Conformational Exchange: A Common Mechanism for Amyloid Assembly Open Access

Simmons, James Austin (2011)

Permanent URL: https://etd.library.emory.edu/concern/etds/jd472x08w?locale=en
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Abstract



Amyloid fibrils cause disease and serve functional roles. The formation of these
structures follows an amyloid assembly pathway which involves the aggregation of
peptide monomers into oligomers that later transition into β-sheet fibrils. The mechanism
responsible for this transition is currently unknown. Using amyloid peptide truncations,
the monomeric and assembled states of amyloid fibril formation share a common
secondary structure, a polyproline II helix, which is often observed for unordered
peptides. This process can occur in the presence of phospholipid membranes.
Phospholipid membrane vesicles are used to mimic the peptide oligomers observed
during amyloid assembly. Using Aβ(13-21), a peptide derived from the full-length
amyloid-β (Aβ) peptide and whose assembly is controllable, the mechanism of amyloid
assembly in the context of membranes is shown to occur on the membrane surface. This
solvent microenvironment likely mimics that of the oligomer-water interface and
strengthens this location as the site that initiates assembly. A novel mechanism for
amyloid assembly - conformational exchange - is proposed in which solvent polarity
microenvironments dictate a secondary structural change that initiates the formation of
amyloid fibrils. This new insight allows thermodynamics and kinetics to control amyloid
peptide orientation, registry, and mixing.



Conformational Exchange: A Common Mechanism for Amyloid Assembly


B.S. Davidson College, 2003
Advisor: David G. Lynn, Ph.D.
A dissertation submitted to the Faculty of the
James T. Laney School of Graduate Studies of Emory University
in partial fulfillment of the requirements for the degree of
Doctor of Philosophy
in Chemistry
2011

Table of Contents

Table of Contents
Chapter 1 Mechanisms of Amyloid Fibril Formation

................................................... 1
1.1 Amyloid Peptide Fibrils - the Good, the Bad, and the Characteristics ........................ 2
1.2 Amyloid Fibril Structural Characterization .................................................................. 3
1.3 Amyloid Fibril Formation - Kinetic Mechanisms ........................................................ 7
1.4 Amyloid Fibril Formation - Thermodynamic Mechanism ......................................... 10
1.5 Aβ Interactions with Phospholipid Membranes .......................................................... 11
1.6 Summary ..................................................................................................................... 14

Chapter 2 Characterization of an Unassembled Amyloid Derived Peptide
Monomer:Aβ(13-21) ....................................................................................................... 15
2.1 Introduction. ................................................................................................................ 16
2.2 Results and Discussion ............................................................................................... 18
2.2.1 Structural Analysis of Aβ(13-21) with CD .............................................................. 18
2.2.2 Effects of pH on Aβ(13-21) ..................................................................................... 20
2.2.3 Structural Analysis of Aβ(13-21) with FT-IR ......................................................... 22
2.2.4 Effects of Temperature on Aβ(13-21) ..................................................................... 24
2.2.5 Structural Analysis of Aβ(13-21) with NMR .......................................................... 24
2.2.6 Effects of Ionic Strength on Aβ(13-21) ................................................................... 28
2.2.7 Aβ(13-21) Assembly by NMR ................................................................................ 29
2.2.8 Characterizing Aβ(13-21) Position on the Assembly Pathway with SANS ............ 31
2.2.9 Characterizing Aβ(13-21) Position on the Assembly Pathway with DLS ............... 33
2.2.10 Analyzing Aβ(13-21) Position on the Assembly Pathway with Fluorescence ...... 33


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