MODULATING AMYLOID PEPTIDE SELF-ASSEMBLY WITH NUCLEOBASE INCORPORATION Open Access

Liu, Peng (2007)

Permanent URL: https://etd.library.emory.edu/concern/etds/fq977v02q?locale=en
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Abstract

In this dissertation, self-assembly of several short peptides originating from amyloid-ß peptide was investigated and was specifically probed with nucleobases incorporation. The Synthesis of β-(cytosine-1-yl)alanine is successful, and for the first time, nucleobases are successfully incorporated into amyloid beta peptide side chain. The nucleobase modified amyloid peptide, Aß(10-21)CyCy-NH2, is sufficient to form homogeneous amyloid fibrils. Cytosine nucleobase incorporation in Aß(10-21) reduced the nucleation phase and initiation of sheet-sheet contacts is crucial for the formation of nucleus. In order to simplify possible geometric constraints on assembly, Aß(13-21)CyCy was designed to exposure of the CyCy dyad at peptide N-terminus. The results established that Aß(13-21)CyCy forms homogenous nanotubes around the pKa of cytosine. The fibrils formed by Aß(10-21)CyCy and nanotubes formed by Aß(13-21)CyCy possess remarkably similar structural elements to those of the normal assembled amyloid fibrils, such as cross-β diffraction pattern and β-sheet secondary structures. Formation of homogenous stable nanotubes by Aß(13-21)CyCy was clearly pH-dependent.

Isotope edited FTIR result of Aß(13-21)CyCy established a parallel ß-sheet arrangement of Aß(13-21)K16A amyloid fibrils. SSNMR suggests two peptide arrangement patterns, a parallel ß-sheet organization and an anti-parallel ß-sheet organization, which probably results from the two clear morphologies. SSNMR results are consistent with isotope edited FTIR spectroscopy result so far. Combination of structural analysis and linear dichroism results, argues that the cytosine base interaction is along the ß-sheet lamination, inducing significant lamination growth and stabilizing the morphology of nanotubes.
These nucleobase modified amyloid peptides now have potential applications in the design of synthetic materials. Peptide self-assembly can be controlled by varying the the length of the peptide, and functional groups exposed on the surfaces can be tailored with different nucleobases. These studies have set the good base for more extensive development of peptide self-assembly for novel material development.

Table of Contents

TABLE OF CONTENTS
ACKNOWLEDGEMENTS
LIST OF FIGURES
LIST OF ABBREVIATIONS


CHAPTER 1: INTRODUCTION: THE AMYLOIDE BETA PEPTIDE SELF ASSEMBLY SYSTEM...1

THE AMYLOID BETA PEPTIDE SELF ASSEMBLY SYSTEM...1
STRUCTURE CHARACTERIZATION OF AMYLOID FIVRILS IN VITRO...2
KINETIC OF AMYLOID FIBRIL FORMATION...6
METALS AND AMYLOID BETA PEPTIDE IN ALZHEIMER'S DISEASE...7
EXPLORING AMYLOID GROWTH IN LAMINATION DIMENSION...8
MOLECULAR RECOGNITION MOTIFS AND SELF-ASSEMBLED PEPTIDE NANOSTRUCTURE...9
SUMMARY...14

CHAPTER 2: MODELING AND SYNTHESIS OF NUCLEOBASE MODIFIED AMYLOID PEPTIDE...15

INTRODUCTION...15
RESULTS...20

Molecular Dynamic Simulation of Nucleobases Modified Aβ(10-21)...20
Synthesis of Nucleobase Modified Amino Acids and Their Oligomerization...21

DISCUSSION...25
MATERIALS AND METHODS...26

CHAPTER 3: INVESTIGATION OF NUCLEOBASE EFFECT ON Aβ (10-21)...34

INTRODUCTION...34
RESULTS...36

Aβ(10-21)CyCy Forms Amyloid Fibrils...36
Aβ(10-21)CyCy Self-Assembly Under Different pH...36
Aβ(10-21)CyCy Secondary Structuren...41
Does Cytosine accelerate self-assembly?...45
Do the Aβ(10-21) and Aβ(10-21)CyCy assemblies have the same structure?...48
Point Mutation at His13 and His14 of Aβ(10-21)...48
Investigation of the surfaces of nucleobases modified amyloid fibrils...53

DISCUSSION...62
MATERIALS AND METHODS...64

CHAPTER 4: EXPLORING AMYLOID LAMINATION BY NUCLEASEBASE INCORPORATION IN Aβ(13-21)...69

INTRODUCTION...69
RESULTS...70

Aβ(13-21)CyCy Forms Homogenous Nanotubes...70
pH dependence of nanotube formation...74
Thermodynamic stability of Aβ(13-21)CyCy tubes...74
X-ray diffraction and Electron Diffraction constrains cross-β peptide arrays...78
Test for Cy/Cy association...79
Free N-termni plays a role in stabilizing the Aβ(13-21)CyCy Nanotubes...82
Aβ(13-21)CyCy Nanotube Acts as templates for metal deposition...89

DISCUSSION...91
MATERIALS AND METHODS...92

CHAPTER 5: STRUCTURAL CHARACTERIZATION OF NANO-TUBES BY ISOTOPE-EDITED IR AND SSNMR...98

INTRODUCTION...98
RESULTS...100

Isotope Edited FT-IR...100
Peptide Organization Study by Solid-state NMR...102
Probing the Cytosine Orientation by Linear Dichroism...109

DISCUSSION...111
MATERIALS AND METHODS...116

CHAPTER 6: CONCLUSIONS AND PERSPECTIVES...122
REFERENCES...126

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