Department of Chemical Engineering
Massachusetts Institute of Technology
77 Massachusetts Ave.
Cambridge, MA 02139 USA
Phone: (617) 258-8037
B.S. Chemical Engineering
Business Foundations Certificate
University of Texas at Austin 2010
Numerous applications of metabolic engineering may be able to benefit from the use of synthetic protein scaffold devices (Dueber et al., 2009; Moon et al., 2010). These scaffolds consist of protein domains that are designed to spatially recruit sequential pathway enzymes tagged with cognate peptide ligands. The resulting in vivo co-localization of these enzymes can increase pathway flux in E. coli.
Conditions for pathways most likely to benefit from the use of scaffolding are unclear at this time. Similarly, the scaffolds are modular, and certain scaffold arrangements have performed better than others depending on the pathway (Whitaker and Dueber, 2011). The ability to correctly predict the scaffold architecture that will result in the greatest enhancement of pathway flux is eventually desired, particularly compared to the only current alternative of experimentally probing many permutations.
To facilitate understanding and adoption of these scaffolds for further metabolic engineering applications, my research focuses on using a model pathway to experimentally and computationally explore the effects of parameters such as scaffold arrangement and metabolite concentrations on the overall pathway flux. The selected pathway features enzymes exclusively with monomeric quaternary structure. Salient advantages of using this pathway are more predictable enzyme-scaffold complex structure and simpler kinetics than in either the mevalonate or glucaric acid pathways.
I am also examining whether protein scaffolds can be used to increase flux through one of the biofuel pathways under investigation in our lab.
Dueber et al. Synthetic protein scaffolds provide modular control over metabolic flux. Nat. Biotech., 2009.
Moon et al. Use of modular, synthetic scaffolds for improved production of glucaric acid in engineering E. coli. Metab. Eng., 2010.
Whitaker and Dueber. Metabolic flux enhancement by synthetic protein scaffolding. Methods Enzymol., 2011.