DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression.

ABSTRACT:

Background

Genome-scale models of metabolism and macromolecular expression (ME models) enable systems-level computation of proteome allocation coupled to metabolic phenotype.

Results

We develop DynamicME, an algorithm enabling time-course simulation of cell metabolism and protein expression. DynamicME correctly predicted the substrate utilization hierarchy on a mixed carbon substrate medium. We also found good agreement between predicted and measured time-course expression profiles. ME models involve considerably more parameters than metabolic models (M models). We thus generate an ensemble of models (each model having its rate constants perturbed), and then analyze the models by identifying archetypal time-course metabolite concentration profiles. Furthermore, we use a meta

SUBMITTER: Yang L 

PROVIDER: S-EPMC6327497 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature