Colloquium on March 8, 2010

Maria Carmen Romano
University of Aberdeen

Traffic dynamics of translation: modelling the synthesis of proteins

We focus on the process of translation, i.e., how "molecular machines" called ribosomes translate the messenger RNA molecules into proteins that can be utilised by the cell for a huge variety of different processes. In order to model the process of translation, we propose a simple stochastic model based on the totally asymmetric exclusion process. We study the role that different distributions of nucleotides, i.e., different mRNA sequences, play in the maximal flow or production rate of proteins that can be achieved. We then relate the rich dynamical behaviour generated by the model to the different biological functions of the analysed proteins.

Moreover, we introduce some extensions of the model, considering the two fundamental steps of the ribosome's biochemical cycle, and the effect of limited resources. We show that these extensions might have a dramatic effect in the predicted production rate of proteins and are crucial when taking into account biologically relevant parameters.