Coordination Chemistry in Protein Cages – Principles, Design, and Applications

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.

Preface Profs. T. Ueno and Y. Watanabe Foreword Harry B. Gray Part 1. Coordination Chemistry in Native Protein Cages 1. The Chemistry of Nature's Iron Biominerals in Ferritin Protein Nanocages Elizabeth C. Theil and Rabindra K. Behera 1.1 Introduction 1.2 Ferritin ion channels and ion entry 1.2.1 Maxi and Mini Ferritin 1.2.2 Iron Entry 1.3 Ferritin catalysis 1.3.1 Spectroscopic characterization of mu-1,2 peroxodiferric intermediate (DFP) 1.3.2 Kinetics of DFP formation and decay 1.4 Protein based-ferritin mineral nucleation and mineral growth 1.5 Iron Exit 1.6 Synthetic uses of ferritin protein nanocages 1.6.1 Nanomaterials synthesized in ferritins 1.6.2 Ferritin protein cages in metalloorganic catalysis and nanoelectronics 1.6.3 Imaging and drug delivery agents produced in ferritins 1.7.Summary and Perspective 2. Molecular Metal Oxides in Protein Cages/Cavities Achim Muller and Dieter Rehder 2.1 Introduction 2.2 Vanadium: Functional Oligovanadates and Storage of VO2+ in Vanabins 2.3 Molybdenum and Tungsten: Nucleation Processes in a Protein Cavity 2.4 Manganese in Photosystem II 2.5 Iron: Ferritins, Dps Proteins, Frataxins and Magnetite 2.6 Some General Remarks: Oxides and Sulfides Part 2. Design of Metalloprotein Cages 3. De novo Design of Protein Cages to Accommodate metal cofactors Flavia Nastri, Rosa Bruni, Ornella Maglio and Angela Lombardi 3.1 Introduction 3.2 De novo designed protein cages housing mono-nuclear metal cofactors 3.3 De novo designed protein cages housing di-nuclear metal cofactors. 3.4 De novo designed protein cages housing heme cofactors. 3.5 Conclusions and Perspectives 4. Generation of Functionalized Biomolecules Using Hemoprotein Matrices with Small Protein Cavities for Incorporation of Cofactors Takashi Hayashi 4.1 Introduction 4.2 Hemoprotein Reconstitution with an Artificial Metal Complex 4.3 Modulation of the O2 affinity of myoglobin 4.4 Conversion of myoglobin into peroxidase 4.4.1 Construction of a substrate-binding site near the heme pocket 4.4.2 Replacement of native heme with iron porphyrinoid in myoglobin 4.4.3 Other systems used in enhancement of peroxidase activity of myoglobin 4.5 Modulation of peroixdase activity of HRP 4.6 Myoglobin reconstituted with a Schiff base metal complex 4.7 A reductase model using reconstituted myoglobin 4.7.1 Hydrogenation catalyzed by cobalt myoglobin 4.7.2 A model of hydrogenase using the heme pocket of cytochrome c 4.8 Conclusion 5. Rational Design of Protein Cages for Alternative Enzymatic Functions Nicolas Marshall, Kyle D. Miner, Tiffany D. Wilson and Yi Lu 5.1 Introduction 5.2 Mononuclear Electron Transfer Cupredoxin Proteins 5.3 CuA Proteins 5.4 Catalytic Copper Proteins 5.4.1 Type 2 Red Copper Sites 5.4.2 Other T2 Copper Sites 5.4.3 Cu, Zn Superoxide Dismutase 5.4.4 Multicopper Oxygenases and Oxidases 5.5 Heme-based Enzymes 5.5.1 Mb based peroxidase and p450 mimics 5.5.2 Mimicking Oxidases in Mb 5.5.3 Mimicking NOR enzymes in Mb 5.5.4 Engineering peroxidase proteins 5.5.5 Engineering cytochrome p450s 5.6 Non-heme ET proteins 5.7 Fe and Mn superoxide dismutase (SOD) 5.8 Non-heme Fe catalysts 5.9 Zinc proteins 5.10 Other Metalloproteins 5.10.1 Cobalt proteins 5.10.2 Manganese proteins 5.10.3 Molybdenum proteins 5.10.4 Nickel proteins 5.10.5 Uranyl proteins 5.10.6 Vanadium proteins 5.11 Conclusions and Future Directions Part 3. Coordination chemistry of protein assembly cages 6. Metal-Directed and Templated Assembly of Protein Superstructures and Cages F. Akif Tezcan 6.1 Introduction 6.2 Metal-Directed Protein Self-Assembly 6.2.1 Background 6.2.2 Design Considerations for Metal-Directed Protein Self-Assembly 6.2.3 Interfacing Non-Natural Chelates with MDPSA 6.2.4 Crystallographic Applications of Metal-Directed Protein Self-Assembly 6.3 Metal-Templated Interface Redesign 6.3.1 Background 6.3.2 Construction of a Zn-Selective Tetrameric Protein Complex through MeTIR 6.3.3 Construction of a Zn-Selective Protein Dimerization Motif through MeTIR 6.4 Conclusion 7. Catalytic Reactions Proceeded in Protein Assembly Cages Takafumi Ueno and Satoshi Abe 7.1Introduction 7.1.1Incorporation of metal compounds 7.1.1 Incorporation of metal compounds 7.1.2 Insight into accumulation process of metal compounds 7.2Ferritin as a platform for coordination chemistry 7.3 Catalytic reaction in ferritin 7.3.1 Olefin hydrogenation 7.3.2 Suzuki-Miyaura coupling 7.3.3 Polymer synthesis 7.4 Coordination process in ferritin 7.4.1 Metal ions 7.4.2 Metal complexes 7.4.3 Various coordination geometries designed in ferritin 7.5 Summary and Perspectives 8. Metal-Catalyzed Organic Transformations inside a Protein scaffold Using Artificial Metalloenzymes V. K. K. Praneeth and Thomas R. Ward 8.1 Introduction 8.2 Enantioselective reduction reactions catalyzed by artificial metalloenzymes 8.2.1 Asymmetric hydrogenation 8.2.2 Asymmetric transfer hydrogenation of ketones 8.2.3 Artificial transfer hydrogenation of cyclic imines 8.3 Palladium catalyzed allylic alkylation 8.4 Oxidation reaction catalyzed by artificial metalloenzymes 8.4.1 Artificial sulfoxidase 8.4.2 Asymmetric cis-dihydroxylation 8.5 Perspectives Part 4. Applications in biology 9. Selective Labeling and Imaging of Protein Using Metal Complex Yasutaka Kurishita and Itaru Hamachi 9.1 Introduction 9.2 Tag-Probe Pair Method Using Metal-Chelation System 9.2.1 Tetracysteine Motif/Arsenical Compounds Pair 9.2.2 Oligo-Histidine Tag/Ni(II)-NTA Pair 9.2.3 Oligo-Aspartate Tag/Zn(II)-DpaTyr Pair 9.2.4 Lanthanide Binding Tag 9.3 Conclusion 10. Molecular Bioengineering of Magnetosomes for Biotechnological Applications Atsushi Arakaki, Michiko Nemoro and Tadashi Matsunaga 10.1 Introduction 10.2 Magnetite biomineralization mechanism in magnetosome 10.2.1 Diversity of magnetotactic bacteria 10.2.2 Genome and proteome analyses of magnetotactic bacteria 10.2.3 Magnetosome formation mechanism 10.2.4 Morphological control of magnetite crystal in magnetosomes 10.3 Functional design of magnetosomes 10.3.1 Protein display on magnetosome by gene fusion technique 10.3.2 Magnetosome surface modification by in vitro system 10.3.3 Protein-mediated morphological control of magnetite particles 10.4 Application 10.4.1 Enzymatic bioassays 10.4.2 Cell separation 10.4.3 DNA extraction 10.4.4 Bioremediation 10.5 Concluding remarks Part 5. Applications in nanotechnology 11. Protein Cage Nanoparticles for Hybrid Inorganic-Organic Materials Shefah Qazi, Janice Lucon, Masaki Uchida and Trevor Douglas 11.1 Introduction 11.2 Biomineral Formation in Protein Cage Architectures 11.2.1 Introduction 11.2.2 Mineralization 11.2.3 Model for Synthetic Nucleation Driven Mineralization 11.2.4 Mineralization in Dps -- a 12 Subunit Protein Cage 11.2.5 Icosahedral Protein Cages -- Viruses 11.2.6 Nucleation of inorganic Nanoparticles Within Icosahedral Viruses 11.3 Polymer Formation inside Protein Cages Nanoparticles (PCNs) 11.3.1 Introduction 11.3.2 Azide-Alkyne Click Chemistry (AACC) in sHsp and P22 11.3.3 Atom Transfer Radical Polymerization (ATRP) in P22 11.3.4 Application as Magnetic Resonance Imaging Contrast Agents (MRI-CAs) 11.4 Coordination Polymers in Protein Cages 11.4.1 Introduction 11.4.2 Metal-Organic Branched Polymer Synthesis by Pre-Forming Complexes 11.4.3 Coordination Polymer Formation from Ditopic Ligands and Metal Ions 11.4.4 Altering Protein Dynamics by Coordination: Hsp-Phen-Fe 11.5 Conclusion 12. Nanoparticles Synthesized and Delivered by Protein in the Field of Nanotechnology Applications Ichiro Yamashita, Kenji Iwahori, Bin Zheng, Shinya Kumagai 12.1.1 Nano particles (NPs) synthesis in a bio-template 12.1.1 NPs synthesis by cage-shaped proteins for nanoelectronic devices and other applications. 12.1.2 Metal oxide or hydro-oxide NP synthesis in the apoferritin cavity 12.1.3 Compound semiconductor NP synthesis in the apoferritin cavity 12.1.4 NPs synthesis in the apoferritin with the metal binding peptides 12.2 Site-directed placement of NPs 12.2.1 Nano-positioning of cage-shaped proteins 12.2.2 Nano-positioning of by porter proteins 12.3 Fabrication of nanodevices by the NP and protein conjugates 12.3.1 Fabrication of floating nanodot gate memory 12.3.2 Fabrication of single electron transistor using ferritin 13. Engineered "Cages" for Design of Nanostructured Inorganic Materials Patrick B. Dennis, Joseph M. Slocik and Rajesh R. Naik 13.1 Introduction 13.2 Metal-binding peptides 13.3 Discrete protein cages 13.4 Heat Shock proteins 13.5 Polymeric protein and carbohydrate quasi-cages 13.6 Conclusion Part 6. Coordination chemistry inspired by protein cages 14. Metal-organic Caged Assemblies Sota Sato and Makoto Fujita 14.1 Introduction 14.2 Construction of polyhedral skeletons by coordination bonds 14.2.1 Geometrical effect on products 14.2.2 Structural extension based on rigid, designable framework 14.2.3 Mechanistic insight into self-assembly 14.3 Development of functions via chemical modification 14.3.1 Chemistry in the hollow of cages 14.3.2 Chemistry on the periphery of cages 14.4 Toward a cage for a protein 14.5 Conclusion