Home Department: Engineering
Mentor: Markus Covert (Bioengineering)

“The Quantitative E. coli Metalloproteome from Computational Whole-Cell Modelling Reveals Novel Physiological Tradeoffs and Elucidates
Unknown Protein Function"

Although E. coli is well-characterized, a quantitative analysis of protein-metal interactions is experimentally intractable. The Covert Lab is developing a computational whole-cell model that predicts exact protein/metal counts and their interactions. Their recent simulations predict that adding zinc rescues cells grown without methionine, industry growth media lacks sufficient molybdenum for optimal growth, and yggX (an uncharacterized protein) may be a nickel chelator. Tim plans to experimentally validate this methionine-zinc/molybdenum hypothesis, run docking simulations to verify yggX-nickel binding, and continue parsing metalloproteome data for other unknown proteins. If successful, the Covert lab would elucidate previously-neglected pathways for bacterial growth and multiple protein functions.