Informatic analysis of proteins with a role in oxidative damage and ageing
Ageing is a complex, universal process that remains very poorly understood, particularly in mammals. This thesis attempts to increase our understanding of ageing by predicting the structure of the uncoupling proteins, membrane proteins with a possible role in the modulation of oxidative damage, and therefore of ageing. A 3-dimensional model of the uncoupling proteins is generated, based on an analysis of known membrane proteins structures. In order to assess the accuracy of this model it is compared to the actual structure of a homologous protein, solved after the modelling was complete. A homology packing model is produced that, in combination with predictions of likely functional residues, will be of use in establishing the mechanism of action of the uncoupling proteins. Additionally, this thesis investigates the regulation of ageing by the insulin-like signalling pathway and the transcription factor DAF-16. Longevity- and ageing-associated transcription factor binding sites are identified, due to their over- or under-representation within genes regulated by this pathway. Direct and indirect DAF-16 target gene classes are identified, and possible mechanisms of feedback control of the pathway are investigated, including the identification of other transcription factors whose expression is regulated by DAF-16. Although this work is a valuable starting point, considerable further work will be required before a full understanding of the regulation of ageing is obtained. Finally, this thesis has provided insights into membrane protein structure and its pre diction. A comprehensive analysis of these structures was performed and the results used to develop a modelling method that is applicable to structure prediction for all membrane proteins. Although buried transmembrane helix faces were identified with relatively high accuracy, a greater understanding of membrane protein structure is required before reliable 3-dimensional models can be produced using this method. The opening of a structural genomics project focused on membrane proteins is helping to bring the realisation of this aim closer to the present. This work was generously supported by the Biotechnology and Biological Sciences Research Council.