Peptide Self-Assembly and Engineering: Fundamentals, Structures, and Applications

✍ Scribed by Yan X. (ed.)

• Publisher: Wiley-VCH
• Year: 2024
• Tongue: English
• Leaves: 675
• Category: Library

✦ Synopsis

State-of-the-art research in peptide self-assembly, with coverage of fundamental aspects of how peptides self-assemble and an extensive number of applications.
Peptide Self-Assembly and Engineering: Fundamentals, Structures, and Applications (2V set) covers the latest progresses in the field of peptide self-assembly and engineering, including the fundamental principles of peptide self-assembly, new theory of nucleation and growth, thermodynamics and kinetics, materials design rules, and precisely controlled structures and unique functions. The broad contents from this book enable readers to obtain a systematical and comprehensive knowledge in the field of peptide self-assembly and engineering.
Contributed by the leading scientists and edited by a highly qualified academic and an authority in the field, Peptide Self-Assembly and Engineering includes information on:
Emerging areas in peptide assembly, such as immune agents, bioelectronics, energy conversion, flexible sensors, biomimetic catalysis, and more.
Existing applications in biomedical engineering, nanotechnology, and photoelectronics, including tissue engineering, drug delivery, and biosensing devices.
History of peptide self-assembly for design of functional materials and peptides’ unique mechanical, optical, electronic, and biological properties.
Various solvent conditions, such as pH, ionic strength, and polarity, that can affect the structure and stability of peptide assemblies.
A very comprehensive reference covering the latest progresses in the field of peptide self-assembly and engineering, Peptide Self-Assembly and Engineering is an essential resource for all scientists performing research intersecting with the subject, including biochemists, biotechnologists, pharmaceutical chemists, protein chemists, materials scientists, and medicinal chemists.

✦ Table of Contents

Volume 1
Cover
Half Title
Peptide Self‐Assembly and Engineering: Fundamentals, Structures, and Applications. Volume 1
Copyright
Contents
Volume 1
Volume 2
Preface
1. Introduction to the Concept, History, and Significance of Peptide Selfassembly and Materials
References
2. Peptides: Molecular Basis, Secondary Structures, and Synthesis Methods
2.1 Molecular Basis of Peptides
2.2 Peptide Secondary Structures
2.2.1 Helices
2.2.2 Sheets
2.2.3 Turns
2.3 Synthesis Strategies of Peptides
2.3.1 Solid-phase Peptide Synthesis
2.3.2 Peptide Ligation
2.3.3 Biological Manufacturing of Peptides
2.4 Conclusion
Acknowledgment
References
3. Principles of Peptide Self-assembly and Material Design Rules
3.1 Introduction
3.2 LLPS-mediated Multistep Nucleation Mechanism
3.3 HOO-mediated Multistep Growth Mechanism of Peptide Self-assembly
3.4 Principles of Peptide Self-assembly
3.4.1 Thermodynamics and Kinetics
3.4.2 The Role of Intermolecular Interactions
3.4.2.1 Electrostatic Interaction
3.4.2.2 Hydrogen Bonding Interaction
3.4.2.3 π–π Stacking
3.4.2.4 Hydrophobic Effect
3.5 Design Rules for Materials Based on Peptide Self-assembly
3.5.1 Designing Amphiphilic Peptide Structures with Desired Functions
3.5.2 Modulation of Intermolecular Interactions
3.5.3 Regulating Self-assembly Thermodynamics and Kinetics
3.6 Conclusions and Outlook
Acknowledgments
References
4. Molecular Simulations and Computational Chemistry of Peptide Self-assembly
4.1 Introduction
4.2 Molecular Models and Computational Methods
4.2.1 Theory
4.2.1.1 Quantum Mechanics
4.2.1.2 Molecular mechanics
4.2.1.3 Molecular dynamics
4.2.2 Molecular Model of Force Field in Molecular Simulation
4.2.2.1 All-atom Force Field
4.2.2.2 United-atom Force Field
4.2.2.3 Coarse-grained Force Field
4.2.3 Acceleration Method of Molecular Simulation
4.2.3.1 Replica-exchanged Molecular Dynamics
4.2.3.2 Discrete molecular dynamics
4.2.4 Nonequilibrium Molecular Dynamics
4.3 Analysis Object of Molecular Simulation in Peptide Self-assembly System
4.3.1 Analysis of Molecular Interactions
4.3.1.1 Types of Noncovalent Interaction in Peptide Self-assembly System
4.3.1.2 Inter- and Intramolecular Interactions
4.3.2 Molecular Conformation and Secondary Structure Analysis
4.3.2.1 α-Helix Secondary Structure
4.3.2.2 β-Sheet Secondary Structure
4.3.2.3 α-Sheet Secondary Structure
4.3.2.4 Random Coil Secondary Structure
4.4 Molecular Simulation of Self-assembling Process
4.4.1 Self-assembling Models of Peptide Systems
4.4.1.1 Hierarchical Self-assembly Model
4.4.1.2 Transition Model from Nanoribbon to Nanotube
4.4.1.3 Surfactant-like Self-assembly Model
4.4.1.4 Self-assembly Model Mediated by Phase Separation
4.4.2 Simulation of Phase Separation
4.4.2.1 Liquid–Liquid Phase Interface
4.4.2.2 Aggregation and Fluidity in Liquid-like State
4.4.3 Simulation of Structural Propensity and Evolution
4.4.3.1 Aggregation Process
4.4.3.2 Molecular Alignment
4.4.4 Simulation of Gelation
4.4.4.1 Structural Propensity Toward Nanofiber
4.4.4.2 Formation of Nanofiber Network
4.4.5 Simulation of Chirality Transfer
4.4.5.1 Chirality of Single Molecule
4.4.5.2 Chirality of Building Blocks
4.5 Conclusion and Outlook
Acknowledgments
References
5. Stimuli-responsive Structural Transformations of Peptide Supramolecular Gels
5.1 Introduction
5.2 Designing Peptide-based Supramolecular Gelators
5.3 Stimuli-responsive Changes in Peptide Supramolecular Gels
5.3.1 Aging
5.3.2 Light-triggered Response
5.3.2.1 Photodimerization
5.3.2.2 Photoisomerization
5.3.2.3 Photoreduction
5.3.3 Chemical-responsive Gels
5.3.3.1 pH-triggered Changes
5.3.3.2 Dynamic Chemical Transformations
5.3.3.3 Redox Response
5.3.4 Mechanical Response
5.4 Conclusion and Future Perspective
References
6. Self-assembling Cyclic Peptide Nanotubes: Methods and Characterization
6.1 Introduction
6.2 Preparation Peptide Nanotubes
6.2.1 Requirements
6.2.2 Design
6.2.3 Synthesis
6.3 Characterization of Self-assembling Cyclic Peptide Nanotubes
6.3.1 NMR
6.3.2 X-ray Diffraction
6.3.3 Microscopy
6.3.3.1 Scanning Electron Microscopy
6.3.3.2 Transmission Electron Microscopy
6.3.3.3 Electron Diffraction
6.3.3.4 Atomic Force Microscopy
6.3.3.5 Fluorescence Microscopy
6.3.4 Fourier-transform Infrared Spectroscopy
6.3.5 Fluorescence Spectroscopy
6.3.6 Scattering Techniques
6.3.7 Size-exclusion Chromatography
6.3.8 Computational Calculations
6.3.8.1 Molecular Modeling
6.3.8.2 Molecular Dynamics Simulations
6.4 Recent Applications
References
7. Design and Control of Self-sorting Patterns of Supramolecular Peptide Nanofibers
7.1 Introduction
7.1.1 Self-sorting in a Biological System
7.1.2 Self-sorting of Supramolecular Peptide Nanofibers
7.2 How to Characterize Self-sorting Patterns of Supramolecular Peptide Nanofibers
7.2.1 Spectroscopy (IR/UV–Vis/CD/NMR)
7.2.2 Small-angle Scattering
7.2.3 Electron Microscopy/Atomic Force Microscopy
7.2.4 Confocal Laser Scanning Microscopy
7.3 How to Design and Control Self-sorting Patterns of Supramolecular Peptide Nanofibers
7.3.1 Kinetics
7.3.2 Chemical Structure
7.4 Multiscale Self-sorting Pattern
7.4.1 Network-level Self-sorting
7.4.2 Macroscopic Segregation
7.5 Functions of Self-sorted Nanofibers
7.5.1 Multiple Stimuli-responsive Hydrogels
7.5.2 Cascade Reaction
7.5.3 Optoelectronics
7.5.4 Biological Application of Self-sorting
7.6 Conclusion
References
8. Protein-decorated Artificial Viral Capsids Self-assembled from β-Annulus Peptides
8.1 Introduction
8.2 Artificial Viral Capsids Self-assembled from β-Annulus Peptides
8.2.1 Self-assembly of β-Annulus Peptides
8.2.2 Encapsulation of Guest Molecules into Artificial Viral Capsids
8.3 Protein-decorated Artificial Viral Capsids
8.3.1 Decoration of Functional Molecules on Artificial Viral Capsids
8.3.2 Human Serum Albumin-decorated Artificial Viral Capsids
8.3.3 Horseradish Peroxidase-decorated Artificial Viral Capsids
8.3.4 Ribonuclease S-decorated Artificial Viral Capsids
8.4 Enveloped Viral Replicas Embedded with Membrane Proteins
8.4.1 Enveloped Artificial Viral Capsids
8.4.2 Embedding of Connexin-43 onto Enveloped Artificial Viral Capsids
8.5 Summary and Perspectives
References
9. Peptide Assemblies on Surfaces: A Study Using Scanning Tunneling Microscopy
9.1 Introduction
9.2 Structural Characterization of Individual Peptides
9.2.1 Isolated Peptide Molecules Immobilized on Surfaces
9.2.2 Single Peptides Immobilized by Molecular Matrix
9.3 Structural Characterization of Peptide Assemblies
9.4 Modulation Effects on Peptide Assemblies
9.4.1 Peptide Assemblies Modulated by Mutations
9.4.2 Peptide Assemblies Modulated by Post-Translational Modifications
9.4.3 Peptide Assemblies Modulated by Chirality
9.5 Peptide–Organic Molecule Co-Assemblies
9.5.1 Peptide Assemblies Interacting with Small Molecules by Peptide Termini
9.5.2 Peptide Assemblies Interacting with Small Molecules by Peptide Side Chains
9.5.3 Assemblies of Peptide–Organic Conjugates
9.6 Conclusions and Perspectives
Abbreviations
Acknowledgments
References
10. Molecular Assembly of Cyclic Dipeptide: Structure to Function
10.1 Introduction
10.2 The Synthesis of CDPs
10.3 Molecular Assembly of CDP
10.3.1 CDP Nanoarchitectures
10.3.1.1 Amino-acid Composition and Stereochemistry
10.3.1.2 The Effect of Molecular Assembly Conditions
10.3.2 CDP Molecular Assembly for Various Applications
10.3.2.1 CDP Amphiphiles for Drug Encapsulation and Delivery
10.3.2.2 CDP-based Catalytic Architecture
10.3.2.3 CDP Assembly: Optical Waveguiding
10.3.2.4 CDP-based Quantum-confined Materials
10.4 Biological Activities
10.4.1 Neuroprotective CDPs
10.4.2 Antitumor activity
10.4.3 Antivirus activity
10.5 Conclusions
Acknowledgments
References
11. Minimalistic Peptide Assemblies for Sustainable Optoelectronics
11.1 Introduction
11.2 Photoluminescent Properties
11.2.1 Quantum Confinement-induced Inherent Photoluminescence
11.2.2 Influence of Solvents
11.2.3 The Effect of Temperature
11.2.4 The Effect of Chemical Conjugations
11.2.5 The Effect of Doping
11.3 Optical Waveguide Properties
11.3.1 Intrinsic Optical Waveguiding Properties
11.3.2 Oriented Optical Waveguide Devices
11.3.3 Second-harmonic Generation (SHG)
11.3.4 Electroluminescent Properties
11.4 Conclusions and Perspectives
Acknowledgment
References
12. Peptide-based Coacervates: A Biomimetic Protocell
12.1 Introduction
12.2 Driving Forces for Coacervation and Types of Phase Separation
12.3 Peptide-based Complex Coacervates
12.3.1 Peptide/Nucleotide-based Coacervates
12.3.2 Peptide/Peptide-based Coacervates
12.3.3 Peptide/Metal-based Coacervates
12.4 Peptide-based Simple Coacervates
12.4.1 Designer Small Peptide Derivatives
12.4.2 Mussel Foot Peptide Derivatives
12.5 Biomimetic Coacervates Protocells
12.5.1 Compartmentalization and Sequestration
12.5.2 Catalytic Nature
12.6 Conclusion and Future Perspectives
Acknowledgment
References
13. Water-induced Peptide Self-assembly and Its Function
13.1 Introduction
13.2 The Structure of Water
13.2.1 Radial Distribution Function of Water
13.2.2 Liquid and Solid Water Cluster Structures
13.2.3 Interface-ordered Water
13.3 Water Determines Protein Structure and Function
13.3.1 Dynamic Hydration
13.3.2 Water Participating in Protein Proton Transfer
13.3.3 Water Inducing Protein Allosteric Effect
13.3.4 Antifreeze Protein Inhibits Water Crystallization
13.4 Water-induced Peptide Self-assembly and Its Function
13.4.1 The Role of Water in Protein Fibrosis
13.4.2 The Impact of Water Molecule Behavior on the Peptide Self-assembly Process
13.4.3 Water Molecules Participating in and Stabilizing the Peptide Crystal Strusture
13.4.4 Water-induced Mechanical Deformation of Self-assembled Materials
13.5 Conclusions
Acknowledgment
Rererences
Volume 2
Cover
Half Title
Peptide Self‐Assembly and Engineering: Fundamentals, Structures, and Applications. Volume 2
Copyright
Content
Volume 1
Volume 2
Preface
14. Functional peptide coatings
14.1 Introduction
14.2 Peptide coating techniques
14.2.1 Drop-casting
14.2.2 Dip-coating
14.2.3 Spin-coating
14.2.4 Layer-by-layer Assembly
14.2.5 Physical Vapor Deposition
14.2.6 Chemical Vapor Deposition
14.3 Applications
14.3.1 Antifouling Coating
14.3.2 Antimicrobial Coating
14.3.3 Implant Coating
14.3.4 Cell Adhesion
14.3.5 Drug Delivery
14.3.6 Sensors
14.3.7 Other Applications
14.4 Conclusion
References
15. Self-assembling Peptide Amyloids: From Structure to Function in Nanotechnology
15.1 Introduction
15.2 Structure of Self-assembled Peptide Amyloids
15.2.1 0D Peptide Amyloids
15.2.2 1D Peptide Amyloids
15.2.3 2D Peptide Amyloids
15.2.4 3D Peptide Amyloids
15.3 Functional Regulation of Self-assembled Peptide Amyloid Nanomaterials
15.3.1 Functional Regulation with Metal NPs
15.3.2 Functional Regulation with 2D Nanomaterials
15.3.3 Functional Regulation with Polymers
15.4 Applications of Peptide Amyloids
15.4.1 Biosensors
15.4.2 Bioimaging
15.4.3 Phototherapy
15.4.4 Drug Delivery
15.4.5 Tissue Engineering
15.4.6 Antibacterial Materials
15.4.7 Energy Materials
15.4.7.1 Optoelectronic Materials
15.4.7.2 Piezoelectric Materials
15.4.8 Environmental Science Applications
15.4.8.1 Absorption of Pollutants
15.4.8.2 Photocatalytic Degradation of Pollutants
15.4.8.3 Detection of Pollutants
15.5 Conclusions
Acknowledgments
References
16. Piezoelectric Self-assembling Peptides for Engineering Applications
16.1 Introduction
16.1.1 What Is Piezoelectricity?
16.2 Research Tools for Piezoelectric Self-assembling Peptides
16.3 Piezoelectricity of Peptide Self-assembling Architectures
16.3.1 Amino Acids
16.3.2 Proteins
16.3.3 Peptides
16.3.3.1 Peptide Crystals
16.3.3.2 Peptide Nanofibers
16.4 Conclusion and Respective
Acknowledgments
References
17. Peptide-based Hydrogels for Soft Electronic Devices and Wearable Biosensors
17.1 Introduction
17.2 Assembly of Electroactive Peptide-based Supramolecular Hydrogels
17.2.1 Peptide–Peptide Interactions
17.2.2 Peptide–π Interactions
17.3 Three-dimensional Processing of Electroactive Peptide-based Hydrogels
17.4 Application of Electroactive Peptide-based Hydrogels
17.4.1 Soft Electronic Devices
17.4.2 Wearable Biosensors
17.4.2.1 Mechanical Sensing
17.4.2.2 pH Sensing
17.4.2.3 Temperature Sensing
17.4.2.4 Sensing of Biological or Chemical Molecules
17.5 Conclusions and Perspectives
Abbreviations
References
18. Self-assembled Peptide-based Biocatalyst
18.1 Introduction
18.2 Assembled Catalytic Peptides, Amyloids, and Polypeptides
18.2.1 Histidine-based Hydrolysis
18.2.2 Proline-based C—C Bond-forming Reactions
18.2.3 Expanded Special Reactions
18.2.4 Catalytic Amyloids
18.2.5 Polypeptides
18.2.6 Metallo-nanozyme
18.2.6.1 Single-valence Metal-based Catalyst
18.2.6.2 Multivalence Metal-based Catalyst
18.3 Photosensitive Artificial Enzyme
18.3.1 Co-assembly of Peptides and Photosensitizers
18.3.2 Conjugates of Peptides and Photosensitizers
18.4 Hybrid Photo-enzyme-coupled Systems
18.4.1 Nanocatalyst with Peptide Scaffold
18.4.2 Photo-enzyme-coupled Nanozymes
18.5 Summary
Acknowledgment
References
19. Short Peptide Supramolecular Hydrogels for Antimicrobial Applications
19.1 Introduction
19.2 Molecular Design of AMP Supramolecular Structures
19.2.1 Peptide Sequence
19.2.2 Secondary Structure
19.2.3 Self-assembly and Higher Ordered Structures
19.2.4 Antimicrobial Drug Delivery Platform
19.3 Methods for Peptide Hydrogel Formation
19.3.1 Spontaneous Peptide Self-assembly
19.3.2 Enzymatically Assisted Hydrogelation
19.3.3 Cross-linking Enhanced Hydrogelation
19.4 Rheological Properties of Peptide Hydrogels
19.5 Mode of Action for Antimicrobial Peptide Hydrogel
19.5.1 Extracellular Interaction
19.5.2 Membrane Disruption
19.5.3 Intracellular Function Inhibition
19.5.4 Enhanced Host Defense/Immunomodulation
19.6 Key Features and Practical Usages of Antimicrobial Peptide Hydrogels
19.6.1 Antimicrobial Peptide Hydrogels with Multiple Functions
19.6.2 Enzymatically Assisted Smart Antimicrobial Drug Delivery
19.6.3 Stimuli-responsive Antimicrobial Agents
19.6.4 Short Peptide Mimicking the Antibacterial Effect of the Immune System
19.7 Conclusion, Challenges, and Future Perspectives
Acknowledgments
References
20. Supramolecular Peptide-based Nanomaterials for the Treatment of Fibrosis
20.1 Introduction
20.2 Antifibrotic Nanomaterials Based on Self-assembly of Peptide–Drug Conjugates
20.3 Antifibrotic Nanomaterials Based on Self-assembly of Bioactive Peptides
20.3.1 Bioactive Peptides Based on Natural Peptides
20.3.2 Bioactive Peptides Based on Synthetic Peptides
20.4 Applications of Peptide-based Nanomaterials in Multiple Antifibrotic Treatments
20.4.1 Peptide Therapy and Protein Therapy
20.4.2 Cell Therapy
20.4.3 Extracellular Vesicle Therapy
20.4.4 Gene Therapy
20.5 Conclusion and Perspective
References
21. Self-assembly of Peptides and Chromophores for Design of Theranostic Nanodrugs and Cancer Precision Therapy
21.1 Introduction
21.2 Molecular Design Principles for Peptides and Chromophores
21.2.1 Design Principles of Chromophore
21.2.2 Design Principles of Peptide
21.3 Chromophore and Peptide Self-assembled Theranostic Nanodrugs
21.3.1 Noncovalent Assembly of Chromophores and Peptides
21.3.2 Self-assembly of Molecular Peptide–Chromophore Conjugates
21.3.2.1 Directly Connected Peptide–Chromophore Conjugates
21.3.2.2 Peptide–Chromophore Conjugates with Connecting Group
21.4 Applications for Cancer Precision Therapy
21.4.1 Phototherapy
21.4.1.1 Photodynamic Therapy
21.4.1.2 Photothermal Therapy (PTT)
21.4.2 Chemotherapy Combined Phototherapy
21.4.3 Targeted Therapy Combined with Phototherapy
21.4.4 Immunotherapy Combined Phototherapy
21.5 Conclusions
Acknowledgments
References
22. Self-assembling Bioactive Peptides for Supramolecular Cancer Immunotherapy
22.1 Introduction
22.2 Bioactive Peptides
22.2.1 Antigenic Peptides
22.2.2 Adjuvant Peptides
22.2.3 Checkpoint Blockade Peptides
22.2.4 Immunomodulatory Peptides
22.3 Immunotherapy Approaches
22.3.1 Supramolecular Tumor Vaccines
22.3.1.1 OVA-based Antigen Peptide Co-assembly
22.3.1.2 Other Antigen Peptides Assembly
22.3.1.3 Antigen Peptide-based Conjugate Assembly
22.3.1.4 Supramolecular Self-adjuvant Assembly
22.3.2 Immune Checkpoint Blockade
22.3.2.1 ICB Peptide-based Assembly
22.3.2.2 Peptide Assembly Synergizing ICB
22.3.3 Immune Cell Regulation
22.3.3.1 Antigen Presentation Cells
22.3.3.2 Effector T Cells
22.3.3.3 Tumor-associated Macrophages
22.3.3.4 Other Immune Cells
22.3.4 Combination Therapy
22.3.4.1 Photodynamic Therapy
22.3.4.2 Photothermal Therapy
22.3.4.3 Chemotherapy
22.4 Conclusion
Acknowledgment
References
23. Self-assembled Stimuli-responsive Nanomaterials Using Peptide Amphiphiles for Targeting Delivery of Drugs
23.1 Introduction
23.2 Design of the PAs for Drug Nanocarriers
23.2.1 Self-assembly Building Blocks and Driving Forces
23.2.2 Programmed, Self-assembled System for Drug Nanocarriers
23.2.3 Cellular Uptake and Intracellular Delivery
23.3 Cell-penetrating PAs for Drug Nanocarriers
23.3.1 PAs with Cell-penetrating Peptide Building Blocks
23.4 Stimuli-responsive PA Drug Nanocarriers
23.4.1 pH-responsive Nanocarriers
23.4.2 Temperature-sensitive Nanocarriers
23.4.3 Redox-sensitive Nanocarriers
23.4.4 Enzyme-sensitive Nanocarriers
23.4.5 Other Stimuli-responsive Carriers
23.4.6 Multimodal-responsive Nanocarriers
23.4.7 Stimuli-responsive Hydrogel Nanocarriers
23.5 Targeting Delivery of PA-based Nanoscaffolds
23.5.1 Cell-targeted Delivery
23.5.2 Subcellular Organelle-targeted Delivery
23.5.3 Cardiovascular System and Brain-targeted Delivery
23.6 Supramolecular Theranostic Nanocarriers
23.6.1 Theranostic Nanocarriers
23.6.2 Antimicrobial Theranostic Nanocarriers
23.7 Other Applications of Stimuli-responsive Nanomaterials
23.7.1 Therapeutic Gas Transmitters
23.7.2 Photothermal Therapeutic Nanoagents
23.7.3 Cellular Cryopreserved Nanoagents
23.7.4 Others
References
Index