The influence of hypermodified nucleosides lysidine and t6A to recognize the AUA codon instead of AUG: a molecular dynamics simulation study

Abstract

Hypermodified nucleosides lysidine (L) and N⁶-threonylcarbamoyladenosine (t⁶A) influence codon–anticodon interactions during the protein biosynthesis process. Lysidine prevents the misrecognition of the AUG codon as isoleucine and that of AUA as methionine. The structural significance of these modified bases has not been studied in detail at the atomic level. Hence, in the present study we performed multiple molecular dynamics (MD) simulations of anticodon stem loop (ASL) of tRNA^Ile in the presence and absence of modified bases ‘L’ and ‘t⁶A’ at the 34th and 37th positions respectively along with trinucleotide ‘AUA’ and ‘AUG’ codons. Hydrogen bonding interactions formed by the tautomeric form of lysidine may assist in reading the third base adenine of the ‘AUA’ codon, unlike the guanine of the ‘AUG’ codon. Such interactions might be useful to restrict codon specificity to recognize isoleucine tRNA instead of methionine tRNA. The t⁶A side chain interacts with the purine ring of the first codon nucleotide adenine, which might provide base stacking interactions and could be responsible for restricting extended codon–anticodon recognition. We found that ASL tRNA^Ile in the absence of modifications at the 34th and 37th positions cannot establish proper hydrogen bonding interactions to recognize the isoleucine codon ‘AUA’ and subsequently disturbs the anticodon loop structure. The binding free energy calculations revealed that tRNA^Ile ASL with modified nucleosides prefers the codon AUA over AUG. Thus, these findings might be useful to understand the role of modified bases L and t⁶A to recognize the AUA codon instead of AUG.