Proteome Constraints in Genome-Scale Models
Book chapter, 2021

Genome-scale metabolic models (GEMs) describe the stoichiometry of all reactions in the cellular metabolic network, and at the same time associate the reactions to the enzymes that catalyze them. This chapter discusses proteome constraints followed by examples on how one particular type of cellular constraint, namely a proteome constraint, is a powerful approach to improve the predictive strength of GEMs. Cells operate under myriad constraints that govern their phenotypes and functioning. A fundamental constraint in the context of metabolism is the conservation of mass and energy. The chapter addresses the recently developed approach GECKO to illustrate how proteome constraints can be integrated into a GEM in a coarse-grained manner. Coarse-grained approaches as GECKO provide a straightforward platform to integrate proteome constraints. Contrasting with the coarse-grained integration, fine-tuned approaches tend to explicitly integrate biological processes into a GEM, example protein synthesis process.

cellular metabolic network

protein synthesis process

coarse-grained approaches

fine-tuned approaches

proteome constraints

genome-scale metabolic models

Author

Yu Chen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Jens B Nielsen

Technical University of Denmark (DTU)

BioInnovation Institute

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Eduard Kerkhoven

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Metabolic Engineering: Concepts and Applications: Volume 13a and 13b

Vol. 13 137-152
9783527823468 (ISBN)

Subject Categories

Biochemistry and Molecular Biology

Bioinformatics (Computational Biology)

Bioinformatics and Systems Biology

DOI

10.1002/9783527823468.ch4

More information

Latest update

7/12/2024