Kemp, Josh Paul2006-07-282006-07-2820012001http://hdl.handle.net/10012/624This thesis focuses on the use of minimal models to study biological molecules such as proteins. The major aim of this work was the design and study of a new minimal model that could be used to study the statistical properties of the anisotropic interactions in helical forming segments. We discuss in detail what effect the potential energy form has on these various states by systematically varying the potential from strongly anisotropic to isotropic. The data demonstrates that the foldability of a helix is strongly related to the anisotropic nature of the potential. The model is further modified to examine the folding process of these segments with emphasis on how nucleation and anisotropy affect folding. The folding times of different helical systems are examined. The results demonstrate that the foldability of the helix segments are strongly correlated to the interplay between nucleation and propagation. This interplay not only affects the foldability of the structure, but significantly affects the scaling behaviour of the folding times. Finally, a classic minimal lattice model is implemented to study the folding properties of prion-like sequences. With this simplified model we attempt to find sequences that exhibit prion-like behavior. The sequences that are identified as prion-like are further studied by analyzing the native state structures for the features that give these sequences their unique properties.application/pdf7293533 bytesapplication/pdfenCopyright: 2001, Kemp, Josh Paul. All rights reserved.Harvested from Collections CanadaDoctoral Thesis