Abstract
In the process of translation, ribosomes read the genetic code on an mRNA and assemble the corresponding polypeptide chain. The ribosomes perform discrete directed motion which is well modeled by a totally asymmetric simple exclusion process (TASEP) with open boundaries. Using Monte Carlo simulations and a simple mean-field theory, we discuss the effect of one or two “bottlenecks” (i.e., slow codons) on the production rate of the final protein. Confirming and extending previous work by Chou and Lakatos, we find that the location and spacing of the slow codons can affect the production rate quite dramatically. In particular, we observe a novel “edge” effect, i.e., an interaction of a single slow codon with the system boundary. We focus in detail on ribosome density profiles and provide a simple explanation for the length scale which controls the range of these interactions.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
C. MacDonald, J. Gibbs and A. Pipkin, Biopolymers 6:1 (1968); C. MacDonald and J. Gibbs, Biopolymers 7:707 (1969).
B. Derrida, E. Domany and D. Mukamel, J. Stat. Phys. 69:667 (1992).
B. Derrida, M. R. Evans, V. Hakim and V. Pasquier, J. Phys. A: Math. Gen. 26:1493 (1993).
G. M. Schütz and E. Domany, J. Stat. Phys. 72:277 (1993).
B. Derrida, Phys. Rep. 301:65 (1998).
G. M. Schütz, in Phase Transition and Critical Phenomena, edited by C. Domb and J. L. Lebowitz (Academic Press, San Diego, 2000).
J. Solomovici, T. Lesnik and C. Reiss, J. Theor. Biol. 185:511 (1997).
C. M. Stenström, H. Jin, L. L. Major, W. P. Tate and L. A. Isaksson, Gene 263:273 (2001).
T. Chou and G. Lakatos, Phys. Rev. Lett. 93:198101 (2004).
M. Robinson, R. Lilley, S. Little, J. S. Emtage, G. Yarranton, P. Stephens, A. Millican, M. Eaton and G. Humphreys, Nucl. Acids Res. 12:6663 (1984).
M. A. Sorensen, C. G. Kurland and S. Pedersen, J. Mol. Biol. 207:365 (1989).
B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts and P. Walter, in Molecular Biology of the Cell, 4th ed. (Garland Science, New York, NY, 2002)
F. Neidhardt and H. Umbarger, in Escherichia coli and Salmonella, 2nd ed., edited by F. C. Neidhardt (ASM Press, Washington, DC, 1996).
R. Heinrich and T. Rapoport, J. Theor. Biol. 86:279 (1980).
C. Kang and C. Cantor, J. Mol. Struct. 181:241 (1985).
L. B. Shaw, R. K. P. Zia and K. H. Lee, Phys. Rev. E 68:021910 (2003).
J. J. Dong, B. Schmittmann and R. K. P. Zia, to be published.
A. Kolomeisky, J. Phys. A: Math. Gen. 31:1153 (1998).
S. Janowsky and J. Lebowitz, Phys. Rev. A 45:618 (1992).
S. Janowsky and J. Lebowitz, J. Stat. Phys. 77:35 (1994).
R. J. Harris and R. B. Stinchcombe, Phys. Rev. E 70:016108 (2004).
M. Ha, J. Timonen and M. den Nijs, Phys. Rev. E 68:056122 (2003). For more details, see also M. Ha, PhD thesis, University of Washington, 2003.
L. B. Shaw, A. B. Kolomeisky, and K. H. Lee, J. Phys. A: Math. Gen. 37:2105 (2004).
Author information
Authors and Affiliations
Corresponding author
Additional information
PACS numbers: 05.70.Ln, 64.90.+b, 87.14.Gg
Rights and permissions
About this article
Cite this article
Dong, J.J., Schmittmann, B. & Zia, R.K.P. Towards a Model for Protein Production Rates. J Stat Phys 128, 21–34 (2007). https://doi.org/10.1007/s10955-006-9134-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10955-006-9134-7