This talk was recorded Jan 28, 2013 as a practice talk for my Candidacy Exam at University of California, San Diego. It discusses my current... » More

This talk was recorded Jan 28, 2013 as a practice talk for 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.

Abstract

The rate at which novel protein folds are discovered has declined rapidly, leading to some hope that currently known protein structures cover the majority of protein fold space utilized by nature, at least within well-sampled classes of proteins [1]. This presents an opportunity to globally analyze fold space. In my proposed thesis I will look for answers to the following ambitions questions:

• How do new folds evolve from existing ones? What are the relative frequencies of known mechanisms for forming new folds?


• Is fold space continuous or discrete? How can it display properties of both?


• How can an understanding of protein fold space translate into insights about specific protein families?

Although these questions are quite broad, I think that the key elements are now in place to make answers accessible in a PhD thesis. I first redefine these questions as clear computational problems. I then propose some algorithms that could be used to solve the problems, as well as summarize some steps, which have already been taken towards understanding, fold space. Finally, I describe an evolutionary model, which places the computational results in a biological framework.

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