List of Contributors xv
1 What Are Bionanocomposites? 1
Agathe Urvoas, Marie ValerioLepiniec, Philippe Minard and Cordt Zollfrank
1.1 Introduction 1
1.2 A Molecular Perspective: Why Biological Macromolecules? 3
1.3 Challenges for Bionanocomposites 3
References 6
2 Molecular Architecture of Living Matter 9
2.1 Nucleic Acids 11
Enora Prado, Mónika ÁdokSipiczki and Corinne Nardin
2.1.1 Introduction: A Bit of History 11
2.1.2 Definition and Structure 12
2.1.2.1 Nomenclature 12
2.1.2.2 Structure 13
2.1.3 DNA and RNA Functions 15
2.1.3.1 Introduction 15
2.1.3.2 TranscriptionTranslation Process 16
2.1.3.3 Replication Process 18
2.1.4 Specific Secondary Structures 19
2.1.4.1 WatsonCrick HBonds 19
2.1.4.1.1 StemLoop 19
2.1.4.1.2 Kissing Complex 20
2.1.4.2 Other Kinds of HBonding 21
2.1.4.2.1 GQuartets 21
2.1.4.2.2 iMotifs 23
2.1.5 Stability 23
2.1.6 Conclusion 25
References 25
2.2 Lipids 29
Carole Aimé and Thibaud Coradin
2.2.1 Lipids SelfAssembly 29
2.2.2 Structural Diversity of Lipids 30
2.2.2.1 Fatty Acyls (FA) 30
2.2.2.2 Glycerolipids (GL) 32
2.2.2.3 Glycerophospholipids (GP) 32
2.2.2.4 Sphingolipids (SP) 33
2.2.2.5 Sterol Lipids (ST) 34
2.2.2.6 Prenol Lipids (PR) 34
2.2.2.7 Saccharolipids (SL) 35
2.2.2.8 Polyketides (PK) 35
2.2.3 Lipid Synthesis and Distribution 35
2.2.4 The Diversity of Lipid Functions 36
2.2.4.1 Cellular Architecture 37
2.2.4.2 Lipid Rafts 37
2.2.4.3 Energy Storage 37
2.2.4.4 Regulating Membrane Proteins by ProteinLipid Interactions 39
2.2.4.5 Signaling Functions 39
2.2.5 Lipidomics 39
References 40
2.3 Carbohydrates 41
Mirjam Czjzek
2.3.1 Introduction 41
2.3.2 Monosaccharides 42
2.3.3 Oligosaccharides 44
2.3.3.1 Disaccharides 44
2.3.3.2 Protein Glycosylations 46
2.3.4 Polysaccharides 47
2.3.4.1 Cellulose 49
2.3.4.2 Hemicelluloses 50
2.3.4.2.1 Xyloglucan 50
2.3.4.2.2 Xylan 50
2.3.4.2.3 Mannan or Glucomannan 52
2.3.4.2.4 MixedLinkage Glucan (MLG) 52
2.3.4.3 Pectins 53
2.3.4.4 Chitin 54
2.3.4.5 Alginate 54
2.3.4.6 Marine Galactans 55
2.3.4.7 Storage Polysaccharides: Starch, Glycogen, and Laminarin 55
References 56
2.4 Proteins: From Chemical Properties to Cellular Function: A Practical Review of Actin Dynamics 59
Stéphane Romero and FrançoisXavier CampbellValois
2.4.1 Introduction 59
2.4.2 Molecular Architecture of Proteins 59
2.4.2.1 Amino Acids 60
2.4.2.2 Peptide Bond 60
2.4.2.3 Primary Structure 64
2.4.3 Protein Folding 66
2.4.3.1 Peptide and Protein: Secondary Structure 66
2.4.3.2 3D Folding: Tertiary Structure 67
2.4.3.3 Quaternary Structure 68
2.4.3.4 Protein Folding and De Novo Design 70
2.4.4 Interacting Proteins for Cellular Functions 73
2.4.4.1 Protein Interactions 73
2.4.4.2 Enzymatic Activity of Proteins 75
2.4.4.3 Molecular Motors 77
2.4.5 Self Assembly and AutoOrganization: Regulation of the Actin Cytoskeleton Assembly 78
2.4.5.1 Origin of the Actin Treadmilling 79
2.4.5.2 Regulation of Actin Treadmilling 83
2.4.5.3 Arp2/3 and ForminInitiated Actin Assembly to Generate Mechanical Forces 83
2.4.5.4 SelfOrganization Properties and Force Generation Understood Using In Vitro Reconstituted ActinBased Nanomovements 85
2.4.5.5 Applications in Bionanotechnologies 85
2.4.6 Conclusion 87
References 88
3 Functional Biomolecular Engineering 93
3.1 Nucleic Acid Engineering 95
Enora Prado, Mónika ÁdokSipiczki and Corinne Nardin
3.1.1 Introduction 95
3.1.2 How to Synthetically Produce Nucleic Acids? 95
3.1.2.1 The Chemical Approach 95
3.1.2.2 Polymerase Chain Reaction 96
3.1.2.3 Combinatorial Synthesis of Oligonucleotides and Gene Libraries: Aptamers 100
3.1.3 Secondary Structures in Nanotechnologies 102
3.1.3.1 WatsonCrick HBonds 102
3.1.3.1.1 StemLoop 102
3.1.3.1.2 Kissing Complex 103
3.1.3.2 Other Kind of HBonding 103
3.1.3.2.1 GQuartets 103
3.1.3.2.2 Origami: Nanoarchitecture on Surface 105
3.1.4 Conclusion 108
References 108
3.2 Protein Engineering 113
Agathe Urvoas, Marie ValerioLepiniec and Philippe Minard
3.2.1 Synthesis of Polypeptides: Chemical or Biological Approach? 113
3.2.2 Proteins: From Natural to Artificial Sources 114
3.2.2.1 How to Get the Coding Sequence of the Protein of Interest? 114
3.2.2.2 E. coli: A Cheap Protein Factory with a Diversified Tool Box 114
3.2.2.3 Common Expression Plasmids 116
3.2.2.4 Limits of Recombinant Protein Expression in E. coli 117
3.2.2.5 Some Solutions Are Available to Solve these Expression Problems 118
3.2.3 Proteins: A Large Repertoire of Functional Objects 118
3.2.3.1 Looking for Natural Proteins with Desired Function 118
3.2.3.2 From Protein Engineering to Protein Design 119
3.2.3.2.1 Modified Proteins Are Often Destabilized 119
3.2.3.2.2 Natural or Engineered Proteins: From Small Step to Giant Leap in Sequence Space 120
3.2.3.2.3 Computational Protein Design 120
3.2.3.2.4 Directed Evolution: A Diverse Repertoire Combined with a Selection Process 121
3.2.3.3 Combining Chemistry with Biological Objects 123
3.2.3.3.1 Labeling Natural Amino Acids 123
3.2.3.3.2 Bioorthogonal Labeling 123
3.2.3.3.3 TagMediated Labeling and Enzymatic Coupling 125
3.2.3.3.4 EnzymeMediated Ligation 126
3.2.3.3.5 Quality Control of Labeled Biomolecules 126
References 126
4 The Composite Approach 129
4.1 Inorganic Nanoparticles 131
Carole Aimé and Thibaud Coradin
4.1.1 Introduction 131
4.1.2 Overview of Inorganic Nanoparticles 132
4.1.3 Synthesis of Inorganic Nanoparticles 132
4.1.3.1 Basic Principles 132
4.1.3.2 Nanoparticles from Solutions 138
4.1.3.2.1 Ionic Solids 138
4.1.3.2.2 Metals 139
4.1.3.2.3 Metal Oxides 140
4.1.3.2.4 Morphological Control 144
4.1.4 Some Specific Properties of Inorganic Nanoparticles 145
4.1.5 Concluding Remarks 149
References 149
4.2 Hybrid Particles: Conjugation of Biomolecules to Nanomaterials 153
Nikola ?. Kne?evi, Laurence Raehm and JeanOlivier Durand
4.2.1 General Considerations 153
4.2.2 Functionalization of Nanoparticle Surface 154
4.2.2.1 Functionalization of Hydroxylated Surfaces 154
4.2.2.2 Functionalization of HydrideContaining Surfaces 154
4.2.2.3 Functionalization of MetalContaining Nanoparticles 155
4.2.2.4 Functionalization of CarbonBased Nanomaterials 155
4.2.3 LinkerMediated Conjugation of Biomolecules to Nanoparticles 155
4.2.3.1 Conjugation through Carbodiimide Chemistry 155
4.2.3.2 Carbamate, Urea, and Thiourea Linkage 156
4.2.3.3 Schiff Base Linkage 158
4.2.3.4 Multicomponent Linkage Formation 159
4.2.3.5 Biofunctionalization through Alkylation 160
4.2.3.6 Bioorthogonal Linkage Formation 161
4.2.3.7 Conjugation through HostGuest Interactions 162
4.2.3.8 Linkage through Metal Coordination 162
4.2.3.9 Ligation through Complementary Base Pairing 164
4.2.3.10 Electrostatic Interactions 164
4.2.4 Conclusions 164
Acknowledgments 165
References 165
4.3 Biocomposites from Nanoparticles: From 1D to 3D Assemblies 169
Carole Aimé and Thibaud Coradin
4.3.1 General Considerations 169
4.3.2 OneDimensional Bionanocomposites 170
4.3.3 TwoDimensional Organization of Nanoparticles 175
4.3.4 ThreeDimensional Organization of Particles 175
4.3.5 Conclusion and Perspectives 180
References 180
5 Applications 185
5.1 Optical Properties 187
Cordt Zollfrank and Daniel Van Opdenbosch
5.1.1 Introduction 187
5.1.2 Interactions of Light with Matter 189
5.1.3 Optics at the Nanoscale 190
5.1.3.1 Nanoscale Optical Processes 190
5.1.3.2 Nanoscale Confinement of Matter 191
5.1.3.3 Nanoscale Confinement of Radiations 191
5.1.4 Optical Properties of Bionanocomposites 191
5.1.4.1 Absorption Properties of Bionanocomposites 192
5.1.4.2 Emission Properties of Bionanocomposites 195
5.1.4.3 Structural Colors with Bionanocomposites 200
5.1.5 Conclusions 201
References 202
5.2 Magnetic Bionanocomposites: Current Trends, Scopes, and Applications 205
Wei Li, Yuehan Wu, Xiaogang Luo and Shilin Liu
5.2.1 Introduction 205
5.2.2 Construction Strategies for Magnetic Biocomposites 208
5.2.2.1 The Blending Method 208
5.2.2.2 In Situ Synthesis Method 209
5.2.2.3 Graftingonto Method 210
5.2.3 Applications of Magnetic Biocomposites 212
5.2.3.1 Environmental Applications 212
5.2.3.1.1 Removal of Toxic Metal Ions 212
5.2.3.1.2 Removal of Dyes 216
5.2.3.1.3 Biocatalysis and Bioremediation 216
5.2.3.2 Biomedical Applications 218
5.2.3.2.1 Magnetic Resonance Imaging (MRI) 218
5.2.3.2.2 Cellular Therapy and Labeling 219
5.2.3.2.3 Tissue Engineering Applications 221
5.2.3.2.4 Drug Delivery 221
5.2.3.2.5 Tissue Regeneration 224
5.2.3.3 Biotechnological and Bioengineering Applications 225
5.2.3.3.1 Biosensing 226
5.2.3.3.2 Magnetically Responsive Films 228
5.2.4 Concluding Remarks and Future Trends 228
Acknowledgments 229
References 229
5.3 Mechanical Properties of Natural Biopolymer Nanocomposites 235
Biqiong Chen
5.3.1 Introduction 235
5.3.2 Overview of Mechanical Properties of Polymer Nanocomposites and Their Measurement Methods 237
5.3.3 Solid Biopolymer Nanocomposites 237
5.3.4 Porous Biopolymer Nanocomposites 245
5.3.5 Biopolymer Nanocomposite Hydrogels 247
5.3.6 Conclusions 249
References 251
5.4 Bionanocomposite Materials for Biocatalytic Applications 257
Sarah Christoph and Francisco M. Fernandes
5.4.1 Bionanocomposites and Biocatalysis 257
5.4.2 Form and Function in Bionanocomposite Materials for Biocatalysis 260
5.4.2.1 Bionanocomposites Structure 260
5.4.2.1.1 Biopolymers 260
5.4.2.1.2 The Inorganic Fraction 264
5.4.2.2 Key Biocatalysts 269
5.4.2.2.1 Nucleotides and Amino Acids 269
5.4.2.2.2 Enzymes 272
5.4.2.2.3 Whole Cells 273
5.4.3 Applications 277
5.4.3.1 Biosynthesis 277
5.4.3.2 Sensing Applications 281
5.4.3.3 Environmental Applications 283
5.4.3.4 Energy Applications of Biocatalytic Bionanocomposites 286
5.4.4 Conclusions and Perspectives 289
References 290
5.5 Nanocomposite Biomaterials 299
Gisela Solange Alvarez and Martín Federico Desimone
5.5.1 Introduction 299
5.5.2 Natural Nanocomposites 301
5.5.2.1 Cellulosic Materials 301
5.5.2.2 Chitosan 305
5.5.2.3 Alginate 305
5.5.2.4 Collagen 307
5.5.2.5 Gelatin 307
5.5.2.6 Silk Fibroin 309
5.5.3 Synthetic Nanocomposites 309
5.5.3.1 PLLA and PLGA 309
5.5.3.2 Polyethylene Glycol 312
5.5.3.3 Methacrylate 312
5.5.3.4 Polyvinyl Alcohol 314
5.5.3.5 Polyurethanes 314
5.5.4 Conclusions 315
Acknowledgments 317
References 317
6 A Combination of Characterization Techniques 321
Carole Aimé and Thibaud Coradin
6.1 Introductory Remarks 321
6.2 Chemical Analyses 322
6.2.1 Inductively Coupled Plasma 322
6.2.2 Infrared Spectroscopy 323
6.2.3 XRay Photoelectron Spectroscopy and Auger Electron Spectroscopy 324
6.2.4 EnergyDispersive XRay Spectroscopy and ElectronEnergy Loss Spectroscopy 328
6.3 Determining Size and Structure 329
6.3.1 Imaging 329
6.3.1.1 Electron Microscopy 330
6.3.1.2 Atomic Force Microscopy 333
6.3.2 Scattering Techniques 335
6.3.2.1 Small Angle Scattering 337
6.3.2.2 Dynamic Light Scattering and Zetametry 337
6.3.3 Monitoring ParticleBiomolecule Interactions 339
6.3.3.1 Electrophoresis 339
6.3.3.2 Circular Dichroism Spectroscopy 340
6.3.3.3 Isothermal Titration Calorimetry and Surface Plasmon Resonance 342
6.4 Materials Properties 344
6.4.1 Optical Properties 344
6.4.2 Mechanical Testing 346
6.4.2.1 Rheology 346
6.4.2.2 Compression Tests 347
6.4.2.3 Tensile Tests 348
6.4.2.4 Relaxation Tests 348
6.4.2.5 Dynamic Mechanical Analysis 349
6.4.2.6 Indentation 349
6.4.2.7 Mechanical Testing of Hydrogels 349
6.4.3 Magnetic Measurements 350
6.4.4 Biological Properties 353
References 355
Index 359
