Near-cognate tRNAs dominate codon decoding times in simulated ribosomes

The codon sequence of messenger RNAs affects ribosome dynamics, translational control, and transcript stability. Here we describe an advanced computational modelling tool and its application to studying the effect of different tRNA species on the codon decoding process. We show that simulated codon decoding times are sensitive to the abundance of near-cognate tRNA species as well as cognate species, an aspect of the decoding system that is not fully considered in other computational modelling studies. We demonstrate that codon decoding times predicted by models that accurately define near-cognate tRNAs and that are parameterised with high-quality tRNA abundance datasets are highly similar to ribosome dwell times determined using experimental ribosome footprinting data, thereby confirming both the importance of near-cognate tRNAs for the codon decoding process and the general accuracy of our modelling tools.