Self-assembly of porousa-helical nanosheets Open Access

Magnotti, Elizabeth Laird (2016)

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Two-dimensional materials, or nanosheets, such as graphene, which is 300 times stronger than steel and the best conductor of electricity, are enticing for applications in electronics, filtration, and energy storage. Proteins, which undergo hierarchical self-assembly into highly ordered structures, as a result of the amino acid sequence, are promising substrates for additional two-dimensional materials. Collagen mimetic peptides and peptoids, or N-substituted polyglycines, have been utilized to create two-dimensional materials, which can template the growth of inorganic materials and can be utilized as substrates for enzymatic reactions. The introduction of pores within biological nanosheets, could grant these materials additional roles in molecular encapsulation and charge transfer. In the following dissertation, α-helical peptides were utilized to create the first example of porous biological nanosheets. A three-fold α-helical design allowed for the generation of highly ordered nanosheets, whose phenotypes may be rationally modulated by manipulating the amino acid sequence. The results of these studies provide an alternate model for the design of interacting α-helices and provide a strategy for the design of porous structures.

Table of Contents

Chapter 1 Two-Dimensional Peptide and Protein Self Assembly. 1

1.1 Introduction. 1

1.2 Biological surface layers (S-layers). 3

1.3 Crystal Structures. 7

1.4 b-sheet peptide based 2D assemblies. 10

1.5 Collagen-based nanosheets. 14

1.6 Peptoid Nanosheets. 26

1.7 Peptide Assembly: Boundary Constrained 2D Assembly. 31

1.8 Protein assemblies: metal-stabilized cytochrome c 1D, 2D, and 3D assemblies. 34

1.9 Protein Assemblies: Protein Fusion Strategies. 39

1.10 Protein Assemblies: Computational Design of 2D Assemblies. 40

1.11 Conclusions and outlook. 43

Chapter 2 Design and characterization of an a-helical peptide 3FD-IL which forms nanosheets. 51

2.1 Introduction. 51

2.2 Design of 3FD-IL nanosheets. 53

2.3 Results and Discussion. 54

2.3.1 Self Assembly of 3FD-IL. 54

2.3.2 Small angle x-ray scattering. 62

2.3.3 The thickness of the 3FD-IL nanosheets and its implications for structure. 67

2.3.4 Solid-state NMR and the effect of hydration on structure. 74

2.3.5 Powder Small Angle X-Ray Scattering. 75

2.3.6 Orientation of the 3FD-IL nanosheets. 77

2.3.5 Hexagonal lattice of 3FD-IL. 81

2.4 Conclusions. 86

2.4.1 Model for Nanosheets. 86

2.4.2 Cryo-electron microscopy to determine the structure of the nanosheets. 87

2.5 Methods and Supporting Information. 90

Chapter 3: Manipulating Electrostatic Interactions to Obtain Information about structure of 3FD-IL and to access new conformations. 102

3.1 Introduction. 102

3.2 Design of peptides with altered charge pattern to probe helix orientation. 107

Self Assembly of Peptides with Altered Charge Patterns. 109

3.3 The effect of charge reversal on self-assembly of 3FD-IL. 118

3.4 Design of arginine and aspartic acid mutants. 123

3.5 Self-Assembly of Aspartate and Arginine Charge Mutants. 124

3.6 Conclusions. 134

3.7 Methods and Supporting Information. 135

Chapter 4 Design and Characterization of Hydrophobic Mutants of Peptide 3FD-IL. 151

4.1 Introduction. 151

4.2 Design of Hydrophobic Peptide Variants. 155

4.3 Results and Discussion. 156

4.3.1 Effect of Changing the Identity of Hydrophobic Amino Acids on Self Assembly 156

4.3.2 Effect of changing the Arrangement of Isoleucines and Leucines on Self-Assembly 169

4.3.3 Small angle x-ray scattering. 172

4.3.4 Atomic Force Microscopy. 174

4.3.5 Orientation of 3FD-LL nanosheets. 176

4.3.6 Hexagonal Packing of 3FD-LL nanosheets. 179

4.4 Conclusions. 180

4.41 Cryo-electron microscopy. 180

4.42 Conclusions. 181

4.5 Supporting Information. 182

Chapter 5: Conclusions. 191

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