Explore a comprehensive, one-stop reference on biological soft matter written and edited by leading voices in the field
Biological Soft Matter: Fundamentals, Properties and Applications delivers a unique and indispensable compilation of up-to-date knowledge and material on biological soft matter. The book presents a thorough overview about biological soft matter, beginning with different substance classes, including proteins, nucleic acids, lipids, and polysaccharides. It goes on to describe a variety of superstructures and aggregated and how they are formed by self-assembly processes like protein folding or crystallization.
The distinguished editors have included materials with a special emphasis on macromolecular assembly, including how it applies to lipid membranes, and proteins fibrillization. Biological Soft Matter is a crucial resource for anyone working in the field, compiling information about all important substance classes and their respective roles in forming superstructures.
The book is ideal for beginners and experts alike and makes the perfect guide for chemists, physicists, and life scientists with an interest in the area. Readers will also benefit from the inclusion of:- An introduction to DNA nano-engineering and DNA-driven nanoparticle assembly- Explorations of polysaccharides and glycoproteins, engineered biopolymers, and engineered hydrogels- Discussions of macromolecular assemblies, including liquid membranes and small molecule inhibitors for amyloid aggregation- A treatment of inorganic nanomaterials as promoters and inhibitors of amyloid fibril formation- An examination of a wide variety of natural and artificial polymers
Perfect for materials scientists, biochemists, polymer chemists, and protein chemists, Biological Soft Matter: Fundamentals, Properties and Applications will also earn a place in the libraries of biophysicists and physical chemists seeking a one-stop reference summarizing the rapidly evolving topic of biological soft matter.
Table of Contents
Preface ix
Part I Natural and Artificial Polymers 1
1 DNA Nanoengineering and DNA-Driven Nanoparticle Assembly 3
Alain Estève and Carole Rossi
1.1 Introduction 3
1.2 From the DNA Molecule to Nanotechnologies 6
1.3 DNA Nanostructures: From Holliday Junctions to 3D Origami 7
1.4 DNA-Directed Assembly of Particles: From Concepts to the Realization of Ordered Assemblies 10
1.4.1 DNA/Nanoparticle Assembly: Primary Functionalization Strategies 12
1.4.2 Toward High-Order Crystalline Structures 12
1.4.3 Crystallization of Heterogeneous Systems 16
1.4.4 DNA/Nanoparticle Assembly: Applications 19
1.5 Nanoengineering of DNA Self-Assembled Al/CuO Nanothermite 20
1.5.1 Fundaments and Characterization of DNA/Surface Chemistry and Grafting Strategies 21
1.5.1.1 DNA/Alumina Interaction Evaluation Through Infrared Spectroscopy and First Principles Calculations 22
1.5.1.2 Functionalization Protocol and Colloidal Characterization 24
1.5.1.3 Quantification of Streptavidin and DNA Surface Densities 26
1.5.2 Kinetics of DNA-Directed Assembly of Al and CuO Nanoparticles 28
1.5.2.1 Design and Impact of the DNA Coding Sequence 29
1.5.3 Structural and Energetic Properties of the Al/CuO Bionanocomposite 32
1.6 Conclusion 35
References 36
2 Polysaccharides and Glycoproteins 43
Sujit Kootala and Susana C.M. Fernandes
2.1 Introdution 43
2.2 Polysaccharides from Plants 45
2.3 Polysaccharides from Microorganisms 47
2.4 Polysaccharides from Marine Organisms 49
2.5 Glycoproteins from Animal Sources - Mammals 52
2.6 Summary 56
References 56
3 Engineered Biopolymers 65
Tugba Dursun Usal, Cemile Kilic Bektas, Nesrin Hasirci, and Vasif Hasirci
3.1 Polyhydroxyalkanoates 65
3.1.1 Medium-Chain-Length Polyhydroxyalkanoates 67
3.1.2 Poly(3-hydroxybutyrate) 70
3.1.3 Poly(4-hydroxybutyrate) 71
3.1.4 Poly(3-hydroxyvalerate) 71
3.1.5 Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) 71
3.2 Poly(lactic acid) (PLA) 72
3.2.1 Poly(L-lactic acid) 73
3.2.2 Poly(D-lactic acid) 75
3.2.3 Poly(DL-lactic acid) 75
3.3 Genetically Modified Polymers 76
3.3.1 Genetically Modified Amino Acid-Based Polymers 76
3.3.1.1 Elastin-Like Recombinamers (ELRs) 76
3.3.1.2 Inorganic-Binding Peptides 78
3.3.2 Genetically Modified Saccharide-Based Polymers 80
3.3.2.1 Bacterial Cellulose 80
3.4 Conclusion 81
References 81
4 Engineered Hydrogels 89
Cemile Kilic Bektas, Tugba Dursun Usal, Nesrin Hasirci, and Vasif Hasirci
4.1 Properties of Hydrogels 89
4.1.1 Modification and Functionalization 90
4.1.1.1 Methacrylation 90
4.1.1.2 PEGylation 93
4.1.1.3 PNIPAm Conjugated Hydrogels 95
4.1.1.4 Hydrogels of Recombinant Polymers 96
4.1.2 New Approaches for 3D Hydrogel Preparation 98
4.1.2.1 Cryogels 98
4.1.2.2 Bottom-Up 3D Hydrogel Preparation Methods 100
4.2 Conclusion 106
References 106
Part II Macromolecular Assemblies 115
5 Lipid Membranes: Fusion, Instabilities, and Cubic Structure Formation 117
Angelina Angelova, Borislav Angelov, and Yuru Deng
5.1 Introduction to Lipid Self-assembly and Membrane Organization 117
5.2 Lipid Membrane Instabilities and Phase Transitions 120
5.3 Shape Deformations and Membrane Curvature 123
5.4 Membrane Fusion 125
5.5 Cubic Membranes In Vivo and Bio-inspired Materials with Cubic Membrane Topology 132
5.6 Conclusion and Outlook 134
Acknowledgments 135
References 135
6 Small Molecule Inhibitors for Amyloid Aggregation 153
Anisha Thomas, Gagandeep Kaur, Rafat Ali, and Sandeep Verma
6.1 Introduction 153
6.2 Targeting Strategies for Inhibition of Amyloid Aggregation 154
6.3 Classes of Inhibitors 155
6.3.1 Peptide-Based Amyloid Inhibitors 156
6.3.1.1 Peptides Derived from the Native Protein Sequence 156
6.3.1.2 Metal Ion Scavenging Peptides 161
6.3.1.3 β-Sheet Breaker Peptides 161
6.3.1.4 Peptides Containing D-Amino Acids 165
6.3.1.5 Molecules Targeting α-Helical State of Amyloid Proteins 165
6.3.1.6 Peptidomimetics 167
6.3.1.7 Cyclic Peptide Amyloid Inhibitors (CPAIs) 171
6.3.2 Non-peptide-Based Small Molecules 174
6.3.2.1 Quinones/Polyphenols/Natural Compounds 175
6.3.2.2 Macrocyclic Inhibitors 179
6.4 Future Outlook 181
Acknowledgments 181
References 182
7 Inorganic Nanomaterials as Promoters/Inhibitors of Amyloid Fibril Formation 195
Monika Holubová
7.1 Introduction 195
7.2 Nanodiamonds 201
7.3 Carbon Nanotubes 202
7.3.1 Multiwalled Carbon Nanotubes 203
7.3.2 Single-Walled Carbon Nanotubes 204
7.4 Fullerenes-C60 205
7.5 Graphene/Graphene Oxide 208
7.6 Quantum Dots 209
7.7 Semiconductor Quantum Dots 211
7.8 Carbon/Graphene Quantum Dots 211
7.9 Iron Nanoparticles 212
7.10 Titanium Dioxide Nanoparticles 214
7.11 Gold Nanoparticles 216
7.12 Other Nanoparticles Based on Metals/Metalloids 218
7.13 Conclusion 218
Acknowledgment 221
References 222
Part III Mechanobiology 229
8 Mechanobiology 231
Menekşe Ermis, Esen Say𝚤n, Ezgi Antmen, and Vasif Hasirci
8.1 Extracellular Matrix (ECM) 231
8.1.1 ECM Structure and Composition 232
8.1.1.1 Proteins of ECM 232
8.1.1.2 Glycosaminoglycans 235
8.1.1.3 Growth Factors 235
8.1.2 ECM Functions 235
8.1.3 ECM Properties 237
8.1.3.1 Physical Properties 237
8.1.3.2 Chemical Properties 237
8.1.3.3 Mechanical Properties 238
8.2 Cell Adhesion 238
8.2.1 Molecules in Cell Adhesion 238
8.2.2 Cell-to-Cell Interactions 240
8.2.2.1 Cell Junctions 240
8.2.2.2 Cell Polarity 241
8.2.3 Signaling Pathways in Cell Adhesion 241
8.2.3.1 Principles of Cell Adhesion Signaling 241
8.2.3.2 Tissue-Specific Cell Adhesion Molecules 242
8.2.3.3 Cell Migration Guidance 242
8.3 Cell-to-ECM Interactions 243
8.4 Interactions with Substrate and Tissue Engineering 244
8.4.1 Properties of Substrates 245
8.4.1.1 Physical Properties 245
8.4.1.2 Chemical Properties 251
8.4.1.3 Mechanical Properties 252
8.5 Mechanobiology, Mechanotransduction, and Force Transmission 252
8.5.1 Concepts 253
8.5.1.1 Mechanobiology 253
8.5.1.2 Force Transduction 253
8.5.1.3 Mechanotransduction 253
8.5.2 Cell Surface Receptors as Mechanosensors 255
8.5.3 Focal Adhesion Kinase Signaling 257
8.5.4 Cytoskeleton as a Force-Transducing Element 258
8.6 Conclusion 263
References 263
Index 271
