Main | Model | Workflow | Data and software | Project "Enzyme dynamics and function"
Enzyme cost minimization Enzyme cost plays a major role in the choice of metabolic routes, both in evolution and bioengineering. Given desired fluxes, necessary enzyme levels can be estimated based on known rate laws and on a principle of minimal enzyme cost. This estimation is greatly facilitated by formulating it as a convex optimality problem. The set of feasible metabolite profiles forms a polytope in log-concentration space, whose points represent all possible steady states of a kinetic model. Enzyme cost is a convex function on this polytope. This makes enzyme cost minimization (ECM) - finding optimal enzyme profiles and corresponding metabolite profiles that realize a desired flux at a minimal cost - a convex optimization problem. By separating the cost contributions from enzyme capacity, energetics, and kinetics, we construct simple enzyme cost functions, applicable even if few or no parameter values are known. |
On this website, you can software for enzyme cost minimization (in matlab and python), as well as all data files for an example, a kinetic model of central carbon metabolism in E. coli.
If you use enzyme cost minimization in your work, please reference our article
Noor E., Flamholz A., Bar-Even A., Davidi D., Milo R., Liebermeister W. (2016),
The protein cost of metabolic fluxes: prediction from enzymatic rate laws and cost minimization
PLoS Comp. Biol. 12 (10): e1005167