The Role of Native State Topology in Protein Folding and Dynamics

The content of this thesis is organized as follows. In the first chapter, the main computational technique used in this work are presented along with a detailed description of the topological approach to the study of protein folding, which has been developed during these years at SISSA. The second chapter is devoted to the study of the folding of intracellular antibodies a class of proteins particularly interesting because of their possible use in functional genomics experiments performed on living cells. These proteins have been selected in SISSA labs as blocking agents of tau protein (15), a molecule involved in the onset of Alzheimer' s neurodegeneration. The third chapter is devoted to the study of the folding characteristics of the prion protein that is considered the pathogenic agent of a class of neurodegenerative diseases known as prion diseases. The fourth chapter is dedicated to the study of the dynamic characteristics of the complex formed by the Nerve Growth Factor (NGF) and its extracellular receptor TrkA. Those proteins are also involved in the complex phenomenology that characterizes the Alzheimer' s disease.