Amyloid: Merging the Properties of Membranes and Enzymes Open Access
Childers, William Seth (2010)
Abstract
Abstract
Amyloid: Merging the Properties of Membranes and Enzymes
By W. Seth Childers
Since the first observation of amyloid deposits more than 150 years
ago, amyloid fibers have
played a critical yet uncertain role in neurodegenerative disease.
At the core of this uncertainty are
the cross-β variations proposed to lead to distinct amyloid
polymorphs that underpin different
phenotypes. Yet it is unclear how peptide sequence directs
polymorphism and functional
differences. Here I have used the critical nucleating core of the
Alzheimer's Disease peptide, Aβ(16-
22), as a model to address the molecular origins of amyloid
polymorphism and understand core
properties that lead to amyloid's diverse functions. Solid-state
NMR and diffraction studies revealed
that simple amino acid changes direct structural polymorphs by
modulating both β-strand and β-
sheet pleat registry. Interestingly, these short peptides form
hollow nanotubes in which peptides
interact via termini interactions to form a peptide bilayer wall.
Like membranes, these amyloid
assemblies have diverse conditionally dependent phases including
fibers, nanotubes, oligomers,
twisted and helical ribbons, and lamellar bundles of nanotubes. The
cross-β assemblies bind small
molecules (e.g. congo red) and precisely template them into
organized molecular arrays providing the
spectroscopic origins of congo red's apple-green birefringence. I
further demonstrated that these
lysine-rich amyloid assemblies serve as retro-aldolase catalysts.
Taken together, I argue that physical
properties of amyloids can best be seen as merging the long-range
order of membranes with the
catalytic features of enzymes and that simple amyloid structures
could provide an early prebiotic
catalyst leading to the emergence of complex chemical systems.
Table of Contents
Table of Contents
Chapter 1: Amyloid - An Enigmatic Peptide Assembly 1Amyloid An Historic Structural Challenge 1
Connecting Morphological Variation with Cross-beta Teriary Structure 5
The Next Structural Challenge: Strain Diversity 7
Molecular Origins of Prion Species Barriers 8
Extension of the Strain Concept to Neurodegenerative Disease 11
Dramatic Impact of Amyloid Co-Assembly in Neurodegenerative Disease 11
Intertwined Nature of Amyloid Dyes and Stain Architecture 13
Mounting Unanswered Questions about a Common Protein Fold 14
Chapter 2: Molecular Origins of Cross-beta Strains 23
Methods 25Secondary Structural Analysis 35
beta-sheet Registry Determined by Solid-State NMR 37
NMR Distance Measurements to Probe Extended Peptide Backbone 44
Probes of beta-sheet Lamination 46
Cross-Strand Pairing Dictates Peptide Registry 52
Orientation of beta-sheet 57
Discussion 60 Chapter 3: Amyloid Peptides Organized as Bilayer Membranes 71 Methods 73Development of Microscopy Methods to Visualize Nanotube Walls 81
Probing the Bilayer Structure 82
Probing Inner and Outer Bilayer Surfaces 89
Calculation of Surface-to-Volume Ratio 93
Conclusions 96 Chapter 4: The Phases of Peptide Oligomerization 104 Methods 107 Initial Phase Transition 109 Internal Oligomer Structure 114Creating Nanotubes and Fiber from Oligomers 121
Impact of Filament Width on Morphology 128
Influence of Salts on Peptide Oligomerization 129
Discussion 131 Chapter 5: Specificity in Amyloid Self-Assembly 139Preliminary Evaluation of Peptide Mixing 141
The Co-assembly of KLVFFAL and KLVFFAV 142
Probing the Degree of Phase Separation 145
Probing Secondary Structural Differences of Assemblies 149
Testing the effect of Decreasing Side-Chain Length 154
Conclusions 157Chapter 6: Templating Molecular Arrays in Amyloid's Cross-b Grooves 162
Methods 166Preliminary Analysis of E22L and E22V Nanotubes 170
CR Binds to E22L Nanotubes that Expose the Termini Surface 172
CR Binding does not alter KLVFFAL's Cross-b Structure 174
CR is Oriented Along the Nanotube Surface 176
CR Docking Model 177 CR Binds at High Density 178Potential Influence of Biphenyl Conformation Change 182
Discussion 183 Chapter 7: Amyloid as a Catalyst 194 Methods 195 Results 198Docking of Methodol to KLVFFAL Nanotube Surface 203
Structural Analysis and Catalysis 205 Conclusions 208Chapter 8: Conclusions - Amyloids as Conformationally Rich Catalytic Membranes 211
Amyloid: Encoding Information Through Conformation 211
Amyloid: Conformational Variation in beta-sheet Strand Registry 211
Amyloid: Conformational Variation in beta-sheet Pleat Registry 213
Amyloid as a Peptide Bilayer Membrane 214
Amyloid as a Catalyst 217Amyloid: A Platform for the Emergence of Chemical Systems 218
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