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 xv1 What Are Bionanocomposites? 1Agathe Urvoas, Marie Valerio‐Lepiniec, Philippe Minard and Cordt Zollfrank1.1 Introduction 11.2 A Molecular Perspective: Why Biological Macromolecules? 31.3 Challenges for Bionanocomposites 3References 62 Molecular Architecture of Living Matter 92.1 Nucleic Acids 11Enora Prado, Mónika Ádok‐Sipiczki and Corinne Nardin2.1.1 Introduction: A Bit of History 112.1.2 Definition and Structure 122.1.2.1 Nomenclature 122.1.2.2 Structure 132.1.3 DNA and RNA Functions 152.1.3.1 Introduction 152.1.3.2 Transcription–Translation Process 162.1.3.3 Replication Process 182.1.4 Specific Secondary Structures 192.1.4.1 Watson–Crick H‐Bonds 192.1.4.1.1 Stem‐Loop 192.1.4.1.2 Kissing Complex 202.1.4.2 Other Kinds of H‐Bonding 212.1.4.2.1 G‐Quartets 212.1.4.2.2 i‐Motifs 232.1.5 Stability 232.1.6 Conclusion 25References 252.2 Lipids 29Carole Aimé and Thibaud Coradin2.2.1 Lipids Self‐Assembly 292.2.2 Structural Diversity of Lipids 302.2.2.1 Fatty Acyls (FA) 302.2.2.2 Glycerolipids (GL) 322.2.2.3 Glycerophospholipids (GP) 322.2.2.4 Sphingolipids (SP) 332.2.2.5 Sterol Lipids (ST) 342.2.2.6 Prenol Lipids (PR) 342.2.2.7 Saccharolipids (SL) 352.2.2.8 Polyketides (PK) 352.2.3 Lipid Synthesis and Distribution 352.2.4 The Diversity of Lipid Functions 362.2.4.1 Cellular Architecture 372.2.4.2 Lipid Rafts 372.2.4.3 Energy Storage 372.2.4.4 Regulating Membrane Proteins by Protein–Lipid Interactions 392.2.4.5 Signaling Functions 392.2.5 Lipidomics 39References 402.3 Carbohydrates 41Mirjam Czjzek2.3.1 Introduction 412.3.2 Monosaccharides 422.3.3 Oligosaccharides 442.3.3.1 Disaccharides 442.3.3.2 Protein Glycosylations 462.3.4 Polysaccharides 472.3.4.1 Cellulose 492.3.4.2 Hemicelluloses 502.3.4.2.1 Xyloglucan 502.3.4.2.2 Xylan 502.3.4.2.3 Mannan or Glucomannan 522.3.4.2.4 Mixed‐Linkage Glucan (MLG) 522.3.4.3 Pectins 532.3.4.4 Chitin 542.3.4.5 Alginate 542.3.4.6 Marine Galactans 552.3.4.7 Storage Polysaccharides: Starch, Glycogen, and Laminarin 55References 562.4 Proteins: From Chemical Properties to Cellular Function: A Practical Review of Actin Dynamics 59Stéphane Romero and François‐Xavier Campbell‐Valois2.4.1 Introduction 592.4.2 Molecular Architecture of Proteins 592.4.2.1 Amino Acids 602.4.2.2 Peptide Bond 602.4.2.3 Primary Structure 642.4.3 Protein Folding 662.4.3.1 Peptide and Protein: Secondary Structure 662.4.3.2 3D Folding: Tertiary Structure 672.4.3.3 Quaternary Structure 682.4.3.4 Protein Folding and De Novo Design 702.4.4 Interacting Proteins for Cellular Functions 732.4.4.1 Protein Interactions 732.4.4.2 Enzymatic Activity of Proteins 752.4.4.3 Molecular Motors 772.4.5 Self‐ Assembly and Auto‐Organization: Regulation of the Actin Cytoskeleton Assembly 782.4.5.1 Origin of the Actin Treadmilling 792.4.5.2 Regulation of Actin Treadmilling 832.4.5.3 Arp2/3 and Formin‐Initiated Actin Assembly to Generate Mechanical Forces 832.4.5.4 Self‐Organization Properties and Force Generation Understood Using In Vitro Reconstituted Actin‐Based Nanomovements 852.4.5.5 Applications in Bionanotechnologies 852.4.6 Conclusion 87References 883 Functional Biomolecular Engineering 933.1 Nucleic Acid Engineering 95Enora Prado, Mónika Ádok‐Sipiczki and Corinne Nardin3.1.1 Introduction 953.1.2 How to Synthetically Produce Nucleic Acids? 953.1.2.1 The Chemical Approach 953.1.2.2 Polymerase Chain Reaction 963.1.2.3 Combinatorial Synthesis of Oligonucleotides and Gene Libraries: Aptamers 1003.1.3 Secondary Structures in Nanotechnologies 1023.1.3.1 Watson–Crick H‐Bonds 1023.1.3.1.1 Stem‐Loop 1023.1.3.1.2 Kissing Complex 1033.1.3.2 Other Kind of H‐Bonding 1033.1.3.2.1 G‐Quartets 1033.1.3.2.2 Origami: Nano‐architecture on Surface 1053.1.4 Conclusion 108References 1083.2 Protein Engineering 113Agathe Urvoas, Marie Valerio‐Lepiniec and Philippe Minard3.2.1 Synthesis of Polypeptides: Chemical or Biological Approach? 1133.2.2 Proteins: From Natural to Artificial Sources 1143.2.2.1 How to Get the Coding Sequence of the Protein of Interest? 1143.2.2.2 E. coli: A Cheap “Protein Factory” with a Diversified Tool Box 1143.2.2.3 Common Expression Plasmids 1163.2.2.4 Limits of Recombinant Protein Expression in E. coli 1173.2.2.5 Some Solutions Are Available to Solve these Expression Problems 1183.2.3 Proteins: A Large Repertoire of Functional Objects 1183.2.3.1 Looking for Natural Proteins with Desired Function 1183.2.3.2 From Protein Engineering to Protein Design 1193.2.3.2.1 Modified Proteins Are Often Destabilized 1193.2.3.2.2 Natural or Engineered Proteins: From Small Step to Giant Leap in Sequence Space 1203.2.3.2.3 Computational Protein Design 1203.2.3.2.4 Directed Evolution: A Diverse Repertoire Combined with a Selection Process 1213.2.3.3 Combining Chemistry with Biological Objects 1233.2.3.3.1 Labeling Natural Amino Acids 1233.2.3.3.2 Bioorthogonal Labeling 1233.2.3.3.3 Tag‐Mediated Labeling and Enzymatic Coupling 1253.2.3.3.4 Enzyme‐Mediated Ligation 1263.2.3.3.5 Quality Control of Labeled Biomolecules 126References 1264 The Composite Approach 1294.1 Inorganic Nanoparticles 131Carole Aimé and Thibaud Coradin4.1.1 Introduction 1314.1.2 Overview of Inorganic Nanoparticles 1324.1.3 Synthesis of Inorganic Nanoparticles 1324.1.3.1 Basic Principles 1324.1.3.2 Nanoparticles from Solutions 1384.1.3.2.1 Ionic Solids 1384.1.3.2.2 Metals 1394.1.3.2.3 Metal Oxides 1404.1.3.2.4 Morphological Control 1444.1.4 Some Specific Properties of Inorganic Nanoparticles 1454.1.5 Concluding Remarks 149References 1494.2 Hybrid Particles: Conjugation of Biomolecules to Nanomaterials 153Nikola Ž. Knežević, Laurence Raehm and Jean‐Olivier Durand4.2.1 General Considerations 1534.2.2 Functionalization of Nanoparticle Surface 1544.2.2.1 Functionalization of Hydroxylated Surfaces 1544.2.2.2 Functionalization of Hydride‐Containing Surfaces 1544.2.2.3 Functionalization of Metal‐Containing Nanoparticles 1554.2.2.4 Functionalization of Carbon‐Based Nanomaterials 1554.2.3 Linker‐Mediated Conjugation of Biomolecules to Nanoparticles 1554.2.3.1 Conjugation through Carbodiimide Chemistry 1554.2.3.2 Carbamate, Urea, and Thiourea Linkage 1564.2.3.3 Schiff Base Linkage 1584.2.3.4 Multicomponent Linkage Formation 1594.2.3.5 Biofunctionalization through Alkylation 1604.2.3.6 Bioorthogonal Linkage Formation 1614.2.3.7 Conjugation through Host–Guest Interactions 1624.2.3.8 Linkage through Metal Coordination 1624.2.3.9 Ligation through Complementary Base Pairing 1644.2.3.10 Electrostatic Interactions 1644.2.4 Conclusions 164Acknowledgments 165References 1654.3 Biocomposites from Nanoparticles: From 1D to 3D Assemblies 169Carole Aimé and Thibaud Coradin4.3.1 General Considerations 1694.3.2 One‐Dimensional Bionanocomposites 1704.3.3 Two‐Dimensional Organization of Nanoparticles 1754.3.4 Three‐Dimensional Organization of Particles 1754.3.5 Conclusion and Perspectives 180References 1805 Applications 1855.1 Optical Properties 187Cordt Zollfrank and Daniel Van Opdenbosch5.1.1 Introduction 1875.1.2 Interactions of Light with Matter 1895.1.3 Optics at the Nanoscale 1905.1.3.1 Nanoscale Optical Processes 1905.1.3.2 Nanoscale Confinement of Matter 1915.1.3.3 Nanoscale Confinement of Radiations 1915.1.4 Optical Properties of Bionanocomposites 1915.1.4.1 Absorption Properties of Bionanocomposites 1925.1.4.2 Emission Properties of Bionanocomposites 1955.1.4.3 Structural Colors with Bionanocomposites 2005.1.5 Conclusions 201References 2025.2 Magnetic Bionanocomposites: Current Trends, Scopes, and Applications 205Wei Li, Yuehan Wu, Xiaogang Luo and Shilin Liu5.2.1 Introduction 2055.2.2 Construction Strategies for Magnetic Biocomposites 2085.2.2.1 The Blending Method 2085.2.2.2 In Situ Synthesis Method 2095.2.2.3 Grafting‐onto Method 2105.2.3 Applications of Magnetic Biocomposites 2125.2.3.1 Environmental Applications 2125.2.3.1.1 Removal of Toxic Metal Ions 2125.2.3.1.2 Removal of Dyes 2165.2.3.1.3 Biocatalysis and Bioremediation 2165.2.3.2 Biomedical Applications 2185.2.3.2.1 Magnetic Resonance Imaging (MRI) 2185.2.3.2.2 Cellular Therapy and Labeling 2195.2.3.2.3 Tissue Engineering Applications 2215.2.3.2.4 Drug Delivery 2215.2.3.2.5 Tissue Regeneration 2245.2.3.3 Biotechnological and Bioengineering Applications 2255.2.3.3.1 Biosensing 2265.2.3.3.2 Magnetically Responsive Films 2285.2.4 Concluding Remarks and Future Trends 228Acknowledgments 229References 2295.3 Mechanical Properties of Natural Biopolymer Nanocomposites 235Biqiong Chen5.3.1 Introduction 2355.3.2 Overview of Mechanical Properties of Polymer Nanocomposites and Their Measurement Methods 2375.3.3 Solid Biopolymer Nanocomposites 2375.3.4 Porous Biopolymer Nanocomposites 2455.3.5 Biopolymer Nanocomposite Hydrogels 2475.3.6 Conclusions 249References 2515.4 Bionanocomposite Materials for Biocatalytic Applications 257Sarah Christoph and Francisco M. Fernandes5.4.1 Bionanocomposites and Biocatalysis 2575.4.2 Form and Function in Bionanocomposite Materials for Biocatalysis 2605.4.2.1 Bionanocomposites Structure 2605.4.2.1.1 Biopolymers 2605.4.2.1.2 The Inorganic Fraction 2645.4.2.2 Key Biocatalysts 2695.4.2.2.1 Nucleotides and Amino Acids 2695.4.2.2.2 Enzymes 2725.4.2.2.3 Whole Cells 2735.4.3 Applications 2775.4.3.1 Biosynthesis 2775.4.3.2 Sensing Applications 2815.4.3.3 Environmental Applications 2835.4.3.4 Energy Applications of Biocatalytic Bionanocomposites 2865.4.4 Conclusions and Perspectives 289References 2905.5 Nanocomposite Biomaterials 299Gisela Solange Alvarez and Martín Federico Desimone5.5.1 Introduction 2995.5.2 Natural Nanocomposites 3015.5.2.1 Cellulosic Materials 3015.5.2.2 Chitosan 3055.5.2.3 Alginate 3055.5.2.4 Collagen 3075.5.2.5 Gelatin 3075.5.2.6 Silk Fibroin 3095.5.3 Synthetic Nanocomposites 3095.5.3.1 PLLA and PLGA 3095.5.3.2 Polyethylene Glycol 3125.5.3.3 Methacrylate 3125.5.3.4 Polyvinyl Alcohol 3145.5.3.5 Polyurethanes 3145.5.4 Conclusions 315Acknowledgments 317References 3176 A Combination of Characterization Techniques 321Carole Aimé and Thibaud Coradin6.1 Introductory Remarks 3216.2 Chemical Analyses 3226.2.1 Inductively Coupled Plasma 3226.2.2 Infrared Spectroscopy 3236.2.3 X‐Ray Photoelectron Spectroscopy and Auger Electron Spectroscopy 3246.2.4 Energy–Dispersive X‐Ray Spectroscopy and Electron–Energy Loss Spectroscopy 3286.3 Determining Size and Structure 3296.3.1 Imaging 3296.3.1.1 Electron Microscopy 3306.3.1.2 Atomic Force Microscopy 3336.3.2 Scattering Techniques 3356.3.2.1 Small Angle Scattering 3376.3.2.2 Dynamic Light Scattering and Zetametry 3376.3.3 Monitoring Particle–Biomolecule Interactions 3396.3.3.1 Electrophoresis 3396.3.3.2 Circular Dichroism Spectroscopy 3406.3.3.3 Isothermal Titration Calorimetry and Surface Plasmon Resonance 3426.4 Materials Properties 3446.4.1 Optical Properties 3446.4.2 Mechanical Testing 3466.4.2.1 Rheology 3466.4.2.2 Compression Tests 3476.4.2.3 Tensile Tests 3486.4.2.4 Relaxation Tests 3486.4.2.5 Dynamic Mechanical Analysis 3496.4.2.6 Indentation 3496.4.2.7 Mechanical Testing of Hydrogels 3496.4.3 Magnetic Measurements 3506.4.4 Biological Properties 353References 355Index 359