Bionanocomposites

CAROLE AIMÉ is a CNRS researcher working in Thibaud Coradin's group in the Laboratoire de Chimie de la Matière Condensée de Paris. After she received a Ph.D. working on self-assembling amphiphilic systems in Reiko Oda's group in Bordeaux University-France, she joined Pr. Nobuo Kimizuka's group in Kyushu University-Japan, where she designed functional coordination nanoparticles from nucleotides and lanthanide ions. She is now developing bio-inspired systems made up of inorganic nanoparticles and biopolymers. THIBAUD CORADIN has been Directeur de Recherche at the CNRS since 2007. He is currently leading the Materials and Biology group in the Laboratoire de Chimie de la Matière Condensée de Paris (UPMC-Paris 06). His research topics include biomineralization, bionanocomposites, biomaterials, bioencapsulation and green materials chemistry. He has co-authored over 170 publications and 17 book chapters and he is a member of the Advisory Editorial Board of Scientific Reports, Current Medicinal Chemistry and Silicon.

List of Contributors xv

1 What Are Bionanocomposites? 1
Agathe Urvoas, Marie Valerio‐Lepiniec, 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 Ádok‐Sipiczki 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 Transcription–Translation Process 16

2.1.3.3 Replication Process 18

2.1.4 Specific Secondary Structures 19

2.1.4.1 Watson–Crick H‐Bonds 19

2.1.4.1.1 Stem‐Loop 19

2.1.4.1.2 Kissing Complex 20

2.1.4.2 Other Kinds of H‐Bonding 21

2.1.4.2.1 G‐Quartets 21

2.1.4.2.2 i‐Motifs 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 Self‐Assembly 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 Protein–Lipid 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 Mixed‐Linkage 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 François‐Xavier Campbell‐Valois

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 Auto‐Organization: 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 Formin‐Initiated Actin Assembly to Generate Mechanical Forces 83

2.4.5.4 Self‐Organization Properties and Force Generation Understood Using In Vitro Reconstituted Actin‐Based 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 Ádok‐Sipiczki 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 Watson–Crick H‐Bonds 102

3.1.3.1.1 Stem‐Loop 102

3.1.3.1.2 Kissing Complex 103

3.1.3.2 Other Kind of H‐Bonding 103

3.1.3.2.1 G‐Quartets 103

3.1.3.2.2 Origami: Nano‐architecture on Surface 105

3.1.4 Conclusion 108

References 108

3.2 Protein Engineering 113
Agathe Urvoas, Marie Valerio‐Lepiniec 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 Tag‐Mediated Labeling and Enzymatic Coupling 125

3.2.3.3.4 Enzyme‐Mediated 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 Ž. Knežević, Laurence Raehm and Jean‐Olivier 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 Hydride‐Containing Surfaces 154

4.2.2.3 Functionalization of Metal‐Containing Nanoparticles 155

4.2.2.4 Functionalization of Carbon‐Based Nanomaterials 155

4.2.3 Linker‐Mediated 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 Host–Guest 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 One‐Dimensional Bionanocomposites 170

4.3.3 Two‐Dimensional Organization of Nanoparticles 175

4.3.4 Three‐Dimensional 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 Grafting‐onto 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 X‐Ray Photoelectron Spectroscopy and Auger Electron Spectroscopy 324

6.2.4 Energy–Dispersive X‐Ray Spectroscopy and Electron–Energy 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 Particle–Biomolecule 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