Dynamic Model of the Process of Protein Synthesis in Eukaryotic Cells

  title={Dynamic Model of the Process of Protein Synthesis in Eukaryotic Cells},
  author={Nadav Skj{\o}ndal-Bara and David R. Morrisb},
  journal={Bulletin of Mathematical Biology},
Protein synthesis is the final step of gene expression in all cells. In order to understand the regulation of this process, it is important to have an accurate model that incorporates the regulatory steps. The model presented in this paper is composed of set of differential equations which describe the dynamics of the initiation process and its control, as well as peptide elongation, starting with the amino acids available for peptide creation. A novel approach for modeling the elongation… Expand
Modeling and control of the protein synthesis process in eukaryotic cells
A reduced model of the initiation process using the eukaryotic initiation factor (eIF)-2 unit is presented and methods to control it are proposed and linearization of the model is presented as a measure to simplify the analysis and the control applications. Expand
A systems view of the protein expression process
The biological facts and mathematical models for each stage of the protein production process are reviewed and it is concluded that advances in experimental techniques leading to a detailed description of the process have not been matched by mathematical models that represent the details of theprocess and facilitate analysis. Expand
Toxin effect on protein biosynthesis in eukaryotic cells: a simple kinetic model.
A model for toxin inhibition of protein synthesis inside eukaryotic cells is presented. Mitigation of this effect by introduction of an antibody is also studied. Antibody and toxin (ricin) initiallyExpand
Basic, simple and extendable kinetic model of protein synthesis.
Protein synthesis is one of the most fundamental biological processes. Despite existence of multiple mathematical models of translation, surprisingly, there is no basic and simple chemical kineticExpand
Analysis of protein synthesis dynamic model in eukaryotic cells: Input control.
  • Nadav S. Bar
  • Mathematics, Medicine
  • Mathematical biosciences
  • 2009
It was proven that the 48S initiation complex can be driven to a desired value by calculating an input control law using measurement techniques available today and if this strategy can be implemented de facto, then a genuine control on protein synthesis process can be obtained. Expand
Basic and simple mathematical model of coupled transcription, translation and degradation
A basic and simple kinetic model of mRNA lifecycle (transcription, translation and degradation) is built by lumping multiple states of translated mRNA into few dynamical variables and introducing a pool of translating ribosomes. Expand
A mathematical modelling framework for elucidating the role of feedback control in translation termination.
A mathematical modelling framework is developed to investigate a complex feedback control mechanism involved in the translation and synthesis of release factor proteins, which has been observed in different systems. Expand
A quantitative model for mRNA translation in Saccharomyces cerevisiae
A deterministic model based on ordinary differential equations that describe mRNA translation in Saccharomyces cerevisiae predicts that the abundance of the eIF1–eIF3– eIF5 complex increases under amino acid starvation conditions, suggesting a possible auxiliary role for these factors in modulating translation initiation in addition to the known mechanisms involving eIF2. Expand
A mechanistic model of nutritional control of protein synthesis in animal tissues.
In conclusion, the regulation of F4e release from Bp by Ins and Leu, and of F2d recycling by uncharged tRNA can be tied together to describe a wide range of FSR values across tissues and physiological states. Expand
Control of translation initiation: a model-based analysis from limited experimental data
It is suggested that the rate of translation initiation is most strongly influenced by one of two reactions: either the guanine nucleotide exchange reaction involving initiation factors eif2 and eIF2B or the assembly of the multifactor complex from its constituent protein/tRNA containing complexes. Expand


A mathematical model for prokaryotic protein synthesis
  • D. Drew
  • Biology, Medicine
  • Bulletin of mathematical biology
  • 2001
A kinetic model for the synthesis of proteins in prokaryotes is presented and analysed and a Michaelis-Menten type of analysis is done, assuming that the rate of protein degradation determines the ’slow' time, and that all the other kinetic rates are ‘fast’. Expand
2 The Pathway and Mechanism of Eukaryotic Protein Synthesis
This chapter focuses on how the soluble factors, namely, initiation factors, elongation factors, and release factors, catalyze the sequential binding and reaction of aminoacyl-tRNAs to ribosomes as dictated by the template messenger RNA. Expand
3 The Protein Biosynthesis, Elongation Cycle
During the last six years, major advances have been made in generating a structural description of the prokaryotic elongation cycle, including an essentially complete structural picture of most of the major functional forms of the elongation factors. Expand
6 Regulation of Ribosomal Recruitment in Eukaryotes
The current understanding of how the activity of the eIF4 initiation factors is regulated by intracellular signaling pathways is described, and the current under-standing of this chapter is summarized. Expand
Gene Expression Analyzed by High-resolution State Array Analysis and Quantitative Proteomics
This work explored the immediate changes in gene expression in response to activation of a mitogen-activated protein kinase pathway in yeast by mating pheromone and found that analysis of transcript level, albeit extremely important, is insufficient by itself to describe completely the phenotypes of cells under different conditions. Expand
Study of Translational Control of Eukaryotic Gene Expression Using Yeast
Abstract: Eukaryotic cells respond to starvation by decreasing the rate of general protein synthesis while inducing translation of specific mRNAs encoding transcription factors GCN4 (yeast) or ATF4Expand
Structural features in eukaryotic mRNAs that modulate the initiation of translation.
  • M. Kozak
  • Medicine, Biology
  • The Journal of biological chemistry
  • 1991
In higher eukaryotes, translation is modulated at the level of initiation by five aspects of mRNA structure: (i) the m7G cap; (ii) the primary sequence or context surrounding the AUG codon; (iii) theExpand
Translational control in stress and apoptosis
Two representative models are examined, the regulation of eukaryotic initiation factor-2α by phosphorylation and internal ribosome initiation through the internal Ribosome-entry site, which illustrate the importance of translational control in the cellular stress response and apoptosis. Expand
Relationship Between Methionyl Transfer Ribonucleic Acid Cellular Content and Synthesis of Methionine Enzymes in Saccharomyces cerevisiae
The results reinforce the idea that the rate of synthesis of methionine group I enzymes can be related to the total content of Methionyl (Met)-tRNA (Met) per cell and render unlikely that MTS could be a constituent of the regulatory signal. Expand
5 Mechanism and Regulation of Initiator Methionyl-tRNA Binding to Ribosomes
In its simplest terms, the process of translation initiation in eukaryotic organisms consists of the binding of methionyl-initiator tRNA (Met-tRNA i Met ) and mRNA to the 40S ribosomal subunit,Expand