Understanding the mechanism of peptide self-assembly

Understanding the molecular mechanism of peptide self-assembly is vital; both as a fundamental biological process but also to combat the pathological disease state known as amyloid. A wide range of techniques, including computer simulations and biophysical assays, will need to be employed to answer this question. The development of experimental techniques that can capture and isolate the fleeting states that occur during peptide self-assembly is thus essential in order to elucidate the underlying mechanism. In order to meet this need, Chapter 1 outlines key concepts that relate to peptide self-assembly by examining two key examples (diphenylalanine and the amyloid-β peptide). In Chapter 2, a combination of experiments (including photo-induced cross-linking and fluorescence quenching) and discontinuous molecular dynamics simulations were used to understand the self-assembly process of a small amyloid peptide, Aβ16-22, at the molecular level. In Chapter 3, both the experimental methods that have been developed and the understanding of the mechanism of Aβ16-22 self-assembly were extended to understand the mechanism by which Aβ16-22 interacts with, and influences the aggregation rate of, a related sequence, Aβ40. Together, the work presented here describes how it is possible to explore complex self-assembling systems, with temporal resolution, at the molecular level.