Postdoctoral Fellow

Microbiology and Immunology

University of California, San Francisco (San Francisco, CA)

Philip Coffino

Exploit cODC, a sequence that directs ubiquitin-independent degradation, to characterize proteasome activity.

Proteasomes, the effectors of the ubiquitin-proteasome system that control protein degradation, are complex molecular machines. Selective degradation of labile regulatory factors and misfolded proteins is essential to cellular function and viability. The misregulation of proteolysis is implicated in a broad array of disease mechanisms, notably carcinogenesis. Our overall goal is to understand how this energy-dependent substrate degradation is accomplished by proteasomes. In particular, we are interested in the mechanisms of substrate association, how substrates are engaged/unfolded and the energetic requirements for degradation. To address these questions, we employ three classes of substrates. Each associates with proteasomes using distinct targeting signals. My work relates to: 1) reconstituting degradation in vitro for available substrate classes; 2) measuring and manipulating the energy consumed during substrate degradation; and 3) probing the mechanism of substrate engagement during unfolding and translocation. The most direct way to test hypotheses biochemically is to reconstitute activity in vitro using purified components, which I have done. The system has been employed to determine relevant kinetic parameters (Km values, turnover numbers and Ki values for competing substrates). I have also developed an assay to measure ATP consumption during degradation. I find that proteasomal degradation stimulates ATPase activity to varying degrees, depending on the nature of the substrate. Current work relates to quantifying the relationship between substrate stability and ATP consumed during degradation.

2006-present Ruth L. Kirschstein National Research Service Award, National Institutes of Health (GM20527)

1999-2002 NIH Molecular and Cellular Biology Training Grant Trainee, to determine primary physiological activity of eIF5A in yeast.