We present a formal analysis of ribosome kinetics using probabilistic model checking and the tool Prism. We compute different parameters of the model, like probabilities of translation errors and average insertion times per codon. The model predicts strong correlation to the quotient of the concentrations of the so-called cognate and near-cognate tRNAs, in accord with experimental findings and other studies. Using piecewise analysis of the model, we are able to give an analytical explanation of this observation.
|Title of host publication||Transactions on Computational Systems Biology XI|
|Editors||C. Priami, R.J. Back, I. Petre|
|Place of Publication||Berlin|
|Publication status||Published - 2009|
|Name||Lecture notes in computer science|
Bosnacki, D., Pronk, T. E., & Vink, de, E. P. (2009). In silico modelling and analysis of ribosome kinetics and aa-tRNA competition. In C. Priami, R. J. Back, & I. Petre (Eds.), Transactions on Computational Systems Biology XI (pp. 69-89). (Lecture notes in computer science; Vol. 5750). Springer. https://doi.org/10.1007/978-3-642-04186-0_4