Amyloid beta-protein (Abeta) has been correlated with Alzheimer's disease (AD) which is the most common form of dementia. Abeta proteins assemble into oligomers, large aggregates, protofibrils before growing into fibrils. Recently more and more evidence has shown that the intermediate, oligomeric states of Abeta, rather than the fibrils are correlated with AD pathology. Among them, the 56 kDa dodecamer species was identified as a proximate toxic agent for AD onset. Therefore to understand the early oligomerization of Abeta proteins and to target the early assembly of Abeta are of significance for therapeutic strategy for AD treatment. In this thesis work, we use mass spectrometry coupled with ion mobility spectrometry method (IM-MS) to investigate the early assembly of Abeta proteins.

In the first, we sought to search for small molecule inhibitors for Abeta and understand their binding interactions and the mechanism of inhibitory actions. Several classes of small molecules, including Z-Phe-Ala-diazomethylketone (PADK), two derivatives of the Abeta C-terminal fragment Abeta(39-42), molecular tweezers, and ML, have been studied and shown different effects. These studies of small molecule inhibitors show that ion mobility spectrometry method has emerged to be a powerful tool for the screening and understanding of small molecule inhibitors for AD and other amyloid diseases.

In the second, we sought to understand the effects of amino acid substitutions on Abeta structure and aggregation. Two recently discovered familial mutations at Ala2 (A2) within Abeta, a protective A2T mutation and a recessive A2V mutation were investigated. Our ion mobility studies reveal different assembly pathways for early oligomer formation for each peptide and provide a basis for understanding how these two mutations lead to, or protect against, AD.

Lastly, we also sought to understand the early assembly of amyloid beta-protein (Abeta) from different rodent species. We investigate the biophysical and biological properties of Abeta peptides from humans, mice (Mus musculus), and rats (Octodon degus).

In conclusion, we have successfully applied ion mobility spectrometry method to understand complicated aggregation systems. This provides a powerful tool to screen small molecule inhibitors for Abeta proteins and sheds light onto their inhibitory mechanisms. The studies of Abeta mutants imply that ion mobility method can be used as new tool in developing an understanding of the effect of familial mutations on Abeta assembly in AD and the assembly of other mutated protein systems.