISBN 978-1-118-07857-0
 

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Оглавление / Contents
 
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 μ-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 Müler 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, Omella 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 с ................................ 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
Rreferences ................................................... 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 of Metal
               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 ds-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 Malsunaga
   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 Moфhological 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 Вioassays ............................ 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


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