Peptide Materials

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 alpha-Helix 46 2.5.2 310-Helix 48 2.5.3 2.27-Helix 50 2.5.4 Pleated-Sheet ß-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 ß-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 alpha-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 ß-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 Martiæ, 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 alpha-Helix/ß-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/alpha-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 14.4.3 The Effect of HA-P140 Nanoparticles in Healthy and Lupus Mice 407 14.5 General Comments 412 Acknowledgements 412 References 412 15 Identification and Application of Polymer-Binding Peptides 417 Toshiki Sawada and Takeshi Serizawa 15.1 Introduction 417 15.2 Biological Identification of Material-Binding Peptides 419 15.3 Recognition of Polymer Stereoregularity by Peptides 421 15.4 Recognition of Other Polymer Nanostructures by Peptides 424 15.5 Applications of Polymer-Binding Peptides 426 15.6 Summary 428 References 428 Index 435