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The Washington Research Foundation Fellowship

Jeff Nivala, Bioengineering - 2009-10 WRFF

Jeff Nivala photoMy passion for tinkering with microscopic life was first cultivated at a young age in the makeshift garage laboratories of my adolescence. From those roots of cataloging the protozoan I found in the rain puddles of my backyard to cooking up homemade bacterial media in my kitchen, I didn’t waste time getting started on formal research once I was accepted into the UW. The summer before I began my freshman year, I joined the bioengineering lab of Gerald Pollack. During the year that I spent in his lab working on probing the physical properties of interfacial water, I learned a great deal about applying the concepts learned in the classroom to problems faced in my research work. After bouncing around a couple of other labs, I was fortunate enough to land in the biochemistry lab of David Baker. Now I am in the midst of a challenging, yet rewarding research project that will also become my senior thesis work. The Washington Research Foundation Fellowship has afforded me the opportunity to purse this project with the best of my abilities, and I am incredibly thankful and humbled to have received such a reward. It has further motivated me and will be a propelling force that will drive me into graduate school. After graduate study, I hope to enter industry with the eventual dream of starting my own biotech company.

Mentor: David Baker, Biochemistry

Project Title: Enzyme Specificity Engineering: Designing a Human Cystosine Deaminase for Prodrug Activation

Abstract: My project seeks to design and create a novel human enzyme, cytosine deaminase, for use in prodrug therapy. Cytosine deaminase catalyzes the deamination of cytosine, converting it into uracil. There is clinical need for a human cytosine deaminase for use as a prodrug activator in suicide gene therapy, where a cytosine deaminase can catalyze the reaction of the cytosine derivative 5-fiuorocytosine (a harmless chemical) into 5-fluorouracil (a cytotoxin). While there are cytosine deaminases that exist in nature, there is no human enzyme capable of catalyzing this reaction. The use of non-human enzymes in prodrug therapy often fails due to the immunogenicity issues that often arise. Therefore, by taking a human enzyme and altering its activity such that it can catalyze the deamination of cytosine, these immunogenicity issues can be avoided. In order to engineer a novel human cytosine deaminase (hCDA) I will build upon previous work that successfully re-engineered a human guanine deaminase (hGDA) to have ammelide deaminase (hAmDA) activity. Since there is considerable structural homology between guanine, ammelide, and cytosine, re-engineering this previously designed ammelide deaminase enzyme to have activity on cytosine should be possible. To do this, I will be using a Rational Design approach aided by computational simulation to alter the active site residues of the previously designed enzyme to better match the active site structure of a bacterial cytosine deaminase (bCD). This will create an active site more complementary to cytosine and hopefully introduce novel cytosine deaminase activity.