9. Reinhard Lipowsky - Stochastic modelling of protein synthesis by ribosomes

In this project we aim to further improve our analysis of the synchronized translation system. We will systematically analyze the composition of the slow codon stretches and compute the consequences of the pausing states when we include them in connection with single codons, adjacent pairs of codons, and more widely separated codons or codon stretches. The second specific goal is to determine the movement of the nascent peptide chain through the exit tunnel. By varying the length of the codon sequence, we will deduce codon-specific elongation rates and a possible context-dependence of these rates in an iterative manner. In our third specific goal, we will address the kinetics of co-translational protein assembly focusing on luciferase which asembles from LuxA and LuxB subunits. We will extend our model to include the kinetics of co-translational folding, subunit diffusion in the cytosol, and interactions with the trigger factor. We will supplement these stochastic models by molecular dynamics simulations in order to elucidate the binding free energy of the two subunits.