Protein-based Engineered Nanostructures (eBook)

Aitziber L. Cortajarena - CIC BiomaGUNE, Biomolecular Nanotechnology Lab, Donostia-San Sebastián, SpainTijana Z. Grove - Virgina Tech, Department of Chemistry, Blacksburg, VA, USA

Contents 6
1: Protein Design for Nanostructural Engineering: General Aspects 8
1.1 Why Proteins? 8
1.2 Needs for Nanostructuration 9
1.3 About This Book 10
References 12
2: Designed Protein Origami 13
2.1 Protein Architecture 14
2.1.1 Designed Protein Assemblies 16
2.1.2 Tethered Oligomerizing Protein Assemblies 16
2.1.3 Oligomerizing Protein Domain Fusion Strategies 16
2.1.4 Designing New Interaction Surfaces for Assemblies Based on Oligomerizing Domains 17
2.1.5 Repeat Domain Proteins 18
2.1.6 The Importance of Long Range Interactions to Define Complex Shapes 18
2.2 Coiled-Coils as Versatile Building Blocks 19
2.2.1 Basic Structure of Coiled-Coils 19
2.2.2 Functional Role of Coiled-­Coils in Nature 20
2.2.3 Engineered Coiled-Coils 21
2.2.4 Engineering Coiled-Coil Orthogonality 21
2.2.5 Computational Tools for the CC Design 21
2.2.6 Attractive Features of CC Dimers 22
2.3 Designed Protein Origami – Modular Topological Protein Fold 23
2.4 Mathematical Abstraction of Modeling of the Topology of Protein Origami 25
2.4.1 String as an Abstract Model 25
2.4.2 Trigonal Bipyramid 27
2.4.3 Extension and Limits of Topological Single-Chain Polyhedra 27
2.5 Future Opportunities and Challenges in Designed Protein Origami 28
2.5.1 Expansion of the of Designed Polyhedral Shapes 28
2.5.2 In Vivo Folding of Protein Origami 28
2.5.3 Regulation of the Protein Origami (Dis)Assembly 29
2.5.4 Functionalization of Designed Protein Origami 29
2.5.5 Extension of Strategies of DNA Nanotechnology for Polypeptide-Based Nanostructures 29
References 30
3: Two-Dimensional Peptide and Protein Assemblies 34
3.1 Introduction 34
3.2 Two Dimensional Architectures in Nature: Biological S-Layers 36
3.3 2D Layers in Crystal Structures 37
3.4 Peptide Assemblies: Beta Sheet Peptides 40
3.5 Peptide Assemblies: Collagen Based Nanosheets 42
3.6 Peptoid Nanosheets 52
3.7 Peptide Assembly: Boundary Constrained 2D Assembly 54
3.8 Protein Assemblies: Metal-­Stabilized Cytochrome C 1D, 2D, and 3D Assemblies 56
3.9 Protein Assemblies: Fusion Protein Strategies 58
3.10 Protein Assemblies: Computational Design of 2D Assemblies 60
3.11 Conclusions and Outlook 60
References 61
4: Designed Repeat Proteins as Building Blocks for Nanofabrication 66
4.1 Protein-Based Supramolecular Assemblies 67
4.2 Repeat Proteins as Scaffolds for Nanofabrication 67
4.3 Repeat Protein-Based Assemblies 68
4.3.1 Protein Nanofibers 71
4.3.2 Protein Monolayers 73
4.3.3 Protein–Based Thin Films 73
4.4 Repeat Proteins as Scaffolds for Biomolecular Patterning 75
4.4.1 Repeat Proteins as Scaffolds for Patterining Metallic Nanoparticles 75
4.4.2 Repeat Proteins as Scaffolds for Stabilization of Metal Nanoclusters 77
4.4.3 Repeat Proteins as Scaffolds for Patterning Organic Molecules 79
4.5 Summary and Conclusions 81
References 82
5: Assembly, Engineering and Applications of Virus-Based Protein Nanoparticles 87
5.1 Introduction 88
5.2 Virions and Virus Capsids 90
5.2.1 Structure of Virus Capsids 91
5.2.2 Biological Functions of Virus Capsids 94
5.2.3 Physico-Chemical Properties of Virus Capsids 97
5.3 Assembly of Virus Capsids 98
5.3.1 Production of Assembled Virions and VLPs 98
5.3.2 Virus Capsid Assembly in the Infected Cell 101
5.3.3 The Biophysics of Virus Capsid Assembly 103
5.4 Engineering Virus Capsids 106
5.4.1 Genetic Engineering of Virus Capsids 106
5.4.2 Chemical Engineering of Virus Capsids 109
5.5 Engineered Virus Particles for Biomedical, Biotechnological or Nanotechnological Applications 110
5.5.1 Directed Evolution of Peptides and Proteins 111
5.5.2 Novel Vaccines 111
5.5.3 Gene Therapy 112
5.5.4 Virotherapy 113
5.5.5 Specific Chemotherapy Using Targeted Drug Delivery 113
5.5.6 Contrast Agents for Medical Imaging 114
5.5.7 Nanobiosensors 115
5.5.8 Improved Enzymatic Reactions 115
5.5.9 Light Harvesting NPs 115
5.5.10 Templated Synthesis of Inorganic 115
5.5.11 Nanoscale Materials 117
5.6 Engineering Physical and Chemical Stability of Virus Capsids 118
5.6.1 Chemically Engineering Thermal Stability 118
5.6.2 Genetically Engineering Chemical Stability 119
5.6.3 Genetically Engineering Thermostability 119
5.6.4 Genetically Engineering Mechanical Properties 119
5.7 Conclusions 120
References 120
6: Dynamic and Active Proteins: Biomolecular Motors in Engineered Nanostructures 125
6.1 Introduction 125
6.2 Biomolecular Motors and Dynamic Self-­Organizing Proteins 127
6.2.1 Cytoskeletal Proteins 129
6.2.1.1 Actin 130
6.2.1.2 Tubulin 130
6.2.1.3 Bacterial Cytoskeleton 131
6.2.2 Biomolecular Motors: Myosin and Kinesin 132
6.2.2.1 Myosin 133
6.2.2.2 Kinesin 133
6.3 Applications of Molecular Motors in Nanotechnology 134
6.3.1 Transport of Individual Molecules 135
6.3.2 Biosensors 136
6.3.3 Assembly at the Nanoscale 137
6.3.4 Manipulation of Single Molecules 138
6.3.5 Actuation at the Micro and Macro-Scale 139
6.3.6 Modulation of Material Properties 139
6.4 Summary and Conclusions 140
References 140
7: Natural Composite Systems for Bioinspired Materials 146
7.1 Introduction 146
7.2 Biological Materials as Inspiration 147
7.2.1 Bone: A Prototypical Biological Composite 147
7.2.2 Hierarchical Biological Composites of Crustaceans and Nacre forming Mollusks: Evolutionary Context, Formation and Structure 148
7.2.2.1 Nacre Structure and Function 149
7.2.2.2 Nacre Proteins 152
7.2.2.3 Cuticle Function and Structure in Crustaceans 154
7.2.2.4 Cuticle Proteins of Marine Crustaceans 157
7.2.3 Novel Biomimetic Composites 158
7.2.3.1 Design Consideration for Mineral Composite Growth 158
7.2.3.2 Engineered Biomimetic Materials 160
7.3 Conclusion 165
References 166
8: Protein-Based Hydrogels for Tissue Engineering 170
8.1 Structural and Mechanical Properties 170
8.2 Self-Assembly 171
8.3 Stimuli-Responsiveness 173
8.4 Pore Size 174
8.5 Degradation 175
8.6 Biocompatibility 178
8.7 Conclusions 178
References 179
9: Design of Self-Assembling Protein-­Polymer Conjugates 181
9.1 Introduction to Protein-­Polymer Materials 181
9.2 Synthetic Approaches Toward Protein-Polymer Conjugates 182
9.2.1 Peptide/Protein Synthesis and Controlled Radical Polymerization (CRP) 182
9.2.2 General Conjugation Methodology 183
9.2.3 Chemoselective Synthetic Approaches Using Natural Amino Acids 184
9.2.3.1 Lysine Conjugation (Including N-Terminus) 185
9.2.3.2 Cysteine Conjugation 186
9.2.3.3 Tyrosine Conjugation 188
9.2.3.4 Tryptophan Conjugation 189
9.2.4 Chemoselective Synthetic Approaches Using Non-­natural Amino Acids 189
9.2.4.1 Conjugation Reactions with Azides 189
9.2.4.1.1 Azide/Alkyne ‘Click’ Chemisty 189
9.2.4.1.2 Staudinger Ligation 190
9.2.5 Oxime/Hydrazone Chemistry 190
9.2.6 Enzyme-Mediated Conjugation 192
9.2.7 Noncovalent Conjugation Through Protein-Ligand Interactions 193
9.3 Rational Design of Conjugate Architecture and Topology 194
9.3.1 Homodimeric and Heterodimeric Conjugate 194
9.3.2 Y- Junction/Branched Conjugate 195
9.3.3 Star-like Multimeric Conjugate 196
9.3.4 Comb-like Conjugates 196
9.3.5 Controlling Topology Through Protein Design 197
9.3.5.1 Precision Polypeptide Copolymers 198
9.3.5.2 Modular Polypeptide Materials 198
9.3.5.3 Native Protein Copolymer Conjugates 199
9.4 Self-Assembly of Protein-­Polymer Conjugates 201
9.4.1 Block-co-Polymer (BCP) Template-Assisted Patterning of Protein Arrays 201
9.4.2 Direct Self-Assembly into Well-Defined Nanostructures 202
9.4.2.1 Self-Assembly in Solution 202
9.4.2.2 Self-Assembly into Well-­Defined Solid-State Nanostructures 203
9.4.3 Protein-Driven Supramolecular Self-Assembly 204
9.5 Emerging and Potential Applications 206
9.5.1 Biomedical Applications and Drug Delivery 206
9.5.2 Non-Biomedical Applications 206
9.6 Conclusion and Perspectives 208
References 208
10: Design of Redox-Active Peptides: Towards Functional Materials 217
10.1 Introduction 217
10.2 Redox Enzymes 220
10.3 FeS Clusters 222
10.3.1 Models of the FeFe Hydrogenase Catalytic Site 222
10.3.2 Electron Conduits 224
10.4 Design of Porphyrin-Binding Peptides 228
10.5 Two-Electron Carriers 232
10.6 Electrode Surface Modification 235
10.6.1 Adsorption 237
10.6.2 Covalent Binding 238
10.6.3 Affinity Interactions 239
10.6.4 Cross-Linking 239
10.6.5 Entrapment 240
10.7 Conclusions 240
References 241
11: S-Layer-Based Nanocomposites for Industrial Applications 246
11.1 What Are S-Layers? 246
11.2 The Molecular Biology of S-Layer Proteins 249
11.3 General Application Potential of Bacterial S-Layers 251
11.3.1 S-Layer Proteins for Stabilizing Functional Lipid Membranes 252
11.3.2 S-Layer Proteins for the Preparation of Vaccines 253
11.3.3 S-Layer Proteins as Biosensors 253
11.3.4 S-Layer Proteins as Matrix in Bio-Mineralization and Production of Nanoparticles 254
11.3.5 S-Layer Proteins as Filter Materials 255
11.4 S-Layer-Based Coatings and Their Production 256
11.5 New S-Layer-Based Nanomaterials 260
11.5.1 Metal/Metalloid Binding by S-Layers and Their Applications 260
11.5.2 S-Layers as Templates for the Production of Nanostructures 263
11.5.3 S-Layers as Immobilization Matrix for Reactive Nanoparticles 266
11.5.4 S-Layers as Immobilization Matrix for Biofunctional and Organic Molecules 269
References 272
12: Protein Design for Nanostructural Engineering: Concluding Remarks and Future Directions 281
12.1 Conclusions 281
12.2 Future Perspectives 283
Index 285