Biology – Quantitative Biology – Biomolecules
Scientific paper
2006-02-27
Journal of Statistical Physics, Volume 128, Numbers 1-2 / July, 2007
Biology
Quantitative Biology
Biomolecules
8 pages, 8 figures
Scientific paper
10.1007/s10955-006-9134-7
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.
Dong Jingcheng
Schmittmann Beate
Zia Royce K. P.
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