title: A resource dependent protein synthesis model for evaluating synthetic circuits.
abstract: Reliable in silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the Ribosome Flow Model and among other things describes the movement of RNA-polymerase and ribosomes on mRNA and DNA templates, respectively. By analyzing the convergence properties of this model based upon geometric considerations, we present additional insights into the dynamic mechanisms of the process of protein synthesis. Further, we demonstrate how this model can be used to evaluate the performance of synthetic gene circuits under different loading scenarios.
authors.affiliation: Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart, Germany. Electronic address: wolfgang.halter@ist.uni-stuttgart.de.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Halter
authors.affiliation: Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart, Germany.
authors.forename: Jan Maximilian
authors.initials: JM
authors.lastname: Montenbruck
authors.affiliation: Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart, Germany.
authors.forename: Zoltan A
authors.initials: ZA
authors.lastname: Tuza
authors.affiliation: Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Allgöwer
mesh_terms: D003198:Computer Simulation; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism; D053263:Gene Regulatory Networks; D008958:Models, Molecular; D009068:Movement; D014176:Protein Biosynthesis; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism; D058615:Synthetic Biology; D013698:Templates, Genetic
chemical_list: D012321:DNA-Directed RNA Polymerases
keywords: Genetic regulatory networks; Host-circuit interactions; Normally hyperbolic manifolds; Resource dependence; Synthetic biology