9781118592403

Preface xiii

List of Contributors xvii

Part I Fundamentals of Peptide Materials 1

1 Physics of Peptide Nanostructures and Their Nanotechnology Applications 3
Nadav Amdursky, Peter Beker and Gil Rosenman

1.1 Introduction to Peptide Nanotubes 4

1.2 Optical Properties and Quantum Confinement of FF-based Nanostructures 8

1.3 Odd-Tensor Related Physical Properties 13

1.4 Thermal Induced Phase Transition in Peptide Nanotubes 17

1.4.1 Changes in the Structure Properties during the Phase Transition Process 18

1.4.2 Phase Transition Classification of the Thermally Induced Process 22

1.5 Deposition Techniques of PNT 22

1.5.1 Wet Deposition Techniques 23

1.5.2 Dry Deposition Technique 25

1.6 Applications of PNTs 29

1.6.1 PNTs for Nanotechnological Applications 30

1.6.2 PNTs as a Deposition Scaffold 32

1.7 Conclusion 32

References 33

2 Chemistry of Peptide Materials: Synthetic Aspects and 3D Structural Studies 39
Fernando Formaggio, Alessandro Moretto, Marco Crisma and Claudio Toniolo

2.1 Introduction 40

2.2 Synthesis of Difficult Peptide Sequences 40

2.3 Peptide (Amide) Bond 43

2.4 Peptide Torsion Angles 44

2.5 Peptide Secondary Structures 46

2.5.1 α-Helix 46

2.5.2 310-Helix 48

2.5.3 2.27-Helix 50

2.5.4 Pleated-Sheet β-Structures 51

2.5.5 2.05-Helix 53

2.5.6 Poly-(l-Pro)n Helices and Collagen Triple Helix 56

References 58

3 Conformational Aspects and Molecular Dynamics Simulations of Peptide Hybrid Materials: From Methods and Concepts to Applications 65
Carlos Alemán, Oscar Bertran, Jordi Casanovas, Juan Torras, Guillermo Revilla-López and David Zanuy

3.1 Computational Chemistry 66

3.2 Quantum Mechanical Calculations: Concepts 67

3.2.1 Ab Initio Methods 68

3.2.2 Semiempirical Methods 70

3.2.3 Density Functional Theory 70

3.2.4 Solvent Effects in Quantum Mechanical Calculations 71

3.3 Quantum Mechanical Calculations on Hybrid Peptide Materials: Some Examples 72

3.4 NCAD: An Information Management System of Quantum Mechanical Calculations on Noncoded Amino Acids for Peptide Design 74

3.5 Molecular Mechanics Calculations: Concepts 77

3.5.1 Force Fields 80

3.5.2 Energy Minimization 81

3.5.3 Molecular Dynamics 81

3.5.4 Boundary Conditions, Pair-List and Long-Range Interactions 82

3.5.5 Temperature and Pressure 83

3.6 Molecular Dynamics Simulations on Peptides 85

3.6.1 Construction of the Molecular Model 85

3.6.2 Practical Strategies for the Application of Molecular Dynamics Techniques 86

3.6.3 Analysis of the Simulation Data 88

3.6.4 Peptide Dynamics 89

3.6.5 Hybrid Peptide Dynamics 91

3.7 Summary 97

Acknowledgements 97

References 98

4 Peptronics: Peptide Materials for Electron Transfer 105
Emanuela Gatto and Mariano Venanzi

4.1 Introduction 106

4.2 Electron Transfer through Peptide Scaffolds in Solution 107

4.2.1 Theoretical Background 107

4.2.2 Seminal Experimental Results 112

4.3 Electron Transfer through Supported Peptide Matrices 121

4.3.1 Theoretical Background 122

4.3.2 Seminal Experimental Results 125

4.4 Conclusions and Perspectives 143

Acknowledgements 143

References 144

Part II Peptide Nanostructures 149

5 Molecular Architecture with Peptide Assembling for Nanomaterials 151
Shunsaku Kimura and Motoki Ueda

5.1 Introduction 151

5.2 Peptide Vesicles 152

5.2.1 Peptosome 153

5.2.2 Polypeptide as a Hydrophilic Block (AB Type and ABA Type) 153

5.2.3 Block Polypeptides Having a Hydrophobic Polypeptide 154

5.2.4 Other ABA Triblock Copolymers 154

5.2.5 Hyper-branched Polymers and Dendrimers 155

5.2.6 Triskelion Structure 155

5.2.7 Cyclic Peptide as Template for Amphiphilicity 155

5.2.8 Lipid-Like Structure 155

5.3 Peptide Building Blocks 157

5.3.1 Oligopeptides 157

5.3.2 Dipeptides 158

5.3.3 β-Peptides 158

5.3.4 Naturally Occurring Peptides 158

5.4 Peptide Architecture 159

5.4.1 Protein Cages 159

5.4.2 Ion-Complex for Self-Assembling 160

5.4.3 Stereo-Complex for Self-Assembling 160

5.4.4 Inside-out Morphology Transformation 161

5.5 Function of Peptide Assemblies 161

5.6 Tumor Imaging with Peptide Nanocarrier 163

5.7 Perspectives 167

References 168

6 Principles of Shape-Driven Nanostructure Design via Self-Assembly of Protein Building Blocks 171
Idit Buch, Chung-Jung Tsai, Carlos Alemán and Ruth Nussinov

6.1 Introduction 172

6.2 Self-Assembly into Preferred Shapes 172

6.2.1 Why Does a Given Building Block Prefer to Self-Assemble into a Particular Shape? 172

6.2.2 The Self-Assembly Formation Mechanism – A Lesson from Lipid Tubules 177

6.2.3 Experimental Results 177

6.3 Designing Protein Nanotubes 180

6.3.1 Shape-Driven Design 180

6.3.2 Structural Properties of Protein Nanotubes and a Design Scheme 181

6.3.3 Incorporation of Nonproteinogenic Amino Acids 183

6.3.4 MD Simulations as a Testing Tool for Novel Designs 184

6.4 Summary and Outlook 185

Acknowledgements 186

References 186

7 Peptide-Based Soft Spherical Structures 191
K. Vijaya Krishna, Nidhi Gour and Sandeep Verma

7.1 Introduction 191

7.2 Short Peptide Sequences 192

7.3 Amphiphilic Peptides 200

7.4 Peptide–Polymer Hybrids 205

7.5 Future Outlook 209

References 211

Part III Peptide Conjugates and Hybrid Materials 217

8 Peptide-Based Carbon Nanotube Dispersal Agents 219
Anton S. Klimenko and Gregg R. Dieckmann

8.1 Introduction 220

8.2 α-Helical Surfactant Peptides 222

8.2.1 Model for Helical Peptide Dispersion of Nanotubes 224

8.2.2 Peptide–Nanotube Interactions 224

8.2.3 Peptide–Nanotube Complex Structure 227

8.3 β-Strand Surfactant-Like Peptides 229

8.4 Extended Peptides 231

8.5 Amorphous Peptides 233

8.6 Cyclic Peptides 234

8.6.1 Reversible Cyclic Peptides 235

8.7 Summary and Outlook 237

Acknowledgements 239

References 239

9 Nanosized Vectors for Transfection Assembled from Peptides and Nucleic Acids 247
Burkhard Bechinger

9.1 Introduction 248

9.2 Condensation of Nucleic Acids by Cationic Peptides and Other Macromolecules 250

9.3 The Size and Shape of Transfection Complexes 251

9.4 Cellular Targeting by Specific Ligands 252

9.5 Enhancing the Cellular Uptake of Nanocomplexes 252

9.6 Assuring Endosomal Escape 253

9.7 A Family of Multifunctional Peptide Sequences 255

9.8 Delivery to the Nucleus and Other Intracellular Compartments 257

9.9 Combining Different Functionalities into Complex Nanovectors 257

Acknowledgements 259

References 259

10 Properties of Disubstituted Ferrocene–Peptide Conjugates: Design and Applications 265
Sanela Marti?, Samaneh Beheshti and Heinz-Bernhard Kraatz

10.1 Introduction 266

10.2 Structural Considerations and Properties 266

10.3 Fc–Peptides to Probe Interactions 274

10.3.1 Interactions with Ions 274

10.3.2 Interactions with Other Molecular Targets 280

10.3.3 Probing Peptide–Protein Interactions 280

10.4 Conclusions 283

References 284

11 Mechanisms of Adsorption of Short Peptides on Metal and Oxide Surfaces 289
Vincent Humblot, Jessem Landoulsi and Claire-Marie Pradier

11.1 Introduction 290

11.2 Why Studying the Interaction of Short Peptides with Solid Surfaces? 291

11.3 Metal and Oxide Surfaces 292

11.4 Factors Influencing Peptide Adsorption 293

11.4.1 Driving Force 293

11.4.2 Influence of Intrinsic Properties 294

11.4.3 Influence of External Parameters 294

11.5 Adsorption at the Solid/Gas interface 295

11.5.1 Adsorption of Dipeptides 295

11.5.2 Adsorption of Tripeptides 299

11.6 Adsorption at the Solid/Liquid Interface 303

11.7 Conclusions and Guidelines for the Future 307

References 308

Part IV Applications of Peptide Materials 313

12 Bioactive Rosette Nanotubes for Bone Tissue Engineering and Drug Delivery 315
Rachel L. Beingessner, Alaaeddin Alsbaiee, Baljit Singh, Thomas J. Webster and Hicham Fenniri

12.1 Introduction 316

12.2 Rosette Nanotubes (RNTs) 317

12.2.1 RNT Design 317

12.2.2 RNT Functionalization 320

12.2.3 RNT Stability 323

12.2.4 RNT Toxicity and Biocompatibility 324

12.3 Applications of RNTs in Bone Tissue Engineering 328

12.3.1 Introduction 328

12.3.2 RNTs as 2D Coatings on Ti Implants 329

12.3.3 RNTs Embedded in Hydrogels 339

12.4 RNTs for Drug Delivery 340

12.5 Conclusions 349

References 350

13 Peptide Secondary Structures as Molecular Switches 359
Fernando Formaggio, Alessandro Moretto, Marco Crisma and Claudio Toniolo

13.1 Introduction 360

13.2 Classical Secondary Structures Switches 360

13.2.1 α-Helix/β-Pleated Sheet Switch 360

13.2.2 Type-I Poly-(l-Pro)n/Type II Poly-(l-Pro)n Switch 363

13.3 Recently Discovered Secondary Structure Switches 365

13.3.1 The 310-Helix/α-Helix Switch 365

13.3.2 The 2.05-Helix/310-Helix Switch 371

13.4 Conclusions 376

References 378

14 Peptide Nanostructured Conjugates for Therapeutics: The Example of P140 Peptide for the Treatment of Systemic Lupus Erythematosus 385
Yves Frère, Louis Danicher and Sylviane Muller

14.1 Introduction 386

14.2 Noninvasive Routes of Peptide Administration 387

14.2.1 The Transcutaneous Route 387

14.2.2 The Transmucosal Routes for Peptide Delivery 387

14.2.3 The Oral Route 388

14.3 Encapsulation of Peptides and Proteins for Oral Delivery 390

14.3.1 Lipidic Vectors 390

14.3.2 Polymeric Vectors 391

14.3.3 The Vector for the Oral Route 397

14.4 P140 Peptide Nanostructured Complex for the Treatment of Systemic Lupus Erythematosus 399

14.4.1 The Therapeutic Peptide P140 399

14.4.2 Development of Nanoparticles Containing Hyaluronic Acid Associated to P140 Peptide (HA-P140) 400