| The class of investigative methods collectively termed evolutionary or comparative genomics embraces the principle that features of a protein or nucleic acid are significantly influenced by ancestry and are the product of extensive natural selection. The application of different computational techniques exploiting this principle yields insight into evolution and function, and also provides a sound theoretical framework for further experimental investigation. This dissertation yields such insights by applying these techniques to selected protein folds, namely the PUA, P-loop NTPase, Rossman, and beta-grasp folds.; Highlights of these investigations include the discovery of a conserved protein domain in the ASC-1 transcriptional coactivator complex with an ancestral linkage to the PUA fold and prediction of an RNA-binding role for the domain. Multiple evolutionary origins for viral DNA packaging ATPases of the P-loop NTPase fold were discovered, and novel components of viral DNA packaging systems were detected. Contrary to previous assumptions, portal proteins of diverse tailed phages, the primary interacting partners of packaging ATPases, were determined to be of monophyletic origin. A third higher-order assemblage of domains belonging to the Rossmann-like fold was established, unified by conserved sequence features which contribute to metal-chelation. Determinants of catalytic activity in the Haloacid Dehalogenase (HAD) and E1-like protein superfamilies of the Rossmann fold were elucidated; these findings show how structural and domain architecture variation have influenced exploration of substrate space by these superfamilies. These investigations also led to the identification and crystallization of the first member of the HAD superfamily lacking catalytic activity, and functional predictions for this inactive HAD domain. The determinants of functional diversity in the beta-grasp fold were also identified resulting in discovery of a novel superfamily of ligand-binding beta-grasp domains, the first dedicated soluble-ligand binding activity identified in the fold. Functional predictions for domains in this superfamily were made for diverse systems such as polysaccharide export, DNA uptake, and intracellular redox reactions. Investigations into the beta-grasp fold also led to the elucidation of the evolutionary origins of the eukaryotic ubiquitin signaling system and the prediction of several distinct, entire modification systems in prokaryotes featuring conjugation and deconjugation of ubiquitin-like proteins. |
