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Protein evolution proceeds through genetic mechanisms, but selection acts on biological assemblies. I define a protodomain as a minimal independently evolving unit with conserved structure. Protodomain rearrangements have minimal impact on biological assemblies, so they represent a valid evolutionary path through fold space.
This report is the written portion of my Candidacy Exam at University of California, San Diego. It discusses my current research in Philip Bourne's lab, as well as proposes research for my thesis over the next two years. Slides for the oral presentation are available at http://www.slideshare.net/sbliven/following-the-evolution-of-new-protein-folds-via-protodomains