NANOSTRUCTURES. Jaime Castillo-Leon Luigi Sasso Winnie E.Svendsen. Pan Stanford. Publishing. edited by ADVANCES AND APPLICATIONS IN NANOBIOTECHNOLOGY

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1 edited by Jaime Castillo-Leon Luigi Sasso Winnie E.Svendsen Pmmim, EPTIDE «m> hhiiiuj nn a ywrnnma^ NANOSTRUCTURES ADVANCES AND APPLICATIONS IN NANOBIOTECHNOLOGY taim m Pan Stanford Publishing

2 0=C< Preface xi 1 Theoretical Basis of Biological Self-Assembly 1 Carl Henrik Gorbitz 1.1 Introduction Formation of a Crystal Self-Assembly Prior to Nucleation Nucleation Crystal Growth and Crystal Habit Polymorphism Intermolecular Interactions The Strong Hydrogen Bonds Main chain -NHj ~00C Main chain >N-H 0=C< Main chain -NH^" and >N-H- -00C Main-chain-side-chain interactions Interactions with solvent water The Weak Hydrogen Bonds C-H.--0=C< hydrogen bonds S-H donors and S acceptors Aromatic-Aromatic Interactions The Role ofthe Solvent Peptide Solvates Crystallization Methods The Entropy Issue Structure Types Linear, Unblocked Peptides Linear C- and N-Blocked Peptides 24

3 The Non-helical structures Helical structures Cyclic Peptides Diketopiperazines Larger ring structures Putting it Together Art of Balancing The Toolbox Lessons Learned from Structure Prediction Algorithms A Working Example: Dipeptide Nanotubes Structure Refinement and Errors 30 Appendix A 32 A.l Algorithms for CSD Searches 32 2 Natural and Designed Self-Assembling Peptides and Their Applications in Bionanotechnology 39 Anna Mitraki and Emmanouil Kasotakis 2.1 Introduction Self-Assembly of Short Synthetic Peptides Corresponding to Natural Sequences Self-Assembly of Non-Natural and De Novo Designed Short Synthetic Peptides Templating Role of Biological Nanostructures Self-Assembling Peptides as Biomineralization Scaffolds Metal Nanoparticles Templated on Self-Assembling Peptides Self-Assembling Peptide Hydrogels Introducing Responsiveness Self-Assembling Peptides as Tissue Engineering Scaffolds Controlled Positioning of Self-Assembling Peptide Materials Summary and Outlook 58 3 Peptide-Based Materials via Molecular Self-Assembly 67 Rein V. Ulijn 3.1 Introduction 68

4 vli 3.2 Peptide Design Strategies Amino Acids: The Structural Building Blocks of Life Peptide Self-Assembly Based on Nature's Hydrogen Bonding Patterns Systems based on ^-sheets Systems based on a-helix/coiled-coils Peptide Self-Assembly Using Novel Sequences Peptide nanotubes from -sheets Aromatic dipeptides Peptide amphiphiles Aliphatic peptide amphiphiles Aromatic peptide amphiphiles Dynamically Controlling Self-Assembly Combining Catalysis and Self-Assembly From Structure to Function Biomedical Materials Based on Peptides Interfacing Peptides with Man-Made Materials Conclusions 85 4 Self-Assembling Peptide Nanostructures: Towards Bioactive Artificial Protein Nanomaterials 93 Yong-beom Lim 4.1 Introduction Lessons from Protein Structures Amide Bond and Reduced Flexibility in Polypeptide Chain Secondary Structures of Proteins Tertiary and Quaternary Structures of Proteins and Macromolecular Assemblies Self-Assembly and Self-Assembled Nanostructures Driving Force for Self-Assembly: Non-Covalent Interactions Non-covalent interactions: Hydrophobic interactions 101

5 vlil Non-covalent interactions: Electrostatic interactions Non-covalent interactions: The van der Waals force Non-covalent interactions: Hydrogen bonds Artificially Designed Self-Assembling Peptide Nanostructures Peptide Nanostructures Self-Assembled within Lipid Bilayer Membrane Self-Assembled Peptide Nanostructures for Intracellular Carriers Structural Peptide Nanomaterials Peptide Nanostructures for Modulating Biomolecular Interactions Conclusions Manipulation ofself-assembled Peptide Nanostructures 125 Jaime Castillo-Leon, LuigiSasso, and Winnie E. Svendsen 5.1 Introduction Considerations When Manipulating Self-Assembled Peptide Nanostructures Temperature Stability in Liquid Solutions Direct Contact Manipulation Techniques Atomic Force Microscopy (AFM) Soft-Lithography Non-Contact Manipulation Techniques Dielectrophoresis [DEP] Magnetic Alignment Microfluidic Manipulation Inkjet printing Chemical Immobilization Antibody functionalization Thiol functionalization Self-Assembly as a Manipulation Method Conclusions 141

6 ix 6 Applications in Bionanotechnology of Self-Assembled Peptide Nanostructures 147 Yihua Loo, Elizabeth C. Wu, Anupama Lakshmanan, Archana Mishra, and Charlotte A. E. Hauser 6.1 Introduction Peptide/Protein Hydrogels for Regenerative Medicine Engineering Synthetic Extracellular Matrix Peptide Hydrogels for Tissue Engineering Applications a-helical Peptide Hydrogels Aligned Monodomain Gels for 3D Cell Culture Functionalized and Hybrid Peptide Hydrogels Ultra Small Peptide Hydrogels Delivery of Bioactive Therapeutics Peptide and Protein-Based Hydrogel Drug Delivery Devices Viral Peptide Self-Assembly in Gene Delivery and Vaccine Development Peptide Self-Assembly in Nanofabrication Biomineralization Synthesis of Inorganic Nanoparticles Molecular Imaging Peptide Organogels Conclusions Biomedical Applications of Assembled Peptide and Protein Micro- or Nanostructures 179 Xuehai Yan, Ying Su, Wei Qi, andjunbai Li 7.1 Introduction Self-Assembled Peptide and Protein Nanostructures Naturally Occurring Proteins Collagen Elastin Biomimetic and Bioinspired Peptide-Building Blocks Diphenylalanine peptide and itsderivatives 185

7 X Amphiphilic peptides Cyclic peptides Polypeptides Layer-by-Layer Assembled Protein Microcapsules Fabrication of Protein Microcapsules Application of Protein Microcapsules Application in biomimetics Application in drug delivery Conclusions and Remarks Self-Assembling Peptides as a New Class of Medical Device for Regenerative Medicine 231 Danielle Miles, Ruth Wilcox, and Amalia Aggeli 8.1 Introduction Self-Assembling De Novo Designed Peptides in Physiological Conditions and Their Applications as Scaffolds in Tissue Engineering /3-Structured Systems Ionic/8-sheet peptides Tape-forming peptides /3-hairpins Aromatic short peptides Peptide amphiphiles a-helix/coiled-coil Systems Conclusions and Future Perspectives 259 Index 271

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