Synthetic Pathway Design for Metabolic Engineering
Using enzymes as biocatalysts would provide a renewable route for the production of specialty and industrial chemicals. The range of desired products often exceeds those for which existing biosynthetic reactions have been reported, therefore, we have created a in silico pipeline for discovering and engineering new (non-natural) biosynthetic routes.
- Assembly of known & novel biochemical pathways to produce target compounds
- Combined systems and molecular-level approaches to assess feasibility of designed biosynthetic routes
- Systems approaches assess feasibility in the context of pathway thermodynamics
- Molecular-level approaches assess feasibility of the reaction mechanism
- substrate promiscuity / substrate ambiguity / catalytic promiscuity
- Computational collaboration with Prof. Vassily Hatzimanikatis and the LCSB (EPFL)
- Reference Publications:
- Brunk, Elizabeth, et al. Biotechnology and bioengineering 109.2 (2012): 572-582.
- Lechner, A; Brunk, E; Keasling, JD. The Need for Integrated Approaches in Metabolic Engineering Cold Spring Harbor Perspectives (2016)
- Brunk, E; et. al. Characterizing Strain Variation in Engineered E. coli Using a Multi-omics based workflow. Cell Systems (2016)