Peptide model systems for amyloid fiber formation: design strategies and validation methods

The rational understanding of the factors involved in the formation of amyloid deposits in tissue is fundamental to the identification of novel therapeutic strategies to prevent or cure pathological conditions such as Alzheimer's and Parkinson's disease or spongiform encephalopathies. Given the complexity of the molecular events driving protein self-association, a frequent strategy in the field has consisted of designing simplified model systems that facilitate the analysis of the elements that predispose polypeptides toward amyloid formation. In fact, these systems have provided very valuable knowledge on the determinants underlying structural transitions to the polymeric beta-sheet state present in amyloid fibers and more disordered aggregates. In this chapter, we will describe different approaches to obtain and design model systems for amyloidogenesis, as well as the methodologies that are typically used to validate them. We will also show how some of the general principles obtained from these studies can be applied for de novo design purposes and for the sequence-based identification of amyloidogenic stretches in proteins.