Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer’s, Creutzfeld-Jacob, diabetes, Parkinson’s and others. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. Amyloid fibrils are composed of proteins that originate in an innocuous α-helix or random-coil structure. The α-helices convert their structure to β-strands that aggregate into β-sheets, and then into protofibrils, and ultimately into fully formed amyloid fibrils. On the basis of experimental data, I have developed a mathematical model for the kinetics of the reaction pathways and determined rate parameters for peptide secondary structural conversion and aggregation during the entire fibrillogenesis process from random coil to fibrils, including the molecular species that accelerate the conversions. The specific steps of the model and the rate constants that are determined by fitting to experimental data provide insight on the molecular species involved in the fibril formation process. To better understand the molecular basis of the protein structural transitions and aggregation, I report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccβ, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow β-hairpin proteins to straighten, and the subsequent formation of interchain hydrogen bonds during aggregation into amyloid fibrils. For my MD simulations, I found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccβ protein experiences during the process of forming protofibrillar structures. Both the mathematical modeling of the kinetics and the MD simulations show that molecular structural heterogeneity is a major factor in the process. The MD simulations also show that intrachain and interchain hydrogen bonds breaking and forming is strongly correlated to the process of amyloid formation.
