This study investigates the role of the wobble nucleotide within the tRNA anticodon and its impact on the functionality of the CAR interaction surface. Using a series of Molecular Dynamics (MD) simulations, the hydrogen bonding and stacking interactions between the CAR interface and the adjacent mRNA codon were analyzed within the ribosome during the early stages of translocation.

The findings suggest that modifications at the tRNA's wobble nucleotide, specifically 2'-O-methylation, significantly alter the hydrogen bonding pattern between the tRNA and the CAR interaction surface. These changes in interaction dynamics may serve as a regulatory mechanism, particularly under stress conditions. We observed that certain mRNA codons, such as UUUGCU, form a higher number of hydrogen bonds with the CAR interaction surface, indicating enhanced sensitivity to the codon sequence and suggesting a potential modulation of the translation by the wobble nucleotide.

The implications of this research extend beyond the molecular insights into translation, pointing to the potential of tRNA modifications to act as fine-tuners of CAR function responding to stress. Future studies are suggested to explore the effect of modifications at base rings of other tRNA sites, such as nucleotide 32, and to consider the broader physiological and adaptive significance of these modifications. This thesis contributes to our understanding of the translation mechanism at the molecular level and emphasizes the role of nucleotide modifications as possible regulatory switches in response to varying cellular conditions.

No results found