Skip to main content
Log in

Dynamic Model of the Process of Protein Synthesis in Eukaryotic Cells

  • Original Article
  • Published:
Bulletin of Mathematical Biology Aims and scope Submit manuscript

An Erratum to this article was published on 23 February 2007

Abstract

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 process permits useful prediction of protein production and consumption of energy and amino acids, as well as ribosome loading rate and ribosome spacing on the mRNA.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Arava, Y., Wang, Y., Storey, J., Liu, C., Brown, P., Herschlag, D., 2003. Genome-wide analysis of mRNA translation profiles in saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 100(7), 3889–3894.

    Article  Google Scholar 

  • Drew, D.A., 2001. A mathematical model for prokaryotic protein synthesis. Bull. Math. Biol. (63), 329–351.

    Article  Google Scholar 

  • Gingras, A.C., Raught, B., Sonenberg, N., 1999. eIF4 initiation factors: Effectors of mRNA recruitment to ribosomes and regulators of translation. Annu. Rev. Biochem. 68, 913–963.

    Article  Google Scholar 

  • Hinnebusch, A.G., 2000. Mechanism and regulation of initiator methionyl-tRNA binding to ribosomes. In: Sonenberg, N., Hershey, J., Mathews, M.B. (Eds.), Translational Control of Gene Expression. Cold Spring Harbor Laboratory Press, New York, pp. 185–243 (Chapter 5).

    Google Scholar 

  • Hinnebusch, A.G., 2004. Study of translational control in eukaryotic gene expression using yeast. Ann. N.Y. Acad. Sci. 1038, 60–74.

    Article  Google Scholar 

  • Holcik, M., Sonenberg, N., 2005. Translational control in stress and apoptosis. Nat. Rev. Mol. Cell Biol. 6(4), 318–327.

    Article  Google Scholar 

  • Khalil, H.K., 2002. Nonlinear Systems, 3rd edition. Prentice Hall, Upper Saddle River, New Jersey.

    Google Scholar 

  • Kimball, S.R., Jefferson, L., 2000. Regulation of translation initiation in mammalian cells by amino acids. In: Sonenberg, N., Hershey, J., Mathews, M.B. (Eds.), Translational Control of Gene Expression. Translational Control. Cold Spring Harbor Laboratory Press, New York, pp. 561–579 (Chapter 16).

    Google Scholar 

  • Kozak, M., October 1991. Structural features in eukaryotic mRNAs that modulate the initiation of translation. The Journal of Biological Chemistry 266(30), 19867–19870.

    Google Scholar 

  • Lewis, J., Ames, B., 1972. Histidine regulation in Salmonella typhimurium. XI. The percentage of transfer RNA his charged in vivo and its relation to the repression of the histidine operon. Journal of Molecular Biology 66(1), 131–142.

    Article  Google Scholar 

  • MacKay, Li, Flory, Turcott, Law, Serikawa, Xu, Lee, Goodlett, Aebersold, Zhao, and Morris]MolCellProteomics:3:478 MacKay, V.L., Li, X., Flory, M.R., Turcott, E., Law, G.L., Serikawa, K.A., Xu, X.L., Lee, H., Goodlett, D.R., Aebersold, R., Zhao, L.P., Morris, D.R., 2004. Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: Response of yeast to mating pheromone. Mol. Cell Proteomics 3(5), 478–489.

    Article  Google Scholar 

  • Mathews, D.H., Sabina, J., Zuker, M., Turner, D.H., 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. (288), 911–940.

    Article  Google Scholar 

  • Merrick, W.C., Hershey, J.W., 1996. The pathway and mechanism of eukaryotic protein synthesis. In: Hershey, J.W., Mathews, M.B., Sonenberg, N. (Eds.), Translational Control, vol. 1 of Translational Control. Cold Spring Harbor Laboratory Press, New York, pp. 31–69 (Chapter 2).

    Google Scholar 

  • Merrick, W.C., Nyborg, J., 2000. The protein biosynthesis elongation cycle. In: Sonenberg, N., Hershey, J., Mathews, M.B. (Eds.), Translational Control of Gene Expresison. Cold Spring Harbor Laboratory Press, New York, pp. 89–125 (Chapter 3).

    Google Scholar 

  • Mikami, S., Masutani, M., Sonenberg, N., Yokoyama, S., Imataka, H., April 2006. An efficient mammalian cell-free translation system supplemented with translation factors. Protein Expression and Purification 46(2), 348–357.

    Article  Google Scholar 

  • Raught, B., Gingras, A.C., Sonenberg, N., 2000. Regulation of ribosomal recruitment in eukaryotes. In: Sonenberg, N., Hershey, J., Mathews, M.B. (Eds.), Translational Control of Gene Expresison. Cold Spring Harbor Laboratory Press, New York, pp. 245–293 (Chapter 6).

    Google Scholar 

  • Rowlands, A.G., Panniers, R., Henshaw, E.C., 1988. The catalytic mechanism of guanine nucleotide exchange factor action and competitive inhibition by phosphorylated eukaryotic initiation factor 2. J. Biol. Chem. 263(12), 5526–5533.

    Google Scholar 

  • Scheuner, D., Mierde, D., Song, B., Flamez, D., Creemers, J., Tsukamoto, K., Ribick, M., Schuit, F., Kaufman, R., Jun 2005. Control of mRNA translation preserves endoplasmic reticulum function in beta cells and maintains glucose homeostasis. Natural Medicine 11(7), 757–64.

    Article  Google Scholar 

  • Surdin-Kerjan, Y., Cherest, H., Robichon-Szulmajster, H., 1973. Relationship between methionyl transfer ribonucleic acid cellular content and synthesis of methionine enzyme in Saccharomyces cerevisiae. J. Bacteriol. 113, 1156–1160.

    Google Scholar 

  • Trachsel, H., 1996. Binding of Initiator Methionyl-t RNA to Ribosomes. In: Hershey, J.W., Mathews, M.B., Sonenberg, N. (Eds.), Translational Control. Translational Control of Gene Expression. Cold Spring Harbor Laboratory Press, New York, pp. 113–138 (Chapter 4).

    Google Scholar 

  • Voet, D., 2004. Biochemistry, 3rd edition. John Wiley & sons, Inc., New York.

    Google Scholar 

  • Wong, K.K.Y., Bouwer, H.G.A., Freitag, N.E., 2004. Evidence implicating the 5’ untranslated region of Listeria monocytogenes actA in the regulation of bacterial actin-based motility. Cell. Microbiol. 6(2), 155–166.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Nadav Skjøndal-Bara.

Additional information

An erratum to this article can be found at http://dx.doi.org/10.1007/s11538-006-9179-4

Rights and permissions

Reprints and permissions

About this article

Cite this article

Skjøndal-Bara, N., Morrisb, D.R. Dynamic Model of the Process of Protein Synthesis in Eukaryotic Cells. Bull. Math. Biol. 69, 361–393 (2007). https://doi.org/10.1007/s11538-006-9128-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11538-006-9128-2

Keywords

Navigation