Mass spectrometry analysis of amyloid formation mechanisms

More than 50 human conditions are characterised by the deposition of aberrantly aggregated proteins into amyloid fibrils. These diseases range from neurodegenerative diseases associated with aging to systemic conditions associated with medical interventions. The protein(s) involved in aggregation varies in each condition. Few of these diseases currently have therapeutics available and they represent a growing health burden to society. Increasing the understanding of the processes of amyloid protein aggregation and the mechanisms by which it can be inhibited is vital to developing strategies to combat these diseases. In this thesis, mass spectrometry and supporting biophysical and biochemical techniques were used to characterise the activity and interactions of two amyloid aggregation modulators, YDL085CA and the peptide QBP1, with amyloidogenic proteins. YDL085CA, a small highly charged protein orthologous to the known modifier of amyloid aggregation MOAG-4/SERF1, was found to have an extremely buffer dependent effect on the aggregation of the amyloid protein Aβ40. In ammonium bicarbonate it was shown to accelerate amyloid formation while in sodium phosphate it was shown to act as an inhibitor. This observation suggests a prominent role for ionic strength and specific ion effects. The activity of YDL085CA was shown, by crosslinking followed by mass spectrometric analysis, to be mediated by interactions with regions of α-helical secondary structure in the YDL085CA protein. QBP1, an 11-residue synthetic peptide, has been shown previously to inhibit the formation of amyloid fibrils by polyglutamine proteins, including ataxin-3. Native mass spectrometry studies on a range of ataxin-3 constructs revealed that QBP1 interacts with the monomeric ataxin-3. Unexpectedly, the site of interaction was localised not to the polyglutamine domain, but to a distal region lacking defined structure.