title: The origins of time-delay in template biopolymerization processes.
abstract: Time-delays are common in many physical and biological systems and they give rise to complex dynamic phenomena. The elementary processes involved in template biopolymerization, such as mRNA and protein synthesis, introduce significant time delays. However, there is not currently a systematic mapping between the individual mechanistic parameters and the time delays in these networks. We present here the development of mathematical, time-delay models for protein translation, based on PDE models, which in turn are derived through systematic approximations of first-principles mechanistic models. Theoretical analysis suggests that the key features that determine the time-delays and the agreement between the time-delay and the mechanistic models are ribosome density and distribution, i.e., the number of ribosomes on the mRNA chain relative to their maximum and their distribution along the mRNA chain. Based on analytical considerations and on computational studies, we show that the steady-state and dynamic responses of the time-delay models are in excellent agreement with the detailed mechanistic models, under physiological conditions that correspond to uniform ribosome distribution and for ribosome density up to 70%. The methodology presented here can be used for the development of reduced time-delay models of mRNA synthesis and large genetic networks. The good agreement between the time-delay and the mechanistic models will allow us to use the reduced model and advanced computational methods from nonlinear dynamics in order to perform studies that are not practical using the large-scale mechanistic models.
authors.affiliation: Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America.
authors.forename: Luis
authors.initials: L
authors.lastname: Mier-y-Terán-Romero
authors.forename: Mary
authors.initials: M
authors.lastname: Silber
authors.forename: Vassily
authors.initials: V
authors.lastname: Hatzimanikatis
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins / Q000235:genetics; D007700:Kinetics; D008957:Models, Genetic; D017711:Nonlinear Dynamics; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D015533:Transcriptional Activation
chemical_list: D029968:Escherichia coli Proteins; D012333:RNA, Messenger