# Near-cognate tRNAs dominate codon decoding times in simulated ribosomes

## TL;DR

This paper shows that near-cognate tRNAs significantly influence how quickly ribosomes decode codons, using computational models and yeast tRNA data.

## Contribution

The study introduces a new computational model that accurately simulates codon decoding times using tRNA abundance data.

## Key findings

- Simulated decoding times depend on the abundance of near- and non-cognate tRNAs.
- Models with accurate near-cognate tRNA definitions match experimental ribosome dwell times closely.
- The study confirms the importance of near-cognate tRNAs in codon decoding.

## Abstract

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. Using tRNA abundance data for Saccharomyce cerevisiae, we show that simulated codon decoding times are sensitive to the abundance of near- and non-cognate tRNAs as well as cognate species. Codon decoding times predicted by models that accurately define near-cognate tRNAs and that are parameterized 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.

Graphical Abstract