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

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  • Format: Hardcover
  • Copyright: 4/22/2013
  • Publisher: Wiley
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Written by highly respected pioneers in the field, Coordination Chemistry in Protein Cages addresses the assembly of and reactions inside protein cages, a rapidly developing area of chemistry. Logically organized into four parts (Coordination Chemistry in Native Protein Cages, Coordination Chemistry to Design Artificial Protein Functions, Applications in Biology, and Applications in Nanotechnology), the text addresses a new chemical approach in the synthesis of bioinorganic molecules which has been applied in a wide variety fields, including catalysis, biomedicine, and electronics.

Author Biography

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.

Table of Contents

Profs. T. Ueno and Y. Watanabe

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 μ-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 Müller 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

7.1 Introduction

7.1.1 Incorporation of metal compounds

7.1.1 Incorporation of metal compounds

7.1.2 Insight into accumulation process of metal compounds

7.2 Ferritin 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

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